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Limited Utility of mtDNA Markers for Determining Connectivity among Breeding and Overwintering Locations in Three Neotropical Migrant Birds
Conservation Biology
Abstract
For the past two decades, population declines in Neotropical migrant songbirds have been both a flagship conservation issue and the subject of intensive research initiatives. Nonetheless, the design of effective conservation measures for Neotropical migrants has been hindered by a lack of information on where and how migrant populations are regulated. This problem stems in large part from the difficulty of following individual long-distance migrants throughout their annual cycles. As a result, there has been increasing interest in using genetic markers to determine patterns of connectivity between particular breeding populations and overwintering regions. In species with geographically structured genetic variation during the breeding season, genetic markers can be used to determine the origin of migrating and overwintering individuals. This information on demographic connectivity could be then used to infer the locations or seasons contributing to population trends of currently unknown origin. To date, genetic markers (primarily mitochondrial DNA) have been used to survey only a few species of migratory songbirds, with varying success. To provide examples of the geographic scale at which mtDNA markers are likely to prove most relevant to Neotropical migrant conservation, we surveyed breeding-season variation in North American populations of three long-distance migrant taxa: the Yellow-breasted Chat (Icteria virens), Common Yellowthroat (Geothlypis trichas), and Nashville Warbler (Vermivora ruficapilla). We then used this information to screen individuals sampled at overwintering sites in Mexico and Central America. Genetic structure was only found at the broadest continent-wide scale in all three species, which allowed us to assign overwintering individuals to eastern or western breeding lineages but did not allow us to assign overwintering individuals to breeding populations of origin on a finer scale suitable for assaying local demographic trends. Owing to mitochondrial homogeneity among widely separated breeding locations, mtDNA markers (especially when used alone) are unlikely to provide a panacea for the problem of interseasonal connectivity among migrant songbirds.
Resumen: En las últimas dos décadas, las declinaciones poblacionales de aves migratorias neotropicales han sido un tema insignia para la conservación así como el objeto de intensas iniciativas de investigación. No obstante, el diseño de medidas de conservación ha estado limitado por la falta de información de dónde y cómo son reguladas las poblaciones migratorias. En gran parte, este problema se deriva de la dificultad de seguir los ciclos anuales de individuos migrantes de larga distancia. En consecuencia, hay un creciente interés en utilizar marcadores genéticos para determinar patrones de conectividad entre determinadas poblaciones reproductivas y sus regiones de hibernación. Los marcadores genéticos pueden ser utilizados para determinar el origen de individuos migrantes e invernantes en especies con variación genética geográficamente estructurada durante la época reproductiva. Esta información sobre conectividad demográfica podría ser utilizada para inferir las localidades o estaciones que contribuyen a las tendencias poblacionales actualmente de origen desconocido. A la fecha, los marcadores genéticos (principalmente ADN mitocondrial) se han utilizado para examinar solo unas cuantas especies de aves migratorias, con éxitos variados. Para proporcionar ejemplos de la escala geográfica en la que los marcadores de ADNmt tienen probabilidad de ser más relevantes para la conservación de migrantes neotropicales, examinamos la variación en la época reproductiva en poblaciones de Norte América de tres taxones migratorios de larga distancia: Icteria virens, Geothlypis trichas y Vermivora ruficapilla. Posteriormente utilizamos esta información para investigar individuos capturados en sitios de hibernación en México y Centroamérica. En las tres especies, la estructura genética se encontró solo en la mayor escala continental, lo que nos permitió asignar a los individuos invernantes a linajes reproductivos orientales u occidentales, pero no nos permitió asignar a los individuos a poblaciones reproductivas de origen en una escala más fina adecuada para analizar tendencias demográficas locales. Debido a la homogeneidad mitocondrial entre localidades reproductivas ampliamente separadas, es poco probable que los marcadores de ADNmt (especialmente cuando se usan solos) sean la panacea para el problema de la conectividad inter-estacional de aves migratorias.
... Fortunately, advances in lightweight technology and computational analyses are continually improving the ways in which we can study birds across their full annual cycle (McKinnon and Love 2018). External trackers such as archival light-level geolocators and GPS tags (McKinnon et al. 2013;Hallworth and Marra 2015), as well as intrinsic markers such as DNA and stable hydrogen isotopes (Hobson and Wassenaar 1997;Lovette et al. 2004;Toews et al. 2017), can be used to better understand breeding, migrating, and non-breeding phases and linking different phases together. ...
... virens) and western (I.v. auricollis), which occupy distinct breeding ranges in the United States and southern Canada (Lovette et al. 2004;Smith et al. 2005; Fig. 1). Their non-breeding range spans coastal Mexico and Central America (IUCN 2016). ...
... We used genetics and stable hydrogen isotopes to determine the breeding origin from chats sampled in their overwintering and migration sites. Previous genetic analyses based on the ATPase gene in the mitochondrial genome identified 18 unique haplotypes within 34 chats sampled from across their North American distribution, including both subspecies (Lovette et al. 2004). Importantly, the authors identified several single nucleotide polymorphisms (SNPs) diagnostic of western and eastern chats. ...
Detailed information spanning the full annual cycle is lacking for most songbird populations. We examined breeding, migration, and non-breeding sites for the Yellow-breasted Chat (Icteria virens, chat). We deployed archival GPS tags and light-level geolocators on breeding chats in British Columbia and light-level geolocators in California from 2013 to 2017 to determine migration routes and non-breeding sites. We examined whether chats overwintered in protected areas and characterized the percent of land cover within 1 km. We used a combination of genetics and stable hydrogen isotopes from feathers collected on non-breeding chats in Nayarit, Mexico (2017-2019) and migrating chats in Chiapas, Mexico (2018) and Veracruz, Mexico (2014-2015) to determine subspecies and infer breeding location. Endangered chats in British Columbia followed the Pacific Flyway and spent the non-breeding period in Sinaloa and Nayarit, Mexico. Two out of five chats spent the non-breeding period in protected areas, and the most common landcover type used was tropical or subtropical broadleaf deciduous forest. We found no mixing of eastern and western chats in our Mexico sites, suggesting strong migratory connectivity at the subspecies level. Western chats likely originating from multiple breeding latitudes spent the non-breeding period in Nayarit. Eastern Yellow-breasted Chats likely breeding across various latitudes migrated through Veracruz and Chiapas. Our results provide precise migration routes and non-breeding locations, and describe habitat cover types for chats, notably an endangered population in British Columbia, which may be valuable for habitat protection and conservation efforts.
Supplementary information:
The online version contains supplementary material available at 10.1007/s10336-021-01931-8.
... Physical barriers will likely act to prevent dispersal in this sedentary songbird. The Rocky Mountains have been shown to act as a barrier to gene flow in many birds (Milot et al. 2000;Lovette et al. 2004;Burg et al. 2005;Peters et al. 2005), and different subspecies of boreal chickadees are found on either side of the mountains. Island populations often have reduced gene flow to the mainland, likely due the presence of an impassable water barrier. ...
... The last glacial maximum occurred approximately 21 kya to 18 kya (Pielou 1991). al. 1997;Rueness et al. 2003;Burg et al. 2005) and migratory (Milot et al. 2000;Lovette et al. 2004;Peters et al. 2005) species. ...
... Contrary to the pattern found in many passerines (Milot et al. 2000;Lovette et al. 2004;Burg et al. 2005), the Rocky Mountains are not acting as a barrier to gene flow in this species. There exists continuous habitat from Alaska to the east coast Gerardi et al. 2010), and although boreal chickadees do not tend to be found at extremely high elevations, there are potential dispersal corridors throughout the Rocky ...
... What about the 10 widespread species ? Kimura 2000, Lovette et al. 2004). In addition, there have long been western and eastern subspecies (even species at times) described for Ovenbird (Seiurus aurocapillus), Orange-crowned Warbler (Vermivora celata), and Yellow-rumped Warbler (Dendroica coronata, Sogge et al. 1994, Van Horn and Donovan 1994, Hunt and Flaspoler 1998. ...
... We were also able to locate mtDNA-based phylogenies that surveyed the western and eastern populations for four of ten species that have widespread distributions. All of these phylogenies suggest distinct eastern and western taxa of Wilson's Warbler, Yellow Warbler, Nashville Wabler, and Common Yellowthroats (Ball and Avise 1992, Zink et al. 2000, Milot 2000, Kimura 2000, Lovette et al. 2004. In summary, of the 21 wood warblers that occur in the West, we found mtDNA studies of 11 species. ...
... Webster et al. (2002) proposed the notion of connectivity for understanding the degree to which breeding individuals from a given demographic unit are shared by various winter locations and vice versa. For four species of widespread wood warblers, recent mtDNA data suggest that distinct haplotypes of western and eastern breeding wood warblers are closely associated with western and eastern wintering locations, respectively (Kimura et al. 2000, Lovette et al. 2004). In addition, there are indications that within western populations the latitude of the breeding range is associated with that of winter residency (Kelly et al. 2002, Clegg et al. 2003. ...
That western and eastern songbird migration routes are distinct ecological systems has been proposed for over 100 years. Nonetheless, this distinction has not been widely recognized nor have there been any comparative studies that quantitatively evaluate the differences and similarities between western and eastern songbird migration systems. We drew from previously published research on wood warblers to highlight patterns in stopover ecology that suggest fundamental differences between western and eastern migrants. In particular, we compared biogeography, evolutionary relationships, and stopover ecology of wood warblers from western and eastern North America and found: (1) multiple lines of evidence that indicate western wood warblers are geographically isolated from eastern conspecifics or congeners throughout the annual cycle, (2) eastern and western wood warbler taxa are distinct evolutionary units, (3) migrant wood warblers captured in the Southwest tended to carry lower fat loads and be comprised of more after-hatch-year birds than is typical of eastern migrants, (4) frugivory is unknown in wood warblers endemic to the Northwest or Southwest and (5) relative to other regions and seasons, riparian vegetation is heavily used by western wood warblers in the spring. We think that further examination and synthesis of these differences would yield a more mechanistic understanding of Nearctic-Neotropical avian migration. On this basis, we elaborate our view that (1) an improved understanding of western songbird migration ought to be a high priority for science, conservation, and education, and (2) large-scale coordinated research efforts would be the most effective strategy for advancing our knowledge of passerine migration in the West.
Una Comparación Este-Oeste de la Migración de las Reinitas de Bosque (Parulidae) de Norte América
Resumen. Por más de 100 años se ha propuesto que las rutas de migración de aves paseriformes del este y del oeste son sistemas ecológicos diferentes. Sin embargo, esta distinción no ha sido reconocida ampliamente, ni se han realizado estudios comparativos que evalúen cuantitativamente las diferencias y similitudes entre los sistemas de migración del este y del oeste. Revisamos estudios previamente publicados sobre aves de bosque de la familia Parulidae (Reinitas) para destacar los patrones ecológicos de las paradas migratorias que sugieran diferencias fundamentales entre las aves paseriformes migratorias el este y del oeste. Particularmente, comparamos la biogeografía, las relaciones evolutivas y la ecología de las paradas migratorias de las Reinitas del este y del oeste de Norteamérica y encontramos: (1) múltiples líneas de evidencia que indican que las Reinitas del oeste se encuentran geográficamente aisladas de sus coespecíficos o cogenéricos del este durante todo el ciclo anual, (2) los taxa del este y del oeste son unidades evolutivas independientes, (3) las Reinitas migratorias capturadas en el suroeste tendieron a presentar menores cargas de grasa y una mayor proporción de aves eclosionadas durante el año, que lo es típicamente observado para las aves migratorias del este, (4) la frugivoría no se conoce en las Reinitas endémicas del noroeste o sudoeste y (5) en relación a otras regiones o estaciones, la vegetación riparia es usada intensamente durante la primavera por las Reinitas del oeste. Creemos que estudios adicionales y una síntesis de estas diferencias podrían producir un mejor entendimiento mecanístico de la migración Neártico-Neotropical de aves. Basados en esto, sugerimos que (1) un mejor entendimiento de la migración de aves paserinas del oeste debería tener alta prioridad para la ciencia, conservación y educación y (2) que los esfuerzos de investigación coordinados a gran escala serían la estrategia más efectiva para progresar en nuestro conocimiento sobre la migración de las aves paserinas en el oeste.
... For example, even rare successful dispersal can result in genetic panmixia; in contrast, if immigrants do not breed successfully, populations that appear to be demographically connected may be genetically isolated (Wright 1931). The Rocky Mountains have been implicated as a physical barrier to gene flow leading to east-west population genetic differentiation in many avian species (e.g., Ruegg and Smith 2002;Lovette et al. 2004) but their importance in waterbirds is unclear (e.g., Peters et al. 2005vs. Mercer 2008Oomen et al. 2011;Reudink et al. 2011). ...
... East-west differentiation in Caspian terns is consistent with other North American avian taxa (e.g., northern flicker Colaptes auratus, Moore and Buchanan 1985; indigo Passerina cyanea and Lazuli buntings P. amoena, Harrison 1993; yellow-breasted chat Icteria virens, Lovette et al. 2004). The Rocky Mountains may be driving this pattern by limiting connectivity among breeding groups. ...
... See Table 1 for sample site names 123 when the glaciers receded (Hewitt 2004). Isolation in multiple refugia has been invoked to explain the marked east-west genetic differentiation in wood ducks (Aix sponsa, Peters et al. 2005) and some neotropical migrant birds (e.g., Ruegg and Smith 2002;Lovette et al. 2004). Since Caspian terns display similar differentiation patterns, they also may have occupied multiple refugia during the late Pleistocene. ...
The Caspian tern (Hydroprogne caspia) is a globally distributed seabird that breeds throughout North America, generally in low numbers. Many colonies are threatened by habitat loss and pollution. Additionally, adult terns compete directly with salmonid stocking programs on the west coast, where a large proportion of the fish they feed their young are stocked salmon smolts. North America colonies have been classified into five ‘breeding groups’ based on banding data and geography. To help delineate effective management units, we characterized variation in mitochondrial DNA (488 base pair fragment of cytochrome b) and five microsatellite loci among 111 terns from six sites representing three of the North American breeding areas. We found significant range-wide population differentiation (cytochrome b: global UST = 0.12, P\0.01; microsatellites: global FST = 0.094, P\0.001). Pacific Coast sites differed genetically from sites east of the Rocky Mountains, and sites in Central Canada differed from those in the Great Lakes region. Gene flow among these three regions appears to be restricted. Thus, our results indicate
that at least three of the breeding regions delineated using banding data and geography should be treated as separate management units.
... In the past 20 years, population genetics has become a well-established means for tracking migratory populations, especially for studies involving large sample sizes or small-bodied individuals (Faaborg et al., 2010). However, the value of genetic markers is often limited by the amount of genetic differentiation in a species and the availability of genetic data from individuals across the annual cycle (Faaborg et al., 2010;Lovette et al., 2004). ...
... Population assignment methods originated in the early 1980s and 1990s as a means of identifying breeding origins of migratory individuals back to distinct tributaries (in the case of fish) or geographic regions (in the case of bears; Grant et al., 1980;Paetkau et al., 1995;Rannala & Mountain, 1997). Early methods relied on genetic markers that were limited to identifying only deep phylogeographic breaks within species (Kimura et al., 2002;Lovette et al., 2004;Ruegg & Smith, 2002). In recent years, next-generation sequencing has facilitated the screening of a significantly larger number of genetic markers allowing for the delineation of breeding populations at finer spatial scales (Battey et al., 2018;DeSaix et al., 2019;Ruegg et al., 2014). ...
Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining
migratory connectivity results with demographic analysis of population abundance
and trends, we consider full annual cycle conservation strategies for preserving
numbers of individuals and genetic diversity. Notably, we highlight the importance
of the Northern Temperate-Greater Antilles migratory population as containing
the largest proportion of individuals in the species. Finally, we highlight valuable
considerations for other population assignment studies aimed at using lcWGS. Our
results have broad implications for improving our understanding of the ecology and
evolution of migratory species through conservation genomics approaches.
... One seeming exception to this pattern is the occurrence of three recoveries in the southeast and central US of birds banded in Alaska; however, this migration pattern may be specific to birds breeding in the extreme northwest (i.e., Alaska), and follows, in part, the pattern of some long distance migrants [52], and may be similar to other short-distance migrants such as White-crowned sparrows (Zonotrichia albicollis) [53]. Other species, including the Yellow Warbler (Setophaga petachia), Wilson's Warbler (Cardellina pusilla), Common Yellowthroat (Geothlypis trichas), Yellow-breasted Chat (Icteria virens), and Nashville Warbler (Oreothlypis ruficapilla) also show separation of populations between eastern and western areas with parallel migration patterns [21,54,55]. These patterns of connectivity in American Robins are consistent with taxonomic descriptions that have divided American Robins into distinct populations [44]. ...
... Some studies based on mitochondrial DNA have failed to detect genetic structure or migratory connectivity at finer scales [55]. However, other methodological approaches, such as geolocators, satellite transmitters, morphology, molecular analysis of single nucleotide polymorphisms, and bird band recoveries, have revealed connectivity in other species at finer scales [22,57,58] and weaker levels [59]. ...
Migration strategies may change in response to climate change with consequences for conservation efforts. We used 80 years (1934−2014) of band recovery data (N = 1,057) to describe spatial and temporal patterns in the migration behavior of American Robins. The distribution of recoveries suggests strong continental scale connectivity with distinct separation between eastern and western North America, with a more moderate degree of connectivity within these regions. We also found little evidence of differential migration between males and females. Despite previous studies that suggest the winter distribution of robins has shifted northward, our analysis shows no obvious change in migration distance over time. Surprisingly, we found that a significant proportion of across season band recoveries occurred locally (20%), in close proximity to the original banding locations. It’s well known that large numbers of robins linger in northern breeding grounds well into the winter of some years, but the proximity of these birds to breeding areas was previously unknown. We found little evidence that the winter latitude of migrants or local recoveries shifted over time. However, there was a trend for increased frequency of local recoveries in recent decades, providing an alternative hypothesis for the northward shift in winter distribution.
... Studies on both black (N msat ) or sequenced for mitochondrial control regions (N mt ), allelic richness averaged across loci (Ar), mean number of alleles/locus (A), haplotype diversity (h; mean ± SD), and nucleotide diversity (; mean ± SD). ) and white spruce (Picea glauca (Moench) Voss) found evidence of multiple refugia with at least one in the east and one in the west (Jaramillo-Correa et al. 2004;de Lafontaine et al. 2010), which could help explain the east-west differentiation that we documented in Golden-crowned Kinglets. A number of other continentally distributed avian taxa show an east-west split (Lovette et al. 2004;Bull et al. 2010;Manthey et al. 2011a;Graham and Burg 2012). Thus, it seems likely that the two Golden-crowned Kinglet mitochondrial lineages persisted in isolated areas during the LGM with limited gene flow. ...
... Current data support the hypothesis that Haida Gwaii Golden-crowned Kinglets are resident year-round and do not migrate seasonally like many other kinglet populations in the north (Ingold and Galati 1997). Sedentary species (McDonald et al. 1999;Coulon et al. 2008;McCormack et al. 2008;Manthey et al. 2011a;Graham and Burg 2012) tend to show higher levels of population structure than migratory species (Ruegg and Smith 2002;Lovette et al. 2004;Boulet and Gibbs 2006), and resident populations of species with mixed migration strategies tend to show increased genetic isolation compared with migratory populations (Boulet and Gibbs 2006;Seki et al. 2007). ...
Relatively recently, temperate regions in North America were covered by extensive ice sheets, making them inhospitable to contemporary flora and fauna. Since the retreat of the ice sheets, these regions have been recolonized by a diversity of taxa, some of which have undergone rapid postglacial divergence. Evidence supports the hypothesis that some taxa persisted in unglaciated refugia during the Last Glacial Maximum, such as on Haida Gwaii (formerly the Queen Charlotte Islands). Many taxa on Haida Gwaii are genetically distinct from mainland populations at neutral molecular markers possibly as the result of isolation in refugia or postglacial colonization. The Golden-crowned Kinglet (Regulus satrapa Lichtenstein, 1823) is a continentally distributed, short-distance migratory passerine inhabiting mature conifer forests including those on Haida Gwaii. We used five microsatellite markers and a 568 base-pair fragment of the mitochondrial control region to determine the likelihood that Haida Gwaii region acted as a refugium for this species during the last ice age. We report significant gene flow between Haida Gwaii and the western North American mainland from mitochondrial markers, but significant population genetic differentiation at nuclear markers. We also report genetic divergence between eastern and western Golden-crowned Kinglets, as well as higher genetic diversity and population substructuring within the western population than within the eastern population. The east–west differentiation probably arose due to isolation in separate Pleistocene refugia south of the ice sheets. However, population differences within the west are likely caused by more recent processes; contemporary differentiation of Haida Gwaii Golden-crowned Kinglets most likely occurred postglacially.
... However, until recently these methods yielded insufficiently resolved data (e.g. individuals assigned to broad geographic ranges and/or assigned with relatively low probabilities of membership) and could be limited by technical issues [29][30][31]. ...
With new motivation to increase the proportion of energy demands met by zero-carbon sources, there is a greater focus on efforts to assess and mitigate the impacts of renewable energy development on sensitive ecosystems and wildlife, of which birds are of particular interest. One challenge for researchers, due in part to a lack of appropriate tools, has been estimating the effects from such development on individual breeding populations of migratory birds. To help address this, we utilize a newly developed, high-resolution genetic tagging method to rapidly identify the breeding population of origin of carcasses recovered from renewable energy facilities and combine them with maps of genetic variation across geographic space (called ‘genoscapes’) for five species of migratory birds known to be exposed to energy development, to assess the extent of population-level effects on migratory birds. We demonstrate that most avian remains collected were from the largest populations of a given species. In contrast, those remains from smaller, declining populations made up a smaller percentage of the total number of birds assayed. Results suggest that application of this genetic tagging method can successfully define population-level exposure to renewable energy development and may be a powerful tool to inform future siting and mitigation activities associated with renewable energy programs.
... Light-level geolocation tagging of Tufted Puffins from the Alaskan breeding colony on Middleton Island has revealed that birds winter, on average, 616 km south and southeast of their breeding colony in the Gulf of Alaska. As Abbott et al. (2014) state, movements outside of the breeding season by seabirds are comparable to the migratory movements of terrestrial species (Lovette et al. 2004), which may promote mixing among breeding colonies. Further Hipfner et al. (2020) found a relationship between segregation in wintering sites and population genetic structure for Rhinoceros Auklets, where genetic differentiation was lower among populations with higher overlap in wintering areas. ...
Tufted Puffins (Fratercula cirrhata) are experiencing population declines in some parts of their distribution, making this a species of increased conservation interest. Genetic data will help to identify Tufted Puffin populations of conservation importance and provide an important tool for developing conservation management plans. This species is broadly distributed across the North Pacific Ocean but little is known about the extent of genetic variation and differentiation across their range. In this study, we examine mitochondrial DNA (mtDNA), 8 microsatellite loci and 1,260 single nucleotide polymorphisms (SNPs) to determine the extent of gene flow among 7 breeding colonies (Oregon to the western Aleutians) in the North American breeding range of the species and identify potential barriers to dispersal. Our results show that most breeding colonies form a single genetic cluster, and mtDNA data show substantial historical gene flow among populations. For the microsatellite dataset, all FST comparisons that include St. Lazaria, in southeast Alaska, except Oregon, which had a small sample size, were significant as were comparisons between Triangle Island and the two westernmost sampling sites of Buldir and Aiktak. For the SNP dataset, FST comparisons were low and nonsignificant, further suggesting that breeding colonies form a single panmictic population. Individuals were more closely related to individuals from the same colony, and we found a weak relationship between genetic and geographic distance. This suggests that dispersal among colonies is high, likely facilitated by an overlap in wintering ranges among colonies. The high connectivity among breeding colonies indicates that Tufted Puffins form a single conservation unit, although future genetic studies should incorporate a whole genome sequencing approach to assessing how functional genetic diversity varies across their distribution.
... The low success of tracking studies (Mostello et al. 2014;Paton et al. 2021) has previously made this challenging. Using population assignment to identify origin of individuals screened on migratory routes or wintering grounds has been investigated as a potential means of understanding overwintering dynamics in migratory birds, but fine scale assessment has largely been unsuccessful due to limited genetic structuring among populations (Connan et al. 2015;Gómez-Díaz et al. 2009) or use of uninformative genetic markers (Lovette et al. 2004). Higher-coverage genomic markers such as SNPs, which can better resolve fine-scale structure, can be used to more effectively link migratory birds to their natal regions (DeSaix et al. 2019). ...
While the effects of barriers to dispersal such as population declines, habitat fragmentation, and geographic distance have been well-documented in terrestrial wildlife, factors impeding the dispersal of highly vagile taxa such as seabirds are less well understood. The roseate tern (Sterna dougallii) is a globally distributed seabird species, but populations tend to be both fragmented and small, and the species is declining across most of its range. We evaluated structuring of roseate tern populations in the Northwestern Atlantic, the Caribbean, and the Azores using both microsatellite markers and single-nucleotide polymorphisms generated through targeted sequencing of Ultra-conserved Elements. For both marker types, we found significant genetic differentiation among all 3 populations and evidence for moderate contemporary unidirectional gene flow from the Caribbean to the Azores, but not between other populations. Within the Caribbean population, we found high rates of unidirectional migration from the Virgin Islands to Florida, potentially indicative of movement from source population to sink or an artifact of dispersal among other unsampled populations in the Caribbean region. These observations have significance for species persistence in the Atlantic, as our results indicate that loss of genetic diversity within populations is unlikely to be buffered by inflow of new alleles from other breeding populations.
... Population contractions persisting in refugia during glacial maxima followed by rapid range expansions can result in low levels of differentiation within regions (Milá et al. 2000, Milot et al. 2000, Ruegg and Smith 2002, Colbeck et al. 2008. Many phylogenetic studies have revealed significant east to west differentiation stemming from two or more refugia during glaciation divided by the Rocky Mountains or Great Plains (Kimura et al. 2002, Lovette et al. 2004, Peters et al. 2005, such as seen in the yellow warbler Dendroica petechia (Milot et al. 2000, Boulet andGibbs 2006) and the Swainson's thrush Catharus ustulatus (Ruegg and Smith 2002). Other species like the American redstart Setophaga ruticilla do not exhibit this pattern; instead they appear to have originated from a single refugia in eastern North America (Colbeck et al. 2008). ...
Genetic variation is a fundamental component of biodiversity, and studying population structure, gene flow and demographic history can help guide conservation strategies for many species. Like other aerial insectivores, the purple martin Progne subis is in decline, and yet their genetic background remains largely unknown. To address this knowledge gap, we assessed population structure in the nominate eastern subspecies (P. s. subis) with relation to natal dispersal and examined historical genetic patterns in all three subspecies (P. s. subis, P. s. arboricola, P. s. hesperia) across their North American breeding range by estimating effective population sizes over time. We used next‐generation sequencing strategies for genomic analyses, integrating whole‐genome resequencing data with continent‐wide band encounter records to examine natal dispersal. We documented population structure across P. s. subis, with the highest differentiation between the northern (Alberta) and more southern colonies and following patterns of isolation‐by‐distance. Consistent with spatial patterns of genetic differentiation, we also found greater longitudinal than latitudinal natal dispersal distances, signifying potential latitudinal constraints on gene flow. Earlier contractions in effective population sizes in the western P. s. arboricola and P. s. hesperia compared to the eastern P. s. subis subspecies suggest these subspecies originated from two different glacial refugia. Together, these findings support latitudinal distinction in P. s. subis, and elucidate the origin of subspecies differentiation, highlighting the importance of conserving populations across the range to maximize genetic diversity and adaptive potential in the purple martin.
... The low success of tracking studies (Mostello et al. 2014) has previously made this challenging. Using population assignment to identify origin of individuals screened on migratory routes or wintering grounds has been investigated as a potential means of understanding overwintering dynamics in migratory birds, but ne scale assessment has largely been unsuccessful due to limited genetic structuring among populations (Connan et al. 2015;Gómez-Díaz et al. 2009) or use of uninformative genetic markers (Lovette et al. 2004). Higher-coverage genomic markers such as SNPs, which can better resolve ne-scale structure, can be used to more effectively identify unknown migratory birds to their natal regions (DeSaix et al. 2019). ...
While the effects of barriers to dispersal such as population declines, habitat fragmentation, and geographic distance have been well-documented in terrestrial wildlife, factors impeding the dispersal of highly vagile taxa such as seabirds are less well understood. The roseate tern ( Sterna dougallii ) is a globally distributed seabird species, but populations tend to be both fragmented and small, and the species is declining across most of its range. Within the Atlantic Basin, past work has shown differentiation among roseate terns breeding on different continents, but these results were generated with a limited number of microsatellite markers. Relationships between breeding populations in the Northwestern Atlantic and the Caribbean have never been analyzed. We evaluated population structuring of roseate tern populations in North America and the Azores using both microsatellite markers and single-nucleotide polymorphisms generated through targeted sequencing of Ultra-conserved Elements. For both marker types, we found significant genetic differentiation among all 3 populations and evidence for moderate contemporary unidirectional gene flow from the Caribbean to the Azores, but not among other populations. Within the Caribbean metapopulation, we found high rates of unidirectional migration from the Virgin Islands to Florida, potentially indicative of movement from source population to sink or an artifact of dispersal among other unsampled populations in the Caribbean region. These observations have significance for species persistence in the Atlantic, as our results suggest that loss of genetic diversity within populations is unlikely to be buffered by inflow of new alleles from other breeding populations.
... Markrecapture approaches, including continental-scale banding efforts, yield extremely low return rates despite years of effort (Webster et al., 2002). Genetic markers, by themselves, are typically uninformative because there is little range-wide population structure (Clegg et al., 2003;Lovette et al., 2004), although recent applications of next-generation sequencing show promise (Ruegg et al., 2014). ...
Aim
Conservation planning for migratory species requires knowing how populations are connected throughout the annual cycle. We measured migratory connectivity for five migratory songbird species by combining stable‐hydrogen isotopes in feathers (δ²HF) with citizen science data on breeding range abundance.
Location
Caribbean Basin and North America.
Taxa
Neotropical migratory birds: Mniotilta varia, Setophaga ruticilla, Seiurus aurocapilla, Setophaga americana, and Setophaga discolor.
Methods
We analyzed δ²HF in feathers grown on North American breeding grounds and sampled at 20 Caribbean Basin sites across most of the non‐breeding range of each species. We made Bayesian assignments to breeding origin by combining δ²HF values and North American Breeding Bird Survey abundance data. For each species, we used cluster analysis to group Caribbean sites into non‐breeding regions that shared birds with similar breeding ground assignment probabilities. We then mapped assignment probabilities for the non‐breeding regions of each species onto breeding ground δ²HF surfaces and estimated the strength of migratory connectivity.
Results
Apart from some general similarities, the five species demonstrated different patterns of migratory connectivity. Species with larger non‐breeding ranges exhibited stronger migratory connectivity compared to those with smaller non‐breeding ranges. Despite geographical overlap, birds from each non‐breeding region had mostly unique breeding ground origins.
Main conclusions
The contrasting patterns of migratory connectivity shown by the five species suggest that geographic distribution during the non‐breeding period is a poor indicator of breeding ground origin. Our results indicate that full annual cycle conservation planning, which requires migratory connectivity information, should proceed on a species‐specific basis.
... This suggests that Wyoming loons are possibly a relic breeding population created from the retreat of glaciers across the western North American and the subsequent creation of nesting lakes (Cameron, 1922). Several studies have investigated the role of the Pleistocene glaciation in speciation and contemporary population structure of North American birds (Dohms et al., 2017;Johnson & Cicero, 2004;Zink, 1996) and several molecular studies have identified divergent lineages corresponding to lineages west and east of the Rocky Mountains in songbird species (Clegg et al., 2003;Lovette et al., 2004;Milot et al., 2000). One hypothesis is that the southern refugia of breeding common loons were associated with two glacial sheets (Cordilleran and Keewatin). ...
Understanding how risk factors affect populations across their annual cycle is a major challenge for conserving migratory birds. For example, disease outbreaks may happen on the breeding grounds, the wintering grounds, or during migration, and are expected to accelerate under climate change. The ability to identify the geographic origins of impacted individuals, especially outside of breeding areas, might make it possible to predict demographic trends and inform conservation decision making. However, such an effort is made more challenging by the degraded state of carcasses and resulting low quality of DNA available. Here we describe a rapid and low‐cost approach for identifying the origins of birds sampled across their annual cycle that is robust even when DNA quality is poor. We illustrate the approach in the common loon (Gavia immer), an iconic migratory aquatic bird that is under increasing threat on both its breeding and wintering areas. Using 300 samples collected from across the breeding range we develop a panel of 158 SNP loci with divergent allele frequencies across six genetic subpopulations. We use this SNP panel to identify the breeding grounds for 142 live nonbreeding individuals and carcasses. For example, genetic assignment of loons sampled during botulism outbreaks in parts of the Great Lakes provide evidence for the significant role the lakes play as migratory stopover areas for loons that breed across wide swaths of Canada, and highlights the vulnerability of a large segment of the breeding population to botulism outbreaks that are occurring in the Great Lakes with increasing frequency. Our results illustrate that the use of SNP panels to identify breeding origins of carcasses collected during the non‐breeding season can improve our understanding of the population‐specific impacts of mortality from disease and anthropogenic stressors, ultimately allowing more effective management.
... Alternatively, genetic and isotopic markers that use information contained within the feathers to pinpoint an individuals population of origin have broad appeal because they are cost-effective, noninvasive and do not require recapture (Rubenstein et al. 2002;Kelly et al. 2005;Rundel et al. 2013). However, intrinsic marking techniques have been plagued in the past by low resolution and/or technical issues related to working with feathers (Segelbacher 2002;Lovette et al. 2004;Wunder et al. 2005). Thus, there remains a need for a broadly applicable method for identifying migratory connectivity at spatial scales that are informative for assessing drivers of regional population declines. ...
Neotropical migratory birds are declining across the Western Hemisphere, but conservation efforts have been hampered by the inability to assess where migrants are most limited–the breeding grounds, migratory stopover sites, or wintering areas. A major challenge has been the lack of an efficient, reliable, and broadly applicable method for connecting populations across the annual cycle. Here we show how high-resolution genetic markers can be used to identify populations of a migratory bird, the Wilson's warbler (Cardellina pusilla), at fine enough spatial scales to facilitate assessing regional drivers of demographic trends. By screening 1626 samples using 96 single nucleotide polymorphisms (SNPs) selected from a large pool of candidates (~450,000), we identify novel region-specific migratory routes and timetables of migration along the Pacific Flyway. Our results illustrate that high-resolution genetic markers are more reliable, accurate, and amenable to high throughput screening than previously described tracking techniques, making them broadly applicable to large-scale monitoring and conservation of migratory organisms.
... These methods include extrinsic markers such as individual marking (Bauthian, Gossmann, Ferrand, & Julliard, 2007), VHF (Taylor et al., 2017) and GPS (Klaassen, Strandberg, Hake, & Alterstam, 2008) telemetry and light-level geolocators (Liechti et al., 2015;Stutchbury et al., 2009). Intrinsic approaches include morphology (Lopes, Marques, & Wennerberg, 2006), genetics (Lovette, Clegg, & Smith, 2004), parasites (Fallon, Fleischer, & Graves, 2006) and variation of trace elements (Szép et al., 2009) and stable isotopes (e.g., Hénaux, Powell, Vrtiska, & Hobson, 2012) in different tissues. Each method has its own advantages and shortcomings. ...
Ecosystems around the world are connected by seasonal migration. The migrant animals themselves are influenced by migratory connectivity through effects on the individual and the population level. Measuring migratory connectivity is notoriously difficult due to the simple requirement of data conveying information about the nonbreeding distribution of many individuals from several breeding populations. Explicit integration of data derived from different methods increases the precision and the reliability of parameter estimates.
We combine ring‐reencounter, stable isotope, and blood parasite data of Barn Swallows Hirundo rustica in a single integrated model to estimate migratory connectivity for three large scale breeding populations across a latitudinal gradient from Central Europe to Scandinavia. To this end, we integrated a non‐Markovian multistate mark‐recovery model for the ring‐reencounter data with normal and binomial mixture models for the stable isotope and parasite data.
The integration of different data sources within a mark‐recapture modeling framework enables the most precise quantification of migratory connectivity on the given broad spatial scale. The results show that northern‐breeding populations and Southern Africa as well as southern‐breeding populations and Western–Central Africa are more strongly connected through Barn Swallow migration than central European breeding populations with any of the African wintering areas. The nonbreeding distribution of Barn Swallows from central European breeding populations seems to be a mixture of those populations breeding further north and south, indicating a migratory divide.
... Determining whether populations are limited by events or processes that operate en route involves a complex series of tasks that collectively require intensive and extensive research using new and emerging technologies. We now know that rates of lipid deposition, as measured with plasma metabolite profiles, may serve as an indicator of habitat quality (Williams et al. 1999, Guglielmo et al. 2002, and genetics and stable isotope analyses can be valuable tools to elucidate links between breeding and wintering areas (Hobson and Wassenaar 1997, Webster et al. 2002, Lovette et al. 2004. Radar imagery (Diehl et al. 2003, Gauthreaux andBelser 2003) and low orbit radar receivers (Cochran and Wikelski, in press) also hold much potential for tracking large-scale movements and habitat use of migrants. ...
... Structured genetic and demographic patterns are predicted for species that exhibit high levels of natal philopatry (Avise 2004:499 subsequent reproduction will lead to gene flow among populations (Cabe 1999, Lovette et al. 2004, Arsenault et al. 2005). Yet several molecular examinations of avian species presumed to exhibit natal philopatry (Ransom et al. 2001, Roeder et al. 2001, Kimura et al. 2002, Pearce et al. 2004, or those documented to exhibit high levels of natal philopatry through banding studies (Avise et al. 1992, Birt-Friesen et al. 1992, Austin et al. 1994, have found sampled populations to be largely homogeneous at neutral genetic loci. ...
Iverson et al. (2004) used estimates of the homing rate for molting adult Harlequin Ducks (Histrionicus histrionicus) in Alaska to draw inferences about population structure. Homing rates, defined as one minus the ratio of birds recaptured elsewhere to those recaptured at the original banding site, were high (0.95–1.00) for males and females. Iverson et al. (2004) concluded that these high rates of homing are indicative of demographic independence among molting groups separated by small distances (tens to hundreds of kilometers) and that conservation efforts should recognize this fine-scale population structure. We re-examined their use of the homing rate, because their assumption of equal detection probability across a wide sampling area could have led to an upward bias in their estimates of site fidelity. As a result, we are hesitant to agree with their conclusion of high adult homing to molting areas and that molt-site fidelity is evidence for demographic independence. Our hesitancy stems from the fact that little is known about juvenile and adult movements within and among years, breeding area origins, and the variation of demographic parameters (e.g., survival and productivity) among molting groups. Furthermore, population genetic data of these molting groups suggest gene flow at both nuclear and mitochondrial loci. Such mixed messages between demographic (i.e., banding) and genetic data are increasingly common in ornithological studies and offer unique opportunities to reassess predictions and make more robust inferences about population structure across broad temporal and spatial scales. Thus, we stress that it is this broader scale perspective, which combines both demography and genetics, that biologists should seek to quantify and conservation efforts should seek to recognize.
... These species, such as vireos and flycatchers, winter along the Pacific coast of Mexico west and south of the Sierra Madre Occidental from southern Sonora to Guatemala (Barlow 1980[vireos], Fitzpatrick 1980, Hutto 1980Hutto , 1992. Further, genetically distinct races of some migrants that are broadly distributed in their breeding ranges, such as Common Yellowthroat (Geothlypis trichas) and Yellow-breasted Chats (Icteria virens), show segregation in wintering areas, with western breeders wintering in western Mexico and eastern breeders wintering along the Atlantic coast of Mexico and Central America (Lovette et al. 2004). Western bird populations wintering in western Mexico may require migration stopover sites within a relatively restricted area in the southwestern U.S. and northern Mexico as they travel north along the western edge of the Sierra Madre Occidental. ...
Migration stopover resources, particularly riparian habitats, are critically important to landbirds migrating across the arid southwestern region of North America. To explore the effects of species biogeography and habitat affinity on spring migration patterns, we synthesized existing bird abundance and capture data collected in riparian habitats of the borderlands region of the U.S. and Mexico. We determined the importance of geographic factors (longitude and latitude) in explaining variation in abundances and capture rates of 32 long-distance and three short-distance migrant species. Abundances and capture rates of 13 and 11 species, respectively, increased with increasing longitude, and four species' abundance and capture rates decreased with increasing longitude. Riparian associates, but not nonriparian species, were more abundant in western sites. Their abundance patterns were only weakly influenced by species biogeography. In contrast, biogeography did influence abundance patterns of nonriparian birds, suggesting that they choose the shortest, most direct route between wintering and breeding areas. We hypothesize that riparian obligate birds may, to some degree, adjust their migration routes to maximize time spent in high-quality riparian zones, but they are able to find suitable habitat opportunistically when crossing more hostile landscapes. In contrast, nonriparian birds adhere more closely to a hierarchical model in which the migratory route is determined by biogeographic constraints. Conservation of riparian habitats is necessary to meet future habitat stopover requirements of many western Neotropical migrant birds. We advocate a coordinated research effort to further elucidate patterns of distribution and habitat use so that conservation activities can be focused effectively.
Geografía de la Migración de Primavera de Aves Terrestres a Través de Hábitats Riparios en el Sudoeste de Norteamérica
Resumen. Los recursos que sirven como paradas migratorias, especialmente los hábitats riparios, son críticamente importantes para las aves migratorias terrestres a través de la región árida del sudoeste de Norteamérica. Para explorar los efectos de la biogeografía de las especies y la afinidad de hábitat sobre los patrones de migración de primavera, sintetizamos los datos existentes de abundancia y capturas de aves colectados en hábitats riparios en la zona fronteriza entre Estados Unidos y México. Determinamos la importancia de factores geográficos (latitud y longitud) en explicar la variación en las abundancias y en las tasas de captura de 32 especies migratorias de larga distancia y 3 de corta distancia. Las abundancias y tasas de captura de 13 y 11 especies, respectivamente, aumentaron con el aumento de la longitud, y cuatro especies mostraron una disminución con el aumento de la longitud. Las aves asociadas a los ambientes riparios fueron más abundantes en los sitios del oeste que las especies no riparias, y su abundancia sólo se vio levemente influenciada por la biogeografía de las especies. De modo contrastante, la biogeografía sí influenció los patrones de abundancia de las especies de aves no riparias, lo que sugiere que éstas escogieron la ruta más corta y directa entre las áreas de invernada y de reproducción. Proponemos la hipótesis de que las aves de hábitat ripario obligatorias pueden, hasta cierto grado, ajustar sus rutas migratorias para maximizar el tiempo en zonas riparias de alta calidad, pero también son capaces de encontrar hábitats adecuados de manera oportunista al cruzar paisajes más hostiles. De modo contrastante, las aves no riparias se adhieren más cercanamente a un modelo jerárquico en el cual la ruta migratoria es determinada por restricciones biogeográficas. La conservación de los hábitats riparios es necesaria para cumplir los requerimientos futuros de las paradas durante la migración de muchas aves migratorias Neotropicales del oeste. Abogamos por un esfuerzo de investigación coordinado para elucidar los patrones de distribución y de uso de hábitat de manera que las actividades para la conservación puedan ser enfocadas de manera eficiente.
... Consequently, there is a call for conservation concern for the newly described and unique evolutionary legacy of C. lupaster. This example illustrates the potential for misaligned policy if conservation units have been established predominantly from mitochondrial DNA (mtDNA), a single linkage group that represents the matriline that is difficult to interpret for interbreeding lineages with incomplete lineage sorting (e.g., [26][27][28]). ...
Range expansion is a widespread biological process, with well‐described theoretical expectations associated with the colonization of novel ranges. However, comparatively few empirical studies address the genomic outcomes accompanying the genome‐wide consequences associated with the range expansion process, particularly in recent or ongoing expansions. Here, we assess two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been under selection during range expansion. Using a restriction‐associated DNA sequencing (RADseq), we genotyped 394 coyotes at 22,935 SNPs and found that overall population structure corresponded to their 19th century historical range and two distinct populations that expanded during the 20th century. Counter to theoretical expectations for populations to bottleneck during range expansions, we observed minimal evidence for decreased genomic diversity across coyotes sampled along either expansion front, which is likely due to hybridization with other Canis species. Furthermore, we identified 12 SNPs, located either within genes or putative regulatory regions, that were consistently associated with range expansion. Of these 12 genes, three (CACNA1C, ALK, and EPHA6) have putative functions related to dispersal, including habituation to novel environments and spatial learning, consistent with the expectations for traits under selection during range expansion. Although coyote colonization of eastern North America is well‐publicized, this study provides novel insights by identifying genes associated with dispersal capabilities in coyotes on the two eastern expansion fronts.
... The use of genomic markers for population assignment models requires geographically structured genetic variation on the breeding grounds. In North America, several species of Nearctic-Neotropic (hereafter: Neotropical) migratory songbirds have been shown to exhibit population structure on a broad longitudinal scale (Kimura et al. 2002;Lovette et al. 2004;Kelly et al. 2005;Boulet et al. 2006;Irwin et al. 2011). However, genetic markers have generally provided weak resolving power in identifying breeding ground population structure in avian species and this has been a limitation in the use of genetic markers for studying migratory connectivity in species with more limited geographic ranges (Oyler-McCance et al. 2016). ...
Understanding migratory connectivity is essential for determining the drivers behind population dynamics and for implementing effective conservation strategies for migratory species. Genetic markers provide a means to describe migratory connectivity, however they can be uninformative for species with weak population genetic structure, which has limited their application. Here, we demonstrated a genomic approach to describing migratory connectivity in the prothonotary warbler, Protonotaria citrea, a Neotropical songbird of conservation concern. Using 26,189 SNPs, we revealed regional genetic structure between the Mississippi River Valley and the Atlantic Seaboard with overall weak genetic differentiation among populations (FST = 0.0055; 95% CI: 0.0051 ‐ 0.0059). Genetic variation had a stronger association with geographic rather than environmental factors, with each explaining 14.5% and 8.2% of genetic variation, respectively. By varying the numbers of genomic markers used in population assignment models with individuals of known provenance, we identified a maximum assignment accuracy (89.7% to site, 94.3% to region) using a subset of 600 highly differentiated SNPs. We then assigned samples from nonbreeding sites to breeding region, and found low migratory connectivity. Our results highlight the importance of filtering markers for informative loci in models of population assignment. Quantifying migratory connectivity for weakly structured species will be useful for expanding studies to a wider‐range of migratory species across taxonomic groups and may contribute to a deeper understanding of the evolution of migratory strategies.
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... Consequently, there is a call for conservation concern for the newly described and unique evolutionary legacy of C. lupaster. This example illustrates the potential for misaligned policy if conservation units have been established predominantly from mitochondrial DNA (mtDNA), a single linkage group that represents the matriline that is difficult to interpret for interbreeding lineages with incomplete lineage sorting (e.g., [26][27][28]). ...
The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover spatial patterns of variation in 281 canids in central Ontario and the Great Lakes region. This represents the first genome-wide single nucleotide polymorphism (SNP) dataset with substantial sample sizes of representative populations. Although they comprise their own genetic cluster, we found evidence of eastern wolf dispersal outside of the boundaries of protected areas, in that the frequency of eastern wolf genetic variation decreases with increasing distance from provincial parks. We detected eastern wolf alleles in admixed coyotes along the northeastern regions of Lake Huron and Lake Ontario. Our analyses confirm the unique genomic composition of eastern wolves, which are mostly restricted to small fragmented patches of protected habitat in central Ontario. We hope this work will encourage an innovative discussion regarding a plan for managed introgression, which could conserve eastern wolf genetic material in any genome regardless of their potential mosaic ancestry composition and the habitats that promote them.
... Consequently, there is a call for conservation concern for the newly described and unique evolutionary legacy of C. lupaster. This example illustrates the potential for misaligned policy if conservation units have been established predominantly from mitochondrial DNA (mtDNA), a single linkage group that represents the matriline that is difficult to interpret for interbreeding lineages with incomplete lineage sorting (e.g., [26][27][28]). ...
The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover spatial patterns of variation in 281 canids in central Ontario and the Great Lakes region. This represents the first genome-wide single nucleotide polymorphism (SNP) dataset with substantial sample sizes of representative populations. Although they comprise their own genetic cluster, we found evidence of eastern wolf dispersal outside of the boundaries of protected areas, in that the frequency of eastern wolf genetic variation decreases with increasing distance from provincial parks. We detected eastern wolf alleles in admixed coyotes along the northeastern regions of Lake Huron and Lake Ontario. Our analyses confirm the unique genomic composition of eastern wolves, which are mostly restricted to small fragmented patches of protected habitat in central Ontario. We hope this work will encourage an innovative discussion regarding a plan for managed introgression, which could conserve eastern wolf genetic material in any genome regardless of their potential mosaic ancestry composition and the habitats that promote them.
... migratory connectivity) 4,23 . However, only a few studies [24][25][26] have addressed so far the origin of individuals gathering at staging areas or stopover sites during migration, as insufficient genetic differentiation among populations of migratory species can render the assignment efforts futile 27 . Since migrating birds are subject to a number of unfavorable conditions that could, in turn, have an effect at a breeding population-level 28 resolving movements of individuals across their annual cycle is necessary in order to assess the impact of local threats to population dynamics 29 as well as to design effective conservation strategies for migratory birds 30,31 . ...
Identifying patterns of individual movements in spatial and temporal scales can provide valuable
insight into the structure of populations and the dynamics of communities and ecosystems. Especially
for migrating birds, that can face a variety of unfavorable conditions along their journey, resolving
movements of individuals across their annual cycle is necessary in order to design better targeted
conservation strategies. Here, we studied the movements of a small migratory falcon, the Lesser
Kestrel (Falco naumanni), by genetically assigning feathers from individuals of unknown origin that
concentrate in large roosts during the pre-migratory period. Our findings suggest that birds from
multiple breeding populations in the Central and Eastern Mediterranean region move towards two premigratory
sites in the Balkans, some of them detouring greatly from their expected flyways, travelling
more than 500 km to reach these sites and prepare for the post-nuptial migration. By identifying the
origin of individuals using the pre-migratory sites, not only we provide a better understanding of the
possible impact of local threats at these sites on multiple breeding populations but also inform the
design of effective conservation actions for the species.
... The western auricollis subspecies has a fragmented breeding distribution in the west, which includes our study area in the south Okanagan valley of British Columbia, Canada, at the northern tip of the geographic range for this subspecies (Fig. 1). Genetic evidence indicates that the western subspecies overwinters on the westcoast of Mexico (southern Baja California, Sinaloa to Oxaca) [20]. Chats in the south Okanagan valley nest in low elevation (>500 m) riparian thickets dominated by wild rose (Rosa spp.), snowberry, and other native shrub species [21]. ...
Background
Long-distance migratory birds in North America have undergone precipitous declines over the past half-century. Although the trend is clear, for many migrating species underpinning the exact causes poses a challenge to conservation due to the numerous stressors that they encounter. Climate conditions during all phases of their annual cycle can have important consequences for their survival. Here, using 15 years of capture-recapture dataset, we determined the effects of various climate factors during the breeding, wintering, and migrating stages on the annual survival of a western yellow-breasted chat (Icteria virens auricollis) population breeding in southwestern Canada. ResultsEl Niño effects over the entire annual cycle had little influence on the annual apparent survival of yellow-breasted chats. However, we found evidence that wind conditions during migration, specifically average westerly wind speed or the frequency of storm events, had significant adverse effects on adult annual apparent survival. In comparison, precipitation levels on wintering ground had little to no influence on adult annual apparent survival, whereas growing degree days on the breeding ground had moderate but positive effects. Conclusions
In the face of climate change and its predicted impacts on climate processes, understanding the influence of weather conditions on the survival of migrating birds can allow appropriate conservation strategies to be adopted for chats and other declining neotropical migrants.
... For DNA sexing, three breast feathers were plucked from each bird and placed in a coin envelope with the band number, measurements, age, date, and capture site information provided on the label. DNA was extracted from plucked breast feathers using a protocol provided by Dr. I. Lovette of Cornell University (Lovette et al. 2004) using the commercially available Qiagen DNeasy Kit®. I clipped small rings from the feather shaft tip (3-4 mm in length) and placed them in a 1.5 mL eppendorf tube. ...
... Die Rohrammer im Zürcher Oberland ist demnach räumlich als «patchy population» organisiert. Dass eine fragmentierte Verbreitung nicht zwangsläufig auf eine Metapopulationsstruktur hinweisen muss, wurde auch bei anderen Vogelarten gefunden (Ball & Avise 1992, Mila et al. 2000, Ruegg & Smith 2002, Lovette et al. 2004, Veit et al. 2005. Hinweise für das Vorliegen einer Metapopulation aufgrund genetischer Daten wurden für verschiedene taxonomische Gruppen gefunden (z.B. ...
Many species persist in fragmented populations as a consequence of past and ongoing habitat destruction. Despite this, the importance of remnant fragments varying in size for the conservation of species is often unclear. From 2002 to 2006, we studied the role of small and large wetland fragments (2-247 ha) within a 200 km2 area in northeastern Switzerland for the persistence of the Reed Bunting Emberiza schoeniclus, a characteristic species of wetlands. Results from both artificial nest experiments and real nests showed that nest success increased with vegetation cover around and above the nest, distance from the water-sided reed edge, and to a lesser extent also with distance from the land-sided reed edge, and the size and shape (expressed as the ratio between edge length and area of the patch) of the reed patch containing the nest. These findings suggest that nest success of the Reed Bunting fundamentally depends on the quality of the reed patches: large and old reed patches with dense vegetation are habitats of good quality and conducive to nest success, whereas young and small patches, such as one-year-old reed stripes («rotational fallows»), are suboptimal habitats. Probability of nest predation was not related to whether or not a nest was visited by observers. Reproductive performance of the Reed Bunting in small and large wetland fragments did not basically differ, although small fragments were better reproductive grounds in one of four years. Recruitment probability, defined as probability that individuals born and ringed in our study area were re-sighted as breeders in a subsequent year, was not related to fragment size either. Based on demographic and population genetic analyses, the local populations in the different fragments were strongly connected, thus forming a patchy population (and not a metapopulation, despite the fragmented distribution). Small and large fragments turned out to be mostly sinks, and the annual growth rate of the entire population network was insufficient for selfmaintenance. Both findings imply that the persistence of the local populations and of the entire patchy population depended on immigration, which was found to annually range from 43.8 to 61.4 %. We conclude from this study that small and large wetland fragments contributed equally to the population network of the Reed Bunting in northeastern Switzerland, even though they have to be considered as sinks from a demographic perspective. For the conservation of the Reed Bunting, future management of wetlands should aim at sparing large reed patches along the water's edge to provide adequate nest sites.
... Die Rohrammer im Zürcher Oberland ist demnach räumlich als «patchy population» organisiert. Dass eine fragmentierte Verbreitung nicht zwangsläufig auf eine Metapopulationsstruktur hinweisen muss, wurde auch bei anderen Vogelarten gefunden (Ball & Avise 1992, Mila et al. 2000, Ruegg & Smith 2002, Lovette et al. 2004, Veit et al. 2005. Hinweise für das Vorliegen einer Metapopulation aufgrund genetischer Daten wurden für verschiedene taxonomische Gruppen gefunden (z.B. ...
Many species persist in fragmented populations as a consequence of past and ongoing habitat destruction. Despite this, the importance of remnant fragments varying in size for the conservation of species is often unclear. From 2002 to 2006, we studied the role of small and large wetland fragments (2–247 ha) within a 200 km2 area in northeastern Switzerland for the persistence of the Reed Bunting Emberiza schoeniclus, a characteristic species of wetlands. Results from both artificial nest experiments and real nests showed that nest success increased with vegetation cover around and above the nest, distance from the water-sided reed edge, and to a lesser extent also with distance from the land-sided reed edge, and the size and shape (expressed as the ratio between edge length and area of the patch) of the reed patch containing the nest. These findings suggest that nest success of the Reed Bunting fundamentally depends on the quality of the reed patches: large and old reed patches with dense vegetation are habitats of good quality and conducive to nest success, whereas young and small patches, such as one-year-old reed stripes («rotational fallows»), are suboptimal habitats. Probability of nest predation was not related to whether or not a nest was visited by observers. Reproductive performance of the Reed Bunting in small and large wetland fragments did not basically differ, although small fragments were better reproductive grounds in one of four years. Recruitment probability, defined as probability that individuals born and ringed in our study area were re-sighted as breeders in a subsequent year, was not related to fragment size either. Based on demographic and population genetic analyses, the local populations in the different fragments were strongly connected, thus forming a patchy population (and not a metapopulation, despite the fragmented distribution). Small and large fragments turned out to be mostly sinks, and the annual growth rate of the entire population network was insufficient for selfmaintenance. Both findings imply that the persistence of the local populations and of the entire patchy population depended on immigration, which was found to annually range from 43,8 to 61,4 %. We conclude from this study that small and large wetland fragments contributed equally to the population network of the Reed Bunting in northeastern Switzerland, even though they have to be considered as sinks from a demographic perspective. For the conservation of the Reed Bunting, future management of wetlands should aim at sparing large reed patches along the water’s edge to provide adequate nest sites.
... The mitochondrial control region is a rapidly evolving locus extensively used for population-level studies (see Pearce 2006), and its potential utility to discriminate among geographic origins has been previously shown in a number of species (Lovette et al. 2004). However, this gene appeared ineffective for the geographic assessment of Cory's Shearwaters beyond the taxon level. ...
... More recently, advances in DNA profiling technology and population genetic theory are being applied to indirectly study migration [15][16][17][18] as population level data may be used to characterize patterns of gene flow and estimate effective population size [17,18]. However, different markers often yield conflicting results [17] and often do not provide sufficient geographic resolution [19]. ...
Migratory patterns of bats are not well understood and traditional methods to study this, like capture-mark-recapture, may not provide enough detail unless there are many records. Stable isotope profiles of many animal species have been used to make inferences about migration. Each year Myotis lucifugus and M. septentrionalis migrate from summering roosts to swarming caves and mines in the fall, but the pattern of movement between them is not well understood. In this study, fur δ13C and δ15N values of 305 M. lucifugus and 200 M. septentrionalis were analyzed to make inferences about migration patterns between summering areas and swarming sites in Nova Scotia, Canada. We expected that there would be greater variability in δ13C and δ15N among individuals at swarming sites because it was believed that these sites are used by individuals originating from many summering areas. There was extensive overlap in the standard ellipse area, corrected for small sample sizes (SEAc), of bats at swarming sites and much less overlap in SEAc among groups sampled at summering areas. Meaningful inference could not be made on M. septentrionalis because their low variation in SEAc may have been the result of sampling only 3 summering areas. However, for M. lucifugus, swarming sites had larger SEAc than summering areas and predictive discriminant analysis assigned swarming bats to multiple summering areas, supporting the contention that swarming bats are mixed aggregations of bats from several summering areas. Together, these data support the contention that swarming sites have catchment areas for bats from multiple summering areas and it is likely that the catchment areas for swarming sites overlap. These data suggest that δ13C and δ15N profiling of bat fur offer some potential to make inferences about regional migration in bats.
... Alternatively, genetic and isotopic markers that use information contained within the feathers to pinpoint an individuals population of origin have broad appeal because they are cost-effective, noninvasive and do not require recapture (Rubenstein et al. 2002;Kelly et al. 2005;Rundel et al. 2013). However, intrinsic marking techniques have been plagued in the past by low resolution and/or technical issues related to working with feathers (Segelbacher 2002;Lovette et al. 2004;Wunder et al. 2005). Thus, there remains a need for a broadly applicable method for identifying migratory connectivity at spatial scales that are informative for assessing drivers of regional population declines. ...
Neotropical migratory birds are declining across the Western Hemisphere, but conservation efforts have been hampered by the inability to assess where migrants are most limited – the breeding grounds, migratory stopover sites, or wintering areas. A major challenge has been the lack of an efficient, reliable, and broadly applicable method for measuring the strength of migratory connections between populations across the annual cycle. Here we show how high-resolution genetic markers can be used to identify genetically distinct groups of a migratory bird, the Wilson's warbler (Cardellina pusilla), at fine enough spatial scales to facilitate assessing regional drivers of demographic trends. By screening 1626 samples using 96 highly divergent single nucleotide polymorphisms (SNPs) selected from a large pool of candidates (~450,000), we identify novel region-specific migratory routes and timetables of migration along the Pacific Flyway. Our results illustrate that high-resolution genetic markers are more reliable, precise, and amenable to high throughput screening than previously described intrinsic marking techniques, making them broadly applicable to large-scale monitoring and conservation of migratory organisms.This article is protected by copyright. All rights reserved.
... These species, such as vireos and flycatchers, winter along the Pacific coast of Mexico west and south of the Sierra Madre Occidental from southern Sonora to Guatemala (Barlow 1980[vireos], Fitzpatrick 1980, Hutto 1980Hutto , 1992. Further, genetically distinct races of some migrants that are broadly distributed in their breeding ranges, such as Common Yellowthroat (Geothlypis trichas) and Yellow-breasted Chats (Icteria virens), show segregation in wintering areas, with western breeders wintering in western Mexico and eastern breeders wintering along the Atlantic coast of Mexico and Central America (Lovette et al. 2004). Western bird populations wintering in western Mexico may require migration stopover sites within a relatively restricted area in the southwestern U.S. and northern Mexico as they travel north along the western edge of the Sierra Madre Occidental. ...
Migration stopover resources, particularly riparian habitats, are critically important to landbirds migrating across the arid southwestern region of North America. To explore the effects of species biogeography and habitat affinity on spring migration patterns, we synthesized existing bird abundance and capture data collected in riparian habitats of the borderlands region of the U.S. and Mexico. We determined the importance of geographic factors (longitude and latitude) in explaining variation in abundances and capture rates of 32 long-distance and three short-distance migrant species. Abundances and capture rates of 13 and 11 species, respectively, increased with increasing longitude, and four species' abundance and capture rates decreased with increasing longitude. Riparian associates, but not nonriparian species, were more abundant in western sites. Their abundance patterns were only weakly influenced by species biogeography. In contrast, biogeography did influence abundance patterns of nonriparian birds, suggesting that they choose the shortest, most direct route between wintering and breeding areas. We hypothesize that riparian obligate birds may, to some degree, adjust their migration routes to maximize time spent in high-quality riparian zones, but they are able to find suitable habitat opportunistically when crossing more hostile landscapes. In contrast, nonriparian birds adhere more closely to a hierarchical model in which the migratory route is determined by biogeographic constraints. Conservation of riparian habitats is necessary to meet future habitat stopover requirements of many western Neotropical migrant birds. We advocate a coordinated research effort to further elucidate patterns of distribution and habitat use so that conservation activities can be focused effectively
... The effective population size of mtDNA is approximately four times smaller than nuclear markers due to both maternal-inheritance (in vertebrates) and haploidy, theoretically allowing differentiation to arise more rapidly between isolated populations. However, the patterns revealed by mtDNA are most often significant only at broad continental scales (Clegg et al. 2003, Lovette et al. 2004. Given their high variability and bi-parental inheritance, microsatellite markers may be a better choice of genetic marker for studies of migratory connectivity (Sunnucks 2000, Avise 2004). ...
... Geographic isolation between North America and South America appears to have been a strong barrier to gene flow within these species after the initial colonization. In addition, east-west genetic differentiation is found among many widespread migratory birds in temperate North America (Milot et al. 2000, Kimura et al. 2002, Ruegg and Smith 2002, Newton 2003, Lovette et al. 2004, Peters et al. 2005b) and suggests two major glacial refugia on either side of the Rocky Mountains or Great Plains during the Pleistocene (Colbeck et al. 2008). Thus, North American Cinnamon Teal and Blue-winged Teal might descend from a common ancestor that colonized North America from South America, then diverged in allopatry on either side of the Rocky Mountains. ...
Divergent selection can lead to substantial morphological and behavioral differences despite slight differentiation in neutral genetic variation. We examined the evolutionary history of two closely related waterfowl, the Cinnamon Teal (Anas cyanoptera) and Blue-winged Teal (A. discors), that are morphologically distinct but paraphyletic in mitochondrial DNA (mtDNA) and share allozyme alleles. Sequences of mtDNA and two nuclear introns revealed that North American Cinnamon Teal (n = 70) and Blue-winged Teal (n = 76) are characterized by high genetic diversity, a large effective population size, and recent population expansion. In contrast, South American Cinnamon Teal (n = 102) have less genetic diversity and a smaller effective population size that has been more stable. We found 91 unique mtDNA haplotypes, only a few of which were shared by the two species or the three subspecies of the Cinnamon Teal, but the haplotypes were intermixed in a polyphyletic relationship, and we found no diagnostic phylogroups. Moreover, populations were more strongly differentiated in mtDNA (ΦST = 0.41) than in the nuclear introns (ΦST = 0.04–0.06). Analyses of isolation with migration indicated that sharing of haplotypes and alleles in the two continents is more likely attributable to incomplete lineage sorting than to gene flow, whereas estimates within each continent yielded higher migration rates. The oldest divergence was between North American Cinnamon Teal and the other taxa, whereas the Blue-winged Teal likely split from South American Cinnamon Teal more recently. Considerable overlap in confidence intervals for these divergences, however, suggests that these taxa diversified rapidly.
... Ryder et al., 2011); however, most use stable isotopes or genetic methods, which have limited spatial resolution (e.g. eastern and western populations winter in different areas; Kimura et al., 2002;Clegg et al., 2003;Lovette, 2004;Boulet et al., 2006). To our knowledge, neither genetic nor isotope methods have been used to assess connectivity of Bobolink populations. ...
In the Northern Hemisphere, bird migration from the tropic to the temperate zone in spring is thought to proceed at a rate determined in large part by local phenology. In contrast, little is understood about where birds go or the factors that determine why they move or where they stop during the post-breeding period.
Study sites were in Oregon, Nebraska and Vermont, and location data we collected extend south to Argentina.
We deployed light-level geolocators on individual Bobolinks from three populations across the breeding range and compare their southbound movement phenology to austral greening as indicated by the Normalized Difference Vegetation Index.
Bobolinks from all breeding populations synchronously arrived and remained for up to several weeks in two sequential, small non-breeding areas that were separated by thousands of kilometres, before staging for pre-alternate moult. Similar to the migration patterns of birds to northern breeding areas, movements into the Southern Hemisphere corresponded to increasing primary productivity.
Our findings suggest that the Bobolink's southbound migration is broadly constrained by resource availability, and its non-breeding distribution has been shaped by the seasonal phenology of grasslands in both time and space. This is the first documentation of individual birds from across a continental breeding range exhibiting phenological matching during their post-breeding southward migration. Known conservation threats overlap temporally and spatially with large concentrations of Bobolinks, and should be closely examined. We emphasize the need to consider how individuals move and interact with their environment throughout their annual cycle and over hemispheric scales.
... Stable isotope markers require known geographic isoscapes, knowledge of when animals incorporate isotopes into tissues, and turnover times within tissue types (Hobson and Wassenaar 1997). Given these limitations, both genetic and isotopic analyses have yielded imprecise and inconclusive results in previous studies (Wenink et al. 1996, Wennerberg 2001, Lovette et al. 2004, Kelly et al. 2008. In recent years, light-level geolocation has enhanced our ability to estimate spatial and temporal movements of individuals (Clark et al. 2010), but this approach is expensive, typically results in data from small numbers of individuals, and provides limited geographic resolution. ...
Five subspecies of Dunlins (Calidris alpina) that breed in Beringia are potentially sympatric during the non-breeding season. Studying their ecology during this period requires techniques to distinguish individuals by subspecies. Our objectives were to determine (1) if five morphometric measures (body mass, culmen, head, tarsus, and wing chord) differed between sexes and among subspecies (C. a. actites, arcticola, kistchinski, pacifica, and sakhalina), and (2) if these differences were sufficient to allow for correct classification of individuals using equations derived from discriminant function analyses. We conducted analyses using morphometric data from 10 Dunlin populations breeding in northern Russia and Alaska, USA. Univariate tests revealed significant differences between sexes in most morphometric traits of all subspecies, and discriminant function equations predicted the sex of individuals with an accuracy of 83-100% for each subspecies. We provide equations to determine sex and subspecies of individuals in mixed subspecies groups, including the (1) Western Alaska group of arcticola and pacifica (known to stage together in western Alaska) and (2) East Asia group of arcticola, actites, kistchinski, and sakhalina (known to winter together in East Asia). Equations that predict the sex of individuals in mixed groups had classification accuracies between 75% and 87%, yielding reliable classification equations. We also provide equations that predict the subspecies of individuals with an accuracy of 22-96% for different mixed subspecies groups. When the sex of individuals can be predetermined, the accuracy of these equations is increased substantially. Investigators are cautioned to consider limitations due to age and feather wear when using these equations during the non-breeding season. These equations will allow determination of sexual and subspecies segregation in non-breeding areas, allowing implementation of taxonomic-specific conservation actions.
... For example, pathogens carried by migratory birds, such as Influenza, West Nile and Salmonella, significantly impact domestic animal and human health and there is an urgent need to understand how spillover of pathogens from local hosts and migratory birds may change under climate warming (Fuller et al. 2012). Further, many songbird populations are declining, but it has often proven difficult to link breeding and wintering populations at fine enough geographic scales to determine the causes of declines in particular populations of migratory birds (Lovette et al. 2004; Faaborg et al. 2010). While there is a great deal of valuable information available on the breeding and wintering localities of North American birds that has been painstakingly collected (Jones & Donovan 1996; Ammon & Gilbert 1999), additional information on the connectivity of individual populations is nevertheless needed for making better informed conservation decisions. ...
Methods for determining patterns of migratory connectivity in animal ecology have historically been limited due to logistical challenges. Recent progress in studying migratory bird connectivity has been made using genetic and stable-isotope markers to assign migratory individuals to their breeding grounds. Here, we present a novel Bayesian approach to jointly leverage genetic and isotopic markers and we test its utility on two migratory passerine bird species. Our approach represents a principled model-based combination of genetic and isotope data from samples collected on the breeding grounds and is able to achieve levels of assignment accuracy that exceed those of either method alone. When applied at large scale the method can reveal specific migratory connectivity patterns. In Wilson's warblers (Wilsonia pusilla), we detect a subgroup of birds wintering in Baja that uniquely migrate preferentially from the coastal Pacific Northwest. Our approach is implemented in a way that is easily extended to accommodate additional sources of information (e.g. bi-allelic markers, species distribution models, etc.) or adapted to other species or assignment problems.
... Such dramatic restrictions on immigration are highly unlikely in most temperate landscapes , perhaps because of the propensity of many species to exhibit long-distance movements during migration and postnatal dispersal. Studies of genetic differentiation support the idea that many neotropical species are quite sedentary (Capparella 1988; Bates 2000), whereas most species from northern temperate areas show little genetic differentiation across their geographic ranges (Lovette et al. 2003). Long-term datasets evaluating extinction and recolonization phenomena are rare for any landscape. ...
Irrespective of geography, forest destruction and fragmentation lead to lower avian species richness. The underlying mechanisms causing local extirpations have been studied most thoroughly in northern temperate landscapes, where higher levels of brood parasitism, nest predation, and possibly decreased food availability are responsible for the loss of some species. Tropical landscapes are being similarly altered, but studies of responses by tropical birds remain relatively scarce. Predicting how tropical birds respond to habitat loss and fragmentation should not be extended directly from the results of temperate investigations. Tropical birds possess different evolutionary and life histories, which make them vulnerable to a different suite of threats than those normally considered for birds from temperate regions. These same traits, including greater physio- logical and sensory specialization, reduced dispersal capabilities, and much lower local and regional popula- tion densities, indicate that strategies for conserving bird diversity will be different in tropical landscapes than those for temperate regions.
One of the biggest threats to the survival of many plant and animal species is the destruction or fragmentation of their natural habitats. The conservation of landscape connections, where animals, plants, and ecological processes can move freely from one habitat to another, is therefore an essential part of any new conservation or environmental protection plan. In practice, however, maintaining, creating, and protecting connectivity in our increasingly dissected world is a daunting challenge. This fascinating volume provides a synthesis on the current status and literature of connectivity conservation research and implementation. It shows the challenges involved in applying existing knowledge to real-world examples and highlights areas in need of further study. Containing contributions from leading scientists and practitioners, this topical and thought-provoking volume will be essential reading for graduate students, researchers, and practitioners working in conservation biology and natural resource management.
The current and rapid anthropogenic environmental changes could disproportionately impact ecosystems, particularly when they affect species with critical roles in ecosystem integrity. As top predators, raptors provide critical top-down ecosystem services and structure food webs. Yet, many avian predators are currently experiencing global population declines and some are threatened with extinction. The dire conservation status of numerous raptor species warrants urgent action, and detailed ecological data are needed to guide management strategy, including empirical knowledge regarding genetic structure. To that end, we compiled published studies investigating population genetic structure in raptors. Out of a total of 83 publications on 50 raptors species published, we identified a lack of empirical genetic studies for species from the Southern Hemisphere and species with a high level of extinction risk according to IUCN Red List criteria. Only 24% of the species studied are considered “threatened” (i.e., with the “Vulnerable”, “Endangered”, or “Critically Endangered” status). We found a significant signal of genetic differentiation in 41 species (82%) at the study-specific population. Isolation-by-Distance is a common pattern of genetic differentiation in raptors. Future steps in raptor conservation could prioritize facilitating genetic studies on species located in the Southern Hemisphere and on species with a conservation status. A better inclusion of some key genetic metrics (e.g., Ne, Ne/Nc, genetic diversity) in published studies will further help management and conservation across various species and ecosystems.
Climate change is a serious challenge faced by all plant and animal species. Climate change vulnerability assessments (CCVAs) are one method to assess risk and are increasingly used as a tool to inform management plans. Migratory animals move across regions and continents during their annual cycles where they are exposed to diverse climatic conditions. Climate change during any period and in any region of the annual cycle could influence survival, reproduction, or the cues used to optimize timing of migration. Therefore, CCVAs for migratory animals best estimate risk when they include climate exposure during the entire annual cycle. We developed a CCVA incorporating the full annual cycle and applied this method to 46 species of migratory birds breeding in the Upper Midwest and Great Lakes (UMGL) region of the United States. Our methodology included background risk, climate change exposure × climate sensitivity, adaptive capacity to climate change, and indirect effects of climate change. We compiled information about migratory connectivity between breeding and stationary non-breeding areas using literature searches and U.S. Geological Survey banding and re-encounter data. Climate change exposure (temperature and moisture) was assessed using UMGL breeding season climate and winter climate from non-breeding regions for each species. Where possible, we focused on non-breeding regions known to be linked through migratory connectivity. We ranked 10 species as highly vulnerable to climate change and two as having low vulnerability. The remaining 34 species were ranked as moderately vulnerable. In general, including non-breeding data provided more robust results that were highly individualistic by species. Two species were found to be highly vulnerable throughout their annual cycle. Projected drying will have the greatest effect during the non-breeding season for species overwintering in Mexico and the Caribbean. Projected temperature increases will have the greatest effect during the breeding season in UMGL as well as during the non-breeding season for species overwintering in South America. We provide a model for adaptive management of migratory animals in the face of projected climate change, including identification of priority species, research needs, and regions within non-breeding ranges for potential conservation partnerships.
We describe the range-wide phylogeography of Blackpoll Warblers (Setophaga striata), a migratory passerine with a broad breeding range in North America's boreal forest that encompasses several possible biogeographic barriers but shows no phenotypic geographic variation. We used mitochondrial control-region sequences from 304 individuals in combination with ecological niche models and coalescent simulations to test alternative historical hypotheses about the number of Pleistocene refugial populations and divergences among modern populations. Population pairwise F-ST. and spatial analyses of molecular variance suggested significant genetic structure among western, eastern, and Newfoundland populations, but no structure among sky-island populations at the southeastern periphery of the breeding range. Inferred gene flow fits a model of isolation-by-distance. Coalescent simulations rejected all multiple-refugia hypotheses in favor of a single refugium. Paleodistribution models and modern migratory pathways suggested that the refugium was located in southeastern North America. In contrast to previous studies that have invoked multiple Pleistocene refugia as the cause of genetic structure in North American bird species, our analyses suggest that geographic structure in Blackpoll Warblers results from isolation-by-distance rather than a history of sundered populations. Received 23 November 2011, accepted 20 March 2012.
Climate change is a serious challenge faced by all flora and fauna on earth. Climate vulnerability
analyses are one method to assess risk and are increasingly used as a tool to inform management plans.
Ideally, risk should be assessed throughout an animal’s entire annual cycle, but migratory animals move
across vast regions and can be difficult to track. Consequently, the challenge of conducting comprehensive
full annual life cycle analyses has not been well addressed. Here, we developed a method to assess full annual
cycle vulnerability to climate change for 46 species of migratory birds that breed in the Upper Midwest and
Great Lakes region (UMGL). Our methodology included background risk, climate exposure × climate sensitivity,
adaptive capacity to climate change, and indirect effects of climate change. Where possible, we used USGS capture-recapture data and conducted literature searches to determine migratory connectivity. Climate vulnerability was then assessed using the UMGL breeding season climate and winter climate from linked non-breeding regions for each species. We ranked nine species as “highly vulnerable to climate change” (Red-necked Grebe, Forster’s Tern, Black Tern, Caspian Tern, Eastern Whip-poor-will, Yellow-bellied Flycatcher, Black-throated Blue Warbler, Worm-eating Warbler, and Rusty Blackbird) and two as having “low vulnerability” (Killdeer and Red-winged Blackbird). In general, vulnerability was driven by poor adaptive capacity to climate change, specifically high breeding site fidelity. Such species may be slow to disperse or expand their range in response to climate change. Projected drying will have its greatest effect on vulnerability in the Mexican and Caribbean non-breeding regions while projected temperature increases will have their greatest effect on the UMGL breeding grounds and South American non-breeding grounds. We identified nine species that were vulnerable to temperature and/or moisture change throughout their annual cycle (Upland Sandpiper, Black Tern, Eastern Whip-poor-will, Acadian Flycatcher, Nashville Warbler, Prairie Warbler, Dickcissel, Bobolink, and Orchard Oriole). All but one of these are considered species of conservation concern in the UMGL. Finally, we provide guidance to how our approach could be applied to adaptive management, including identifying: priority species and habit types, regions within the non-breeding range for potential conservation partnerships, and research gaps.
Data from eight microsatellite markers screened in 246 rhinoceros auklets (Cerorhinca monocerata) from across the North Pacific revealed multiple genetic groups. The east (North America) to west (Japan) split was clearly evident in all analyses. Within the eastern Pacific, a minimum of three genetic groups are present. Surprisingly, rhinoceros auklets from Triangle Island, British Columbia, were genetically isolated from other nearby populations, including the breeding colony on Pine Island (~100 km to the east). A fourth genetic cluster (Chowiet Is) was detected using principal coordinate’s analysis; however, sample sizes were limited. Patterns of differentiation correspond to nonbreeding distributions with the eastern and western Pacific birds spending time off the west coast of North America and Japan, respectively, and may represent historical isolation in separate refugia during the Pleistocene glaciations. The patterns of genetic structure result from a combination of historical and contemporary factors influencing dispersal of rhinoceros auklets.
The previous two chapters present detailed case studies describing the connectivity in two Nearctic-Neotropical migratory songbirds, the American Redstart (Setophaga ruticilla) and the northern yellow warbler (Dendroica petechia; group aestiva). Using different approaches, these studies demonstrate how multiple sources of information and assignment techniques can be combined to reveal broad patterns of connectivity between breeding, wintering, and migration periods. Here, we summarize the results of these studies and briefly discuss whether these tools can be applied to other systems. We also explicitly address the assumptions, limitations, and potential sources of variation in these approaches. Next, we discuss how patterns of connectivity can be used to advance our understanding of population dynamics and make sound conservation decisions. Finally, we outline a few key ideas for future projects that we believe would make significant contributions to improving our ability to link migratory populations, placing emphasis on projects that would be suitable for graduate students interested in pursuing research in this field.
Population-specific genetic tags and stable isotope ratios are markers that can be used to track migratory birds throughout their annual cycle and determine their degree of migratory connectivity or the geographic linking of individuals or populations between different stages of the annual cycle. Until recently, few data had been obtained on the connectivity of small-bodied migrant birds such as warblers. Here, we combined geographic differences in mitochondrial DNA (mtDNA), stable hydrogen isotope (δD) analysis, and banding records to assess migratory connectivity in the northern yellow warbler (Dendroica petechia; aestiva group) populations and describe their migration patterns. To use mtDNA variation to identify the geographic breeding region from which birds originated (eastern lineage: eastern and central North America; western lineage: western and central North America; southern lineage: southwest United States), we genotyped 133 wintering birds obtained from 23 sites in Mexico, Central America, and Venezuela; 438 spring migrants from 32 stopovers in North America; and 428 fall migrants from 30 stopovers in North America. There was strong segregation between lineages throughout the annual cycle: the eastern lineage was present in eastern and central North America during migration, and in Yucatan (Mexico), Panama, and Venezuela during the wintering season; the western lineage was present in central and western North America during migration and in Mexico and Panama during the wintering season; the southern lineage was restricted to western Mexico during the wintering season. The distributions of eastern and western lineages indicated strong continental-scale connectivity and a parallel migration system. We conducted δD analysis on 94 feather samples collected from wintering birds captured on eight wintering areas and on 347 feather samples taken from migrants captured on six spring stopovers and five fall stopovers located in the United States and Mexico. For a large portion of these samples (n 407), genotypic information was also available, and we combined these two types of information to create lineage-specific isotopic subregions to which birds were then assigned. The addition of the isotopic marker suggested weak connectivity between Mexican states along the Pacific coast and the west coast of North America, as well as between southeastern Mexican states along the Gulf Coast and central North America. Overall, the combined genetic and isotopic information identified the following migratory routes: in spring, there were three main flyways: a trans-Gulf route taken by eastern migrants passing through New York and Louisiana; a circum-Gulf route taken by eastern and western migrants passing through Veracruz, Mexico; and a western route taken by western birds passing through Nevada. In fall, there were two main flyways: the trans-Gulf route taken by eastern migrants passing through Alabama and the western-circum-Gulf routes taken by western migrants passing through California and possibly through New Mexico. We obtained 6 banding records between breeding and wintering grounds and 46 banding records of migration movements through Canada and the United States, ranging from 1921 to 2002. For records between the breeding and wintering grounds, we recorded a wide diversity in breeding origins, providing independent support that Central America received migrants from a very wide array of breeding locales in North America. Mapping of migration movements suggested strong links between breeding grounds in eastern Canada and stopovers in the eastern United States; strong links between breeding grounds and stopovers along the Pacific coast from Alaska to California; and poorly defined links between breeding grounds and stopovers within central North America, concordant with patterns observed in the other markers. In summary, the combined use of three types of markers provided sufficient resolution to detect general patterns of migratory connectivity in a widely distributed species. In terms of conservation, the finding of a parallel migration system suggests that migrant species with similar broad ranges could be managed using "phylogeographic flyways" to define demographically cohesive management units.
Iverson et al. (2004) used estimates of the homing rate for molting adult Harlequin Ducks (Histrionicus histrionicus) in Alaska to draw inferences about population structure. Homing rates, defined as one minus the ratio of birds recaptured elsewhere to those recaptured at the original banding site, were high (0.95–1.00) for males and females. Iverson et al. (2004) concluded that these high rates of homing are indicative of demographic independence among molting groups separated by small distances (tens to hundreds of kilometers) and that conservation efforts should recognize this fine-scale population structure. We re-examined their use of the homing rate, because their assumption of equal detection probability across a wide sampling area could have led to an upward bias in their estimates of site fidelity. As a result, we are hesitant to agree with their conclusion of high adult homing to molting areas and that molt-site fidelity is evidence for demographic independence. Our hesitancy stems from the fact that little is known about juvenile and adult movements within and among years, breeding area origins, and the variation of demographic parameters (e.g., survival and productivity) among molting groups. Furthermore, population genetic data of these molting groups suggest gene flow at both nuclear and mitochondrial loci. Such mixed messages between demographic (i.e., banding) and genetic data are increasingly common in ornithological studies and offer unique opportunities to reassess predictions and make more robust inferences about population structure across broad temporal and spatial scales. Thus, we stress that it is this broader scale perspective, which combines both demography and genetics, that biologists should seek to quantify and conservation efforts should seek to recognize.
We compiled and analyzed 101 accessible reports of 194 individual Kirtland's Warblers (Dendroica kirtlandii) from the Bahama Archipelago, 1841-1997. Most individuals were reported from northern islands (88%), and most sight reports (84%) and specimen/banding records (76%) were on island groups that support or formerly supported open woodlands of Caribbean pine (Pinus caribaea). Where habitat descriptions were provided, 60% mentioned specifically pines or pine understory. After analyses for potential biases from misidentification in sight reports and unequal effort across islands, we found no evidence to support previous claims that Kirtland's Warblers prefer scrub or avoid pine habitats. Rather, based upon 1995-1997 winter surveys using acoustic broadcasts, Kirtland's Warblers were detected in pine woodlands of Abaco and Grand Bahama more frequently than expected compared to encounter rates generated by a null model of random habitat use. Two periods of apparent decline of the Kirtland's Warbler this century, and a modest population increase on the breeding grounds since 1990, occurred contemporaneously with degradation and recovery, respectively, of the fire-dependent pine ecosystem in the northern Bahamas. We recommend a rigorous re-evaluation of conservation priorities now premised largely upon breeding-season limitation.
Estimating genealogical relationships among genes at the population level presents a number of difficulties to traditional methods of phylogeny reconstruction. These traditional methods such as parsimony, neighbour-joining, and maximum-likelihood make assumptions that are invalid at the population level. In this note, we announce the availability of a new software package, TCS, to estimate genealogical relationships among sequences using the method of Templeton et al. (1992) .
Abundances of forest birds in an unfragmented, undisturbed, and relatively mature temperate deciduous forest at the Hubbard Brook Experimental Forest, New Hamp-shire, changed markedly between 1969 and 1998. Total numbers of birds (all species com-bined) declined from 210–220 individuals/10 ha in the early 1970s to 70–90/10 ha in the 1990s. Of the 24 regularly occurring species, 12 decreased significantly (four to local extinc-tion), three increased significantly, and nine remained relatively constant in abundance. Nine of the 12 declining species were Neotropical migrants. Most species exhibited similar trends on Breeding Bird Survey (BBS) routes in New Hampshire during the same 30 year period and on three replicate study sites in nearby sections of the White Mountains from 1986–1998. Probable causes of trends were diverse and differed among species. Most could be accounted for by individual species' responses to events occurring primarily in the local breeding area. The most important local factor affecting bird abundance was temporal change in forest veg-etation structure, resulting from natural forest succession and local disturbances. Four spe-cies that declined markedly and in some cases disappeared completely from the study plot (Least Flycatcher, Empidonax minimus; Wood Thrush, Hylocichla mustelina; Philadelphia Vir-eo, Vireo philadelphicus; and American Redstart, Setophaga ruticilla) appear to attain peak abundance in early or mid successional forests. Species preferring more mature forests, such as Black-throated Green Warbler (Dendroica virens) and Ovenbird (Seiurus aurocapillus), in-creased significantly in abundance over the 30 year study. Other important factors influ-encing bird abundances were food availability and events in the migratory and winter pe-riods. Nest-predation rates, although varying among years, showed no long-term pattern that would account for population declines, and brood parasites were absent from this forest. Findings from this study demonstrate that major changes in bird abundances occur over time even in undisturbed and relatively mature forests, and illustrate the need for considering habitat requirements of individual species and how habitat suitability changes over time when trying to assess the causes of their long-term population trends. The results also imply that any conclusions about the effects of other factors affecting forest bird abundances, such as increased nest predation or brood parasitism associated with habitat fragmentation, must also account for successional changes that may be affecting habitat suitability. Received 28 July 2000, accepted 28 February 2001. MANY SPECIES AND POPULATIONS of North American birds have undergone declines in abundance in recent decades, especially migra-tory songbirds. Some species have declined throughout their breeding range (Robbins et al. 1989, Peterjohn et al. 1995), whereas others have declined in some regions but remained stable or even increased in others (James et al. 1996). The extent and causes of such changes in abundance are much debated (Askins et al.
Migration is the regular seasonal movement of animals from one place to another, often from a breeding site to a nonbreeding site and back. Because the act of migration makes it difficult to follow individuals and populations year round, our understanding of the ecology and evolution of migrating organisms, particularly birds, has been severely impeded. Exciting new advances in satellite telemetry, genetic analyses and stable isotope chemistry are now making it possible to determine the population and geographical origin of individual birds. Here, we review these new approaches and consider the relevance of understanding migratory connectivity to ecological, evolutionary and conservation issues.
Recent declines in Neotropical-Nearctic migrant songbird populations are often attributed to events during the nonbreeding season, such as tropical habitat conversion and drought. Support for this hypothesis in most species, however, is largely anecdotal or conjectural. There is a dearth of demographic information about migrants on their Neotropical winter grounds. Such data are needed to identify specific ecological factors influencing survival, dispersal, and, ultimately, population abundances aggregated over multiple habitats at regional spatial scales. In this paper, we review several lines of evidence, emphasizing results of our research on paruline warblers in Jamaica, which indicate that migrant passerines often compete intraspecifically in winter for preferred quality habitats and that their populations may be limited at least in part by ecological conditions in winter. The demographic and ecological evidence supporting this hypothesis for migrant passerines includes: (1) differing densities among habitats, suggesting variation in habitat suitability; (2) strong territoriality, site attachment, and site fidelity; (3) experimental demonstrations of habitat saturation; (4) nonrandom distributions of sex and age classes among habitats; (5) overwinter decline of body mass by individuals occupying the most drought-stressed habitats; and (6) different residence times among habitats, suggesting differences in survival or dispersal. We review ecological and behavioral explanations for these demographic patterns, and make conservation recommendations based on our understanding of how local demographic circumstances affect broader scale population processes.
Using data from the North American Breeding Bird Survey, we determined that most neotropical migrant bird species that breed in forests of the eastern United States and Canada have recently (1978-1987) declined in abundance after a period of stable or increasing populations. Most permanent residents and temperate-zone migrants did not show a general pattern of decrease during this period. Field data from Mexico were used to classify a subset of the neotropical migrants as using forest or scrub habitats during winter. Population declines during 1978-1987 were significantly greater among the forest-wintering species, while populations of scrub-wintering species increased. The same subset of neotropical migrants also showed overall declines in forest-breeding species, but no significant differences existed between species breeding in forest and scrub habitats. Neotropical migrant species that primarily use forested habitats in either wintering or breeding areas are declining, but a statistically significant association between habitat and population declines was detected only in the tropics.
For migratory birds, early arrival and physical condition on the breeding grounds are important determinants of reproductive
success and fitness. Differences in arrival times often exceed a month, and later arriving individuals are often in poorer
condition. Habitat-specific isotopic signatures indicate that the quality of winter habitats occupied by American redstarts
(Setophaga ruticilla) determines their physical condition and spring departure dates, which in turn result in variable arrival schedules and condition
on temperate breeding grounds. These findings link events in tropical winter grounds with those in temperate breeding areas
for a migratory songbird and provide evidence that winter habitats may be limiting.
An ambitious, comprehensive assessment of the current status of neotropical migratory birds in the USA, and the methods and strategies for conserving migrant populations. This book covers the full scope of the subject, with chapters reviewing and assessing the topics written as consensus documents by several of the leading workers. Contents include population trends, seasonal variations, habitat requirements during migration, impacts and effects of silviculture and agricultural practices, landscape ecology, habitat grazing effects, and single-species versus multiple-species approaches.
We constructed phylogenetic hypotheses for Greater and Lesser Antillean Mimidae, including five endemic species of tremblers and thrashers that represent the best plausible example of an avian radiation within the Lesser Antilles. Phylogenetic relationships were inferred from analysis of 3,491 base pairs (bp) of mitochondrial DNA (mtDNA) and roughly 780 bp of the nuclear-encoded myoglobin gene. We used a subset of mtDNA gene sequences and pcrRFLP analysis to evaluate the phylogeographic relationships among individuals representing island populations of the Brown and Gray tremblers (Cinclocerthia ruficauda and C. gutturalis), Pearly-eyed Thrasher (Margarops fuscatus), Scaly-breasted Thrasher (Margarops fuscus), and Antillean and continental populations of the Tropical (Mimus gilvus) and Northern mockingbirds (Mimus polyglottos). Phylogeographic analysis distinguished three strongly differentiated mtDNA clades among tremblers, as well as distinct southern (St. Lucia and Martinique) and northern (Dominica to Montserrat) mtDNA lineages of the Scaly-breasted Thrasher. Minor geographic subdivision was also observed between continental and Antillean populations of the Tropical Mockingbird. Phylogenetic analyses of species-level Mimidae relationships that are based on mtDNA and nuclear sequences provide strong support for the monophyly and Antillean origin of a clade that consists of the tremblers, Pearly-eyed Thrasher, and Scaly-breasted Thrasher, but reject the monophyly of the genus Margarops. Phylogenetic analysis cannot confirm the monophyly of all endemic Antillean mimids because of the apparently contemporaneous diversification of the Antillean White-breasted Thrasher (Ramphocinclus brachyurus) with the continental Gray Catbird (Dumetella carolinensis) and Black Catbird (Melanoptila glabrirostris). However, an insertion and a deletion in the myoglobin intron 2 sequence support grouping the West Indian thrashers and tremblers, from which we infer that the endemic Lesser Antillean mimids are an indigenous radiation. Assuming a constant mtDNA clock for the Mimidae, the splitting of the Northern and Tropical mockingbird lineages is roughly contemporaneous with the separation of the three trembler clades, as well as the two Scaly-breasted Thrasher clades. Application of a mitochondrial DNA clock ticking at 2% sequence divergence per million years (Ma), suggests that the history of the endemic thrasher and trembler lineage in the West Indies extends back about 4 Ma, and the three distinct clades of tremblers split about 2 Ma ago.
Abundances of forest birds in an unfragmented, undisturbed, and relatively mature temperate deciduous forest at the Hubbard Brook Experimental Forest, New Hampshire, changed markedly between 1969 and 1998. Total numbers of birds (all species combined) declined from 210–220 individuals/10 ha in the early 1970s to 70–90/10 ha in the 1990s. Of the 24 regularly occurring species, 12 decreased significantly (four to local extinction), three increased significantly, and nine remained relatively constant in abundance. Nine of the 12 declining species were Neotropical migrants. Most species exhibited similar trends on Breeding Bird Survey (BBS) routes in New Hampshire during the same 30 year period and on three replicate study sites in nearby sections of the White Mountains from 1986–1998. Probable causes of trends were diverse and differed among species. Most could be accounted for by individual species' responses to events occurring primarily in the local breeding area. The most important local factor affecting bird abundance was temporal change in forest vegetation structure, resulting from natural forest succession and local disturbances. Four species that declined markedly and in some cases disappeared completely from the study plot (Least Flycatcher, Empidonax minimus; Wood Thrush, Hylocichla mustelina; Philadelphia Vireo, Vireo philadelphicus; and American Redstart, Setophaga ruticilla) appear to attain peak abundance in early or mid successional forests. Species preferring more mature forests, such as Black-throated Green Warbler (Dendroica virens) and Ovenbird (Seiurus aurocapillus), increased significantly in abundance over the 30 year study. Other important factors influencing bird abundances were food availability and events in the migratory and winter periods. Nest-predation rates, although varying among years, showed no long-term pattern that would account for population declines, and brood parasites were absent from this forest. Findings from this study demonstrate that major changes in bird abundances occur over time even in undisturbed and relatively mature forests, and illustrate the need for considering habitat requirements of individual species and how habitat suitability changes over time when trying to assess the causes of their long-term population trends. The results also imply that any conclusions about the effects of other factors affecting forest bird abundances, such as increased nest predation or brood parasitism associated with habitat fragmentation, must also account for successional changes that may be affecting habitat suitability.
Modern molecular methods yield descriptions of the phylogenetic deployment of genetic variation within species, or phylogeography. A developing field is the comparison of geographic patterns of genetic variation in codistributed species, or comparative phylogeography. One determines whether species that currently share the same broad area exhibit congruent phylogeographic patterns, which would indicate that they were historically codistributed and differentiated in response to same geological or environmental events. I reviewed studies of mitochondrial DNA (mtDNA) variation in five codistributed, widespread species of North American birds. In addition to phylogeographic patterns, data were available on levels of genetic variation, gene flow, and evolutionary distance from common ancestors (an index of a species' relative age) for each species, all important factors involved in geographic differentiation. Two species, Canada goose (Branta canadensis) and fox sparrow (Passerella iliaca), exhibited incongruent phylogeographic patterns of mtDNA variation, whereas three other codistributed species, the song sparrow (Melospiza melodia), chipping sparrow (Spizella passerina), and red-winged blackbird (Agelaius phoeniceus), lacked geographically structured mtDNA patterns. Thus, the first two species have had demonstrably different histories, whereas the histories of the latter three are speculative. However, the three species without geographic variation in mtDNA exhibit shallow mtDNA haplotype trees, which are consistent with recent population expansion. Thus, lack of geographic variation in mtDNA is likely due to these three species arriving relatively recently at their current distributions, and after historical isolating events produced genetic divisions in the fox sparrow and Canada goose. Within the geographically uniform species, or parts thereof, dispersal seems a likely homogenizing factor; no consistent explanations emerged from consideration of levels of genetic variation. Lack of congruent phylogeographic patterns suggests that currently codistributed species have not had a long history of co-association. These results and comparison of other North American species for which less extensive mtDNA surveys are available, reveal that the North American avifauna is probably a composite of species with different histories.
Within a group of interbreeding organisms, the balance of gene flow among populations and microevolutionary forces acting within populations is expected to result in clinal transitions in the phenotypes possessed by members of differentiated populations. Discontinuous variation between geographically adjacent populations suggests the presence of a significant barrier to gene flow. Here I present genetic evidence for restricted gene flow between migratory and nonmigratory populations of prairie warblers. The nonmigratory form of this species is restricted to coastal mangroves in Florida and is morphologically distinguishable from the typical, migratory form that occurs across the remainder of the eastern United States. Pairs of migratory populations exhibited little population subdivision (ΦST ⩽ 0.09), whereas pairs of migratory and nonmigratory populations are much more differentiated (ΦST = 0.27-0.42). A phylogenetic analysis of mitochondrial DNA haplotypes did not offer evidence of long-term isolation of migratory and nonmigratory populations. Together with the population genetic analysis, the phylogenetic relationship of haplotypes suggests that isolation between these forms must have arisen relatively recently in their history. Evidence for significant population structure is unexpected, given the geographic proximity of migratory and nonmigratory populations, the capacity for long-distance movements (e.g., migration) by prairie warblers, and several previous studies of population structure in North American birds. However, the findings are consistent with the geographic distribution of morphological and behavioral variation and demonstrate that significant boundaries between populations of vagile organisms may be relatively cryptic.
Habitats of Kirtland's Warbler (Dendroica kirtlandii) on the wintering grounds in the Bahama Archipelago are presented based upon data from 29 specimens, two bandings, and 67 sightings of at least 61 individuals on 13 islands scattered through the region. We placed a major emphasis on a study site in central Eleuthera, with additional information from sites on Grand Turk, North Caicos. and Crooked Island. The warblers used upland habitats that have a low shrub/scrub component with a mosaic of small openings and openings within the vegetation at the ground level. Six broad habitats were used: natural shrub/scrub, secondary shrub/scrub, low coppice, pineland understory, saline/upland ecotone, and suburban; high coppice was not used. The structure and floristic composition of the habitats are described. Observations (n = 451) of a Kirtland's Warbler male (uniquely color banded) and female over three months indicated the birds generally stayed within 3 m of the ground (98% of observations), and used a territory of 8.3 ha. A crude estimate of potential winter habitat suggests that not only is there more than an adequate amount in the Bahama Archipelago for the current small population of warblers (733 singing males in 1997), but also enough for a considerably larger population. No serious future threat to the amount of that habitat is foreseen.
The population trends of 100 species of Neotropical migrants were estimated using the route-regression method. Using the data from the North American Breeding Survey (BBS), the long-term and recent trends were determined.
Breeding Bird Survey (BBS) data for the 22-year period 1966-1987 for the southeastern and south central United States show trends in populations of the eight common species of Neotropical migrant wood-warblers. Using the nonparametric nonlinear route regression (NNRR) analysis method to analyze the data for upland and lowland areas within the southeastern continental region and by 12 physiographic strata, substantial geographic variation in the populations trends of each species was found. This result confirm the effectiveness of the NNRR method to study BBS data.
The chapter discusses ways in which molecular techniques are applied to the study of geographic variation in birds. It evaluates how studies of mitochondrial DNA (mtDNA) have contributed to understanding the evolution of geographic variation, population structure, and gene flow. Detecting genetic variation, documenting its geographic deployment, and inferring evolutionary processes are central themes of evolutionary analysis of populations. New methods of molecular analysis successively provide greater resolving power. Direct sequencing of DNA stands to be the next most influential method to provide insight into the nature of the avian population structure. Contrary to allozyme studies, almost 40% of species examined exhibit geographic variation in mtDNA. Most occurrences of significant phylogeographic structure are found in species that also exhibit morphological differentiation; often mtDNA and subspecies boundaries are congruent, whereas this is not the case with allozymic studies. The resultant question is whether there are consistent geographic correlates of structured haplotype trees. Although past barriers are difficult to judge from current conditions, mtDNA phylogeographic structure seems to be associated with a barrier other than the distance, although most general barriers appear to be associated with phylogeographic structure.
Modern molecular methods yield descriptions of the phylogenetic deployment of genetic variation within species, or phylogeography. A developing field is the comparison of geographic patterns of genetic variation in codistributed species, or comparative phylogeography. One determines whether species that currently share the same broad area exhibit congruent phylogeographic patterns, which would indicate that they were historically codistributed and differentiated in response to same geological or environmental events. I reviewed studies of mitochondrial DNA (mtDNA) variation in five codistributed, widespread species of North American birds. In addition to phylogeographic patterns, data were available on levels of genetic variation, gene flow, and evolutionary distance from common ancestors (an index of a species' relative age) for each species, all important factors involved in geographic differentiation. Two species, Canada goose (Branta canadensis) and fox sparrow (Passerella iliaca), exhibited incongruent phylogeographic patterns of mtDNA variation, whereas three other codistributed species, the song sparrow (Melospiza melodia), chipping sparrow (Spizella passerina), and red-winged blackbird (Agelaius phoeniceus), lacked geographically structured mtDNA patterns. Thus, the first two species have had demonstrably different histories, whereas the histories of the latter three are speculative. However, the three species without geographic variation in mtDNA exhibit shallow mtDNA haplotype trees, which are consistent with recent population expansion. Thus, lack of geographic variation in mtDNA is likely due to these three species arriving relatively recently at their current distributions, and after historical isolating events produced genetic divisions in the fox sparrow and Canada goose. Within the geographically uniform species, or parts thereof, dispersal seems a likely homogenizing factor; no consistent explanations emerged from consideration of levels of genetic variation. Lack of congruent phylogeographic patterns suggests that currently codistributed species have not had a long history of co-association. These results and comparison of other North American species for which less extensive mtDNA surveys are available, reveal that the North American avifauna is probably a composite of species with different histories.
A portion of the mitochondrial control region (494 bp) was sequenced in 106 great reed warblers sampled in six breeding populations in Europe and one wintering population in Africa. In total, 33 different haplotypes were found. There was little evidence of divergence between populations in northern and western Europe whereas the sample from Greece differed significantly from the other European breeding populations. The lowest haplotype diversity was found near the distribution range limit in Sweden and in The Netherlands suggesting recent effects of bottlenecks/founder events in these areas. A neighbour-joining analysis of the different haplotypes placed the haplotypes into two distinctive clades, A and B. The divergence of the two clades was on average 1.29%. Accounting for the within clade variation suggested a divergence time between these lines approximately 70 000 years BP. The frequency of the two clades changed longitudinally across Europe with the A haplotype in the west and the B haplotype in the east. All birds from Kenya carried the B haplotype suggesting an origin of these birds east of Latvia/Greece. The long-term female effective population size was estimated to be 20 000 individuals, which is approximately 2% of current population size.
Within a group of interbreeding organisms, the balance of gene flow among populations and microevolutionary forces acting within populations is expected to result in clinal transitions in the phenotypes possessed by members of differentiated populations. Discontinuous variation between geographically adjacent populations suggests the presence of a significant barrier to gene flow. Here I present genetic evidence for restricted gene flow between migratory and nonmigratory populations of prairie warblers. The nonmigratory form of this species is restricted to coastal mangroves in Florida and is morphologically distinguishable from the typical, migratory form that occurs across the remainder of the eastern United States. Pairs of migratory populations exhibited little population subdivision (ΦST ≤ 0.09), whereas pairs of migratory and nonmigratory populations are much more differentiated (ΦST = 0.27-0.42). A phylogenetic analysis of mitochondrial DNA haplotypes did not offer evidence of long-term isolation of migratory and nonmigratory populations. Together with the population genetic analysis, the phylogenetic relationship of haplotypes suggests that isolation between these forms must have arisen relatively recently in their history. Evidence for significant population structure is unexpected, given the geographic proximity of migratory and nonmigratory populations, the capacity for long-distance movements (e.g., migration) by prairie warblers, and several previous studies of population structure in North American birds. However, the findings are consistent with the geographic distribution of morphological and behavioral variation and demonstrate that significant boundaries between populations of vagile organisms may be relatively cryptic.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
The 27 species of Dendroica wood-warblers represent North America's most spectacular avian adaptive radiation. Dendroica species exhibit high levels of local sympatry and differ in plumage and song, but the group contrasts with other well–know avian adaptive radiations such as the Hawaiian honeycreepers and Galapagos finches in that Dendroica species have differentiated modestly in morphometric traits related to foraging. Instead, sympatric Dendroica tend to partition resources behaviourally and they have become a widely cited example of competitive exclusion. We explore the temporal structure of Dendroica diversification via a phylogeny based on 3639 nucleotides of protein–coding mitochondrial DNA (mtDNA). The taxa sampled include 60 individuals representing 24 Dendroica species and a variety of other paruline warbler and outgroup species. Mitochondrial divergences among Dendroica species were generally large (mean pairwise interspecific distances, 10.0%) and many species were rooted in a basal polytomy.
The prevalence of long terminal branches indicates that these species have evolved efficient isolating mechanisms that hav prevented mtDNA introgression despite the many opportunities for hybridization resulting from local sympatry. Comparison with a null model of random bifurcation–extinction demonstrate that cladogenesis in Dendroica has been clustered non–randomly with respect to time, with a significant burst of speciation occurring early in the histor of the genus, possibly as long ago as the Late Miocene or Early Pliocene periods. Although this non–random clustering of speciatio is consistent with the pattern expected of an adaptive radiation, the age of the Dendroica radiation suggests it is an ‘ancient species flock’ in which most extant species represent lineages that have long been evolutionaril independent.
We studied the ecology of the Golden-cheeked Warbler (Dendroica chryso- paria) during three winter seasons, 1995-1998, in Honduras, Guatemala, and Mexico. In- dividuals of this species occurred almost exclusively as members of mixed-species flocks, occupying sites with greater densities of encino oak and ground cover and fewer pines than random sites. Most foraging observations were recorded in mid-story, encino oak. Com- monly-observed foraging maneuvers were gleaning and sally-hovering. Eighty-three percent of foraging maneuvers were directed at the outermost portions of the oak foliage. Flocks in which Golden-cheeked Warblers occurred contained an average of 20.5 individuals and 12.9 species other than Golden-cheeked Warblers. The most frequently co-occurring species were Wilson's Warbler (Wilsonia pusilla), Black-throated Green Warbler (Dendroica virens), Her- mit Warbler (D. occidentalis), Townsend's Warbler (D. townsendi), and Blue-headed Vireo (Vireo solitarius). The ratio of males to females observed was not substantially different from 1: 1, and there was little evidence of sexual differences in habitat use. Golden-cheeked Warblers appeared to be tolerant of moderate levels of logging and grazing, but understory clearing to promote grazing for cattle may pose a significant threat to winter habitat avail- ability.
The wood-warblers (family Parulidae) fall within a radiation of passerine birds commonly known as the New World nine-primaried oscines. Defining familial rela- tionships within that radiation has previously been challenging because of its extremely high diversity, a paucity of phylogenetically informative morphological characters, and an ap- parent high rate of cladogenesis early in the radiation's history. Here, analyses of mitochon- drial and nuclear DNA sequences demonstrate that the 25 extant genera traditionally placed in the Parulidae do not form a monophyletic group. Instead, all reconstructions identify a well-resolved clade of 19 genera (Vermivora, Parula, Dendroica, Catharopeza, Mniotilta, Seto- phaga, Protonotaria, Helmitheros, Limnothlypis, Seiurus, Oporornis, Geothlypis, Wilsonia, Cardel- lina, Ergaticus, Myioborus, Euthlypis, Basileuterus ,a ndPhaeothlypis) that are all morphologi- cally typical wood-warblers traditionally placed in the Parulidae. Six genera traditionally assigned to the Parulidae—Microligea, Teretistris, Zeledonia, Icteria, Granatellus ,a ndXenoli- gea—fall outside this highly supported clade in all mtDNA-based and nuclear DNA-based reconstructions, and each is probably more closely allied to taxa traditionally placed in other nine-primaried oscine families. The long, well-supported, and independently confirmed in- ternode at the base of this wood-warbler clade provides the opportunity to define a mono- phyletic Parulidae using several complementary molecular phylogenetic criteria. Support for those relationships comes from reconstructions based on a range of nucleotide-intensive (from 894 to 3,638 nucleotides per taxon) and taxon-intensive (45 to 128 species) analyses of mtDNA sequences, as well as independent reconstructions based on nucleotide substitutions in the nuclear-encoded c-mos gene. Furthermore, the 19 typical wood-warbler genera share a synapomorphic one-codon c-mos deletion not found in other passerines. At a slightly deep- er phylogenetic level, our mtDNA-based reconstructions are consistent with previous mor- phologic and genetic studies in suggesting that many nine-primaried oscine taxa have un- anticipated affinities, that many lineages arose during an early and explosive period of cladogenesis, and that the generation of a robust nine-primaried oscine phylogeny will re- quire robust taxonomic sampling and extensive phylogenetic information. Received 29 June 2001, accepted 15 March 2002.
1. Dispersal is of critical ecological and evolutionary importance for several issues of population biology, particularly population synchrony, colonization and range expansion, metapopulation and source–sink dynamics, and population genetic structure, but it has not previously been possible to compare dispersal patterns across a wide range of species or to study movement outside the confines of local study areas.
2. Using resampling methods, we verified that statistically unbiased estimates of average dispersal distance and of intraspecific variance in dispersal distance could be extracted from the bird ringing data of the British Trust for Ornithology.
3. Using data on 75 terrestrial bird species, we tested whether natal and breeding dispersal were influenced by a species’ habitat requirements, diet, geographical range, abundance, morphology, social system, life history or migratory status. We used allometric techniques to ascertain whether these relationships were independent of body size, and used the method of phylogenetically independent contrasts to ascertain whether they were independent of phylogeny.
4. Both natal and breeding dispersal distances were lower among abundant species and among species with large geographical ranges. Dispersal distances and life-history variables were correlated independent of phylogeny, but these relationships did not persist after controlling for body size. All morphometrical variables (wing length, tarsus length and bill length) were not significantly correlated with dispersal distances after correcting for body size or phylogenetic relatedness.
5. Migrant species disperse further than resident ones, this relation was independent of body size but not of phylogeny. A significant positive relation was observed between breeding dispersal distance and long-term population decline among migrants, but not among residents.
6. The species living in wet habitats disperse further than those living in dry habitats, which could be explained by the greater patchiness of wet habitats in space and/or time. This relationship was observed only for breeding dispersal, suggesting that this habitat variable does not impose the same constraint on natal dispersal.
A portion of the mitochondrial control region (494 bp) was sequenced in 106 great reed warblers sampled in six breeding populations in Europe and one wintering population in Africa. In total, 33 different haplotypes were found. There was little evidence of divergence between populations in northern and western Europe whereas the sample from Greece differed significantly from the other European breeding populations. The lowest haplotypc diversity was found near the distribution range limit in Sweden and in The Netherlands suggesting recent effects of bottlenecks/founder events in these areas. A neighbour-joining analysis of the different haplotypes placed the haplotypes into two distinctive clades, A and B. The divergence of the two clades was on average 1.29%. Accounting for the within cladc variation suggested a divergence time between these lines approximately 70 000 years BP. The frequency of the two clades changed longitudinally across Europe with the A haplotypc in the west and the B haplotypc in the east. All birds from Kenya carried the B haplotypc suggesting an origin of these birds east of Latvia/Greece. The long-term female effective population size was estimated to be 20 000 individuals, which is approximately 2% of current population size.
Identification of relationships among geographically distinct populations of migratory species can provide an understanding of breeding and natal philopatry, migration pathways, and population mixing during winter. We used random amplified polymorphic DNA (RAPD) analyses to search for markers specific to difficult-to-differentiate shorebird species (e.g. long-billed dowitcher Limnodromus scolopaceus and short-billed dowitcher L. griseus) as well as geographically distinct breeding populations of Hudsonian godwits Limosa haemastica, red-necked phalaropes Phalaropus lobatus, semipalmated plovers Charadrius semipalmatus, dunlin Calidris alpina, pectoral sandpipers C. melanotos, semipalmated sandpipers C. pusilla and western sandpipers C. mauri. Markers clearly differentiated all shorebird species. Estimates of population differentiation varied greatly among species (FST= 0.095–0.685) and correlated with interspecific variation in philopatry and geographical separation of breeding populations. We assigned individuals to putative breeding locales with greater certainty in well-differentiated species than in poorly differentiated species. Our findings indicate specific phylogeographical structure varies among species, which has strong implications for conservation of habitats within migratory corridors. We suggest that RAPDs are useful in identifying geographical populations of migratory species and that molecular markers should be considered for tracking migratory birds throughout the annual cycle.
Progress toward understanding factors that limit abundances of migratory birds, including climate change, has been difficult
because these species move between diverse locations, often on different continents. For black-throated blue warblers (Dendroica caerulescens), demographic rates in both tropical winter quarters and north temperate breeding grounds varied with fluctuations in the
El Niño Southern Oscillation. Adult survival and fecundity were lower in El Niño years and higher in La Niña years. Fecundity,
in turn, was positively correlated with subsequent recruitment of new individuals into winter and breeding populations. These
findings demonstrate that migratory birds can be affected by shifts in global climate patterns and emphasize the need to know
how events throughout the annual cycle interact to determine population size.
Mitochondrial DNA (mtDNA) control-region sequences of 52 migratory and wintering Dunlins (Calidris alpina) from around the world were determined with direct sequencing of PCR products. The genetic lineages detected in these birds are identical to those found previously in a much larger sample of 155 breeding Dunlins from their northern circumpolar range. Samples of nonbreeding Dunlins from both sides of the Pacific reveal a mixture of two lineages that breed separately in eastern Siberia and Alaska. The presence of Dunlins with an eastern Siberian haplotype along the west coast of North America indicates that the Bering Strait does not represent a biogeographic barrier to Dunlin migration. Dunlins wintering in eastern Asia most likely originated from the discrete breeding population in northern Alaska because they possess haplotypes that were found predominantly in birds from this region. Similarly, Dunlins front staging and wintering sites in Europe and western Asia reveal a mixture of two mtDNA lineages that were previously found confined largely to European and central Siberian breeding grounds. Limited gene flow between these breeding areas, however, precludes definitive allocation of individuals to their population of origin on the basis of mtDNA analysis alone. Body mass, time of migration, and molting pattern seem to be associated with the mtDNA types of migratory Dunlins in Europe, but data are too sparse to determine whether these characters are useful adjuncts in assigning nonbreeding birds to populations that correspond to the major genetic lineages. Overall, the genetic composition of nonbreeding populations indicates the confluence of breeding populations on southward migration. Because of strong phylogeographic population structure in Dunlins on their breeding grounds, mtDNA analysis can be extremely useful in defining broad migration corridors or flyways, and in determining staging and wintering areas used by the major breeding populations.
The fascinating story of how a harsh terrain that resembled modern Antarctica has been transformed gradually into the forests, grasslands, and wetlands we know today. "One of the best scientific books published in the last ten years."âOttowa Journal "A valuable new synthesis of facts and ideas about climate, geography, and life during the past 20,000 years. More important, the book conveys an intimate appreciation of the rich variety of nature through time."âS. David Webb,Science
The 16,775 base-pair mitochondrial genome of the white Leghorn chicken has been cloned and sequenced. The avian genome encodes the same set of genes (13 proteins, 2 rRNAs and 22 tRNAs) as do other vertebrate mitochondrial DNAs and is organized in a very similar economical fashion. There are very few intergenic nucleotides and several instances of overlaps between protein or tRNA genes. The protein genes are highly similar to their mammalian and amphibian counterparts and are translated according to the same variant genetic code. Despite these highly conserved features, the chicken mitochondrial genome displays two distinctive characteristics. First, it exhibits a novel gene order, the contiguous tRNA(Glu) and ND6 genes are located immediately adjacent to the displacement loop region of the molecule, just ahead of the contiguous tRNA(Pro), tRNA(Thr) and cytochrome b genes, which border the displacement loop region in other vertebrate mitochondrial genomes. This unusual gene order is conserved among the galliform birds. Second, a light-strand replication origin, equivalent to the conserved sequence found between the tRNA(Cys) and tRNA(Asn) genes in all vertebrate mitochondrial genomes sequenced thus far, is absent in the chicken genome. These observations indicate that galliform mitochondrial genomes departed from their mammalian and amphibian counterparts during the course of evolution of vertebrate species. These unexpected characteristics represent useful markers for investigating phylogenetic relationships at a higher taxonomic level.
Pleistocene biogeographic events have traditionally been ascribed a major role in promoting speciations and in sculpting the present-day diversity and distributions of vertebrate taxa. However, this paradigm has recently come under challenge from a review of interspecific mtDNA genetic distances in birds: most sister-species separations dated to the Pliocene. Here we summarize the literature on intraspecific mtDNA phylogeographic patterns in birds and reinterpret the molecular evidence bearing on Pleistocene influences. At least 37 of the 63 avian species surveyed (59%) are sundered into recognizable phylogeographic units, and 28 of these separations (76%) trace to the Pleistocene. Furthermore, use of phylogroup separation times within species as minimum estimates of 'speciation durations' also indicates that many protracted speciations, considered individually, probably extended through time from Pliocene origins to Pleistocene completions. When avian speciation is viewed properly as an extended temporal process rather than as a point event, Pleistocene conditions appear to have played an active role both in initiating major phylogeographic separations within species, and in completing speciations that had been inaugurated earlier. Whether the Pleistocene was exceptional in these regards compared with other geological times remains to be determined.
Dispersal and vicariance are often contrasted as competing processes primarily responsible for spatial and temporal patterns of biotic diversity. Recent methods of biogeographical reconstruction recognize the potential of both processes, and the emerging question is about discovering their relative frequencies. Relatively few empirical studies, especially those employing molecular phylogenies that allow a temporal perspective, have attempted to estimate the relative roles of dispersal and vicariance. In this study, the frequencies of vicariance and dispersal were estimated in six lineages of birds that occur mostly in the aridlands of North America. Phylogenetic trees derived from mitochondrial DNA sequence data were compared for towhees (genus Pipilo), gnatcatchers (genus Polioptila), quail (genus Callipepla), warblers (genus Vermivora) and two groups of thrashers (genus Toxostoma). Different area cladograms were obtained depending on how widespread and missing taxa were coded. Nonetheless, no cladogram was obtained for which all lineages were congruent. Although vicariance was the dominant mode of evolution in these birds, approximately 25% of speciation events could have been derived from dispersal across a preexisting barrier. An expanded database is now needed to estimate the relative roles of each process. Applying a molecular clock calibration, nearly all speciation events are of the order of a million or more years old, much older than typically presumed.
Phylogeographic patterns of intraspecific variation can provide insights into the population-level processes responsible for speciation and yield information useful for conservation purposes. To examine phylogeography and population structure in a migratory passerine bird at both continental and regional geographical scales, we analysed 344 bp of mitochondrial DNA (mtDNA) control region sequence from 155 yellow warblers (Dendroica petechia) collected from seven locations across Canada and from Alaska. There is a major subdivision between eastern (Manitoba to Newfoundland) and western (Alaska and British Columbia) populations which appears to have developed during the recent Pleistocene. Some localities within these two regions also differ significantly in their genetic composition, suggesting further subdivision on a regional geographical scale. Eastern and western birds form distinct phylogeographic entities and the clustering of all western haplotypes with two eastern haplotypes suggests that the western haplotypes may be derived from an eastern lineage. Analyses based on coalescent models support this explanation for the origin of western haplotypes. These results are consistent with important features of Mengel's model of warbler diversification. From a conservation perspective they also suggest that individual populations of migrant birds may form demographically isolated management units on a smaller scale than previously appreciated.