Article

Global Mitochondrial DNA Phylogeography of Holarctic Breeding Dunlins (Calidris alpina)

November 1995
Evolution 50(1)

November 1995
50(1)

DOI:10.2307/2410803

Authors:

Hans-Ulrich Rösner

World Wide Fund For Nature, Germany

Marcel G.J. Tilanus

Maastricht University

Comparison of mitochondrial DNA (mtDNA) control-region sequences of 155 dunlins from 15 breeding populations confirmed the existence of five major phylogeographic groups in the circumpolar breeding range of this migratory shorebird species. Time estimates of the origin of groups, based on sequence divergences and a molecular clock for birds, suggest a scenario of repeated fragmentation of populations in isolated tundra refugia during the late Pleistocene. The distribution of about three-quarters of all detected molecular variance between phylogeographic groups attests to the strongly subdivided genetic population structure in dunlins that is being maintained by natal philopatry. Each mtDNA phylogeographic group can be related to a morphometrically defined subspecies, but several other recognized subspecies are not supported by monophyletic mtDNA lineages within their purported ranges. More detailed analysis of several European populations reveals low amounts of gene flow and the partitioning of a substantial fraction of molecular variance between them. This ongoing evolution of population-genetic structuring within the European phylogeographic group most likely started with the last retreat of the ice sheets some 10,000 years ago. Dunlins thus provide one of the clearest examples of the linkage between historical and contemporary components of mtDNA phylogeographic structuring in birds.

New Records of Calidris alpina arcticola from Korea Confirmed by Resightings of Color-marked Birds

Article

Full-text available

Jan 2010

In the Republic of Korea, two subspecies of the Dunlin Calidris alpina have been recognized: the abundant and common C. a. sakhalina and the vagrant C. a. pacifica. As a result of color-marked bird resightings on the west coast of Korea from 2007 to 2009, three C. a. arcticola, which bred in Barrow, northern Alaska, were observed in the Saemangeum reclamation project area. Given skipping migration strategies and high site fidelity of many shorebird species in Korea, this result strongly suggests, at least during their southward autumn migration, that the tidal wetlands of the Saemangeum area play an important role as a key staging site for the newly recorded C. a. arcticola in Korea. Further studies on the current status of the three Dunlin subspecies in Korea and the implementation of effective mitigation measures at Saemangeum are strongly recommended. key word: Calidris alpina arcticola, Dunlin, Saemangeum reclamation project, newly recorded subspecies, color-marked birds

Phylogeographic structure and mitochondrial DNA variation in true lemmings (Lemmus) from the Eurasian Arctic

Article

Mar 1999

Vadim B Fedorov

The geographic pattern of mtDNA variation in lemmings from 13 localities throughout the Eurasian Arctic was studied by using eight restriction enzymes and sequencing of the cytochromebregion. These data are used to reveal the vicariant history ofLemmus, and to examine the effect of the last glaciation on mtDNA variation by comparing diversity in formerly glaciated areas to the diversity in non-glaciated areas. Phylogenetic congruence across different Arctic taxa and association between observed discontinuities, and probable Pleistocene barriers, suggest that glacial-interglacial periods were crucial in the vicariant history ofLemmus. Differences in amount of divergence (2.1–9.1%) across different historical barriers indicate chronologically separate vicariant events during the Quaternary. Populations from a formerly glaciated area are no less variable than those in the non-glaciated area. Regardless of glaciation history, no population structure and high haplotype diversity were found within geographic regions. The lack of population structure indicates that populations with high ancestral haplotype diversity shifted their distribution during the Holocene, and that lemmings tracked a changing environment during the Quaternary without reduction of effective population size.

A TEST OF THE GLACIAL REFUGIUM HYPOTHESIS USING PATTERNS OF MITOCHONDRIAL AND NUCLEAR DNA SEQUENCE VARIATION IN ROCK PTARMIGAN (LAGOPUS MUTUS)

Article

Dec 1999
EVOLUTION

The glacial refugium hypothesis (GRH) proposes that glaciers promoted differentiation and generation of intraspecific diversity by isolating populations in ice-free refugia. We tested three predictions of this hypothesis for the evolutionary divergence of rock ptarmigan (Lagopus mutus) during the Wisconsin glaciation of the late Pleistocene. To do this, we examined subspecies distributions, population genetic structure, and phylogenetic relationships in 26 populations across North America and the Bering Sea region. First, we analyzed sequence variation in the mitochondrial control region, in a nuclear intron (Gapdh), and in an internal transcribed spacer (ITS1). Control region sequences of 154 rock ptarmigan revealed strong population and phylogeographic structure. Variation in intron sequences of 114 rock ptarmigan also revealed significant population structure compatible with results for the control region. Rock ptarmigan were invariant for ITS1. Second, we show that five known Nearctic refugia and an Icelandic refugium are concordant with the current distribution of morphologically distinct subspecies; five of these six refugia are geographically concordant with the distribution of closely related control region haplotypes. Third, our estimates of the time since phylogenetic lineages diverged predated the last glacial maximum for all but two lineages. In addition, all lines of evidence suggest that two unknown refugia in the Bering Sea region supported rock ptarmigan during the Wisconsin glaciation. Overall, our results are most consistent with the hypothesis that isolated populations of rock ptarmigan diverged in multiple refugia during the Wisconsin and that geographic variation reflects patterns of recolonization of the Nearctic after the ice receded. The GRH may therefore offer the most plausible explanation for similar biogeographic patterns in a variety of Nearctic vertebrates.

Conservation genetics of the Java sparrow (Padda oryzivora) and an analysis of its viability

Thesis

Full-text available

Dec 2008

Pramana Yuda

The problem of how to conserve small and declining populations is currently receiving considerable attention in the ecological literature, particularly through the theoretical development of conservation biology and its application to endangered species conservation. This is true despite basic information on the natural history of most endangered species being very limited; not only for species that are very rare, elusive or living in remote areas, but also for species which occupy more accessible habitat (i.e. cultivated areas), such as the Java sparrow (Padda oryzivora). In the research outlined in this thesis, field studies and molecular analyses were combined to establish the current population status, level of continued threat, contemporary connectivity among remnant populations and the genetic diversity of the endangered Java sparrow. Field work included intensive censuses at 6 sites across Central and East Java during the 2004 and 2005 breeding seasons. To gain information about the current scale of trading and trafficking of Java sparrows, the numbers of birds for sale were surveyed at 7 bird markets, mostly situated close to the bird census sites. Further interviews with bird trappers established the level of trapping and distribution of trapping sites. DNA was extracted from both fresh whole blood (field samples) and tissue samples (museum specimens) and analysed using two different molecular marker systems – part one and two of the mtDNA control region and 5 independent nuclear microsatellite loci. MtDNA sequence data were used to infer phylogeography and historical demography of the Java sparrow, while, multi-locus microsatellite genotyping was used to assess contemporary connectivity and levels of genetic variation. In order to predict the future fate of the Java sparrow, a PVA and sensitivity analysis was also undertaken. Stochastic modelling was carried out using the program VORTEX. The results of this study highlight that remnant populations of Java sparrow in Central and East Java are currently small and highly fragmented. Based on roost counts at 6 sites, population estimates range from 5.8 (± 0.2 SE) to 125.2 (± 1.7 SE). The total estimated population for Central and East Java did not exceed 1000 individuals. If other regions of Indonesia within the species’ natural range have similar abundances, then the total Java sparrow population in Indonesia is likely to be at the lower end of the range of 2500 – 10,000 individuals that is currently used to classify the species as ‘Vulnerable’. The major threat from trapping and trading is still ongoing at a high level, with an average 59.3 % of the total population estimates being trapped during the study period. This threat is particularly severe in central Java, where market demands were mainly supplied by local wild caught birds. In contrast, in the east Java bird markets, introduced and captive bred birds were substituted to satisfy high market demand. These findings emphasize the potential abundance of Java sparrows that may occur in currently unstudied introduced populations on outer islands (e.g. Kalimantan), and the important role that introduced and captive bred birds currently have in mitigating further declines. They also highlight the potential usefulness of these introduced populations as part of future conservation schemes for the Java sparrow. Analysis of mtDNA sequence data was used to infer the effects of historic habitat changes on population demography and genetic diversity in the Java sparrow. Despite an expectation that this species would have increased habitat availability during glacial maxima, analysis based on standard mtDNA mutation rates revealed that major climatic shifts have caused bottlenecking in Java sparrows similar to those observed in temperate species impacted by expanding ice sheets. Alternatively, using more recently derived and contrasting mtDNA mutation rates suggests the Java sparrow was bottlenecked during the expansion of rainforest in the early Holocene, and likely expanded during deforestation associated with the arrival of cultivation to Java. If correct, this finding adds to an increasing number of studies highlighting the impact of human colonization on the distribution and abundance of endemic species. Microsatellite genotyping demonstrated that genetic variation in remnant Java sparrow populations was low, in the middle range of genetic variation observed for other endangered species. Levels of diversity among contemporary populations did not differ from historic samples. In addition, significant structuring was found among remnant but not historic populations, implying recent fragmentation and limited current inter-population movement. Therefore, it is likely that while recent population declines have, as yet, had limited impact on genetic diversity, they have had a significant impact on levels of inter-population gene flow. Stochastic PVA modelling suggested that, under a best case scenario, Java sparrows would be able to recover. Sensitivity analysis revealed that the PVA models were most sensitive to mortality and fecundity schedules. However, the results highlighted that further field studies of these parameters are necessary to gain a more realistic assessment of the potential fate of the Java sparrow over both the short and longer term. PVA also suggested that if the current level of trapping continues Java sparrow will become extinct within a very short period of time. Given that terminating trapping seems an unlikely short-term management option, these findings highlight the immediate need to formulate a trapping/harvesting strategy that minimizes the risk of extinction. The implications of the results of this research are as follows: 1. It is proposed that the conservation status of Java sparrow to be transferred from Vulnerable to Endangered (A2a,b,d; E). This research also provides a more robust, high quality data set that can be used for conservation status assessment. 2. Trapping remains the main threatening process and must be reduced before other conservation measures can be effective. The use of captive bred and/or introduced birds should be encouraged to meet market demands. Further population studies on introduced populations (e.g. in Kalimantan) are a necessity to develop the sustainable use of these resources. 3. For management purposes the Java sparrow can be considered as a single Management Unit. However, to develop a sound conservation strategy for this species, it is important to take into account the concept of “ecological exchangeability”. For this purpose we need studies of behaviour, life history, and morphology relative to environment. Such studies will allow more meaningful assessment of biologically relevant differentiation among the remnant populations of the Java sparrow. 4. There is also a need for further research on demographic parameters and breeding biology to gain more realistic predictions of population viability. 5. There is a critical short-term need to formulate a trapping/harvesting strategy to minimize the extinction risk. Working thresholds need to be established as a short-term management priority and as a basis for more effective and sustainable management strategies over the longer term.

Morphology, molecules and mating behavior : an integrative study of population divergence and speciation in widespread sepsid flies (Sepsidae: Diptera)

Article

Jan 2013

Nalini Puniamoorthy

The work presented in this dissertation explores processes of selection and speciation acting on diverging populations in two widespread sepsid species (Sepsidae: Diptera). The main focus was on investigating sexual selection, sexual size dimorphism (SSD) and incipient speciation in the nearctic and palaearctic species Sepsis punctum (Fabricius 1794) (Chapters 1-4). In addition, divergence in reproductive behavior and morphology was also addressed in the neotropical species Archisepsis diversiformis (Ozerov 1993) (Chapter 5).

Population structure of Calidris alpina and separation of subspecies at a stopover on the intertidal mudflats of Jiangsu Province, China

Preprint

Apr 2023

Dunlin (Calidris alpina) is a polymorphic species with a complex of subspecies. A migration stopover site on the intertidal mudflats of Jiangsu Province, China, has a pivotal role in the migratory connectivity of dunlin along the East Asian–Australasian Flyway (EAAF). However, to date, the dunlin subspecies that visit the coast of China during migration remains uncertain. To determine the subspecies, an integrated approach based on mitochondrial DNA, ring recoveries, and morphological traits was used to analyze dunlins sampled at the Jiangsu stopover site. Alaskan and Beringian lineages were the two dominant lineages that migrated through Jiangsu, and the number of dunlins from the Alaskan lineage greatly exceeded that from other lineages. According to genetic analysis, the proportion of identified lineages was greater than 70%. At least four subspecies were detected in eastern Jiangsu Province, including C. a. actites, C. a. kistchinski, C. a. sakhalina, and C. a. arcticola. There were significant differences in morphological characters between years, suggesting that proportions of subspecies at the stopover varied over time and that different subspecies adopted different migratory strategies and timings. The findings of this study highlight the need to further consider how subspecies contribute to the composition of populations and migratory connectivity of dunlin.

Late Quaternary Range Dynamics in the Common Grackle Quiscalus quiscula

Article

Full-text available

Jun 2020

Climate variability is one of the most important forces affecting the distributional range dynamics of species and consequentially plays a significant role in shaping biogeographic patterns. This study aims to infer the role of climate in the recent evolutionary history of the Common Grackle Quiscalus quiscula. Studies of other migratory North American birds have shown that their populations were isolated in two or three refugia in southern North America during the Last Glacial Maximum (LGM). In contrast, preliminary genetic work suggests that Common Grackles may have occupied a single refugium during that time. They subsequently became widespread and northern populations evolved highly migratory behaviour. We used an ecological niche modelling approach that involved the use of three general climate models for the past (the LGM, approximately 22,000 years before present) and for present environmental conditions to identify climatically stable areas. Extrapolations to the past showed contraction to a large continuous refugium located in the southern part of North America, and projection to the present showed expansion that covers much of eastern and middle North America. The most important bioclimatic variable for model predictions was annual mean temperature, which explained 74% of the variation in the model. Results suggest that the Common Grackle has expanded its distributional range by more than 300% after the LGM.

Population genomics of two congeneric Palaearctic shorebirds reveals differential impacts of Quaternary climate oscillations across habitats types

Article

Full-text available

Dec 2019

Intracontinental biotic divisions across the vast Palaearctic region are not well-characterized. Past research has revealed patterns ranging from a lack of population structure to deep divergences along varied lines of separation. Here we compared biogeographic patterns of two Palaearctic shorebirds with different habitat preferences, Whimbrel (Numenius phaeopus) and Eurasian curlew (N. arquata). Using genome-wide markers from populations across the Palaearctic, we applied a multitude of population genomic and phylogenomic approaches to elucidate population structure. Most importantly, we tested for isolation by distance and visualized barriers and corridors to gene flow. We found shallow Palaearctic population structure in subpolar bog and tundra-breeding whimbrels, consistent with other species breeding at a similarly high latitude, indicating connectivity across the tundra belt, both presently and during southward shifts in periods of global cooling. In contrast, the temperate grassland-breeding Eurasian curlew emerged in three distinct clades corresponding to glacial refugia. Barriers to gene flow coincided with areas of topographic relief in the central Palaearctic for whimbrels and further east for Eurasian curlews. Our findings highlight the interplay of historic and ecological factors in influencing present-day population structure of Palaearctic biota.

Mitochondrial DNA and Morphological Variation of White-Winged Doves in Texas

Article

Nov 2000

White-winged Doves (Zenaida asiatica) in Texas are separated into four subspecies primarily based on morphological variation. However, problems differentiating the subspecies by morphological measurements alone and a recent range expansion have led to questions about their systematic status and population structure. We evaluated both morphological characters and a 289 base-pair segment of the mitochondrial control region from 183 White-winged Doves taken from 31 locations in Texas, New Mexico, and Arizona. Twenty-seven variable base changes were observed, which resulted in 44 haplotypes. An analysis of haplotypes yielded little phylogenetic signal; however, analyses of haplotype frequencies indicated geographic heterogeneity between doves collected in the four historic subspecies ranges. Doves from the range expansion areas were intermediate in size and genetically homogenous. Morphological analyses suggested congruency between control region variation and body size. Our data support the recognition of two subspecies of White-winged Doves with a zone of intergradation in the range expansion areas. The dispersal of White-winged Doves into the expansion areas appears to be a congruent process by both subspecies.

Mitochondrial DNA reveals genetic structure within the Atlantic but not Pacific populations of a holarctic seabird, the Black-legged Kittiwake Rissa tridactyla

Article

Full-text available

Aug 2019

To predict evolutionary processes, such as speciation and local adaptation, we need to understand the mechanisms causing genetic differentiation of populations. We used mitochondrial control region sequence variation to investigate the genetic structure within and between Atlantic and Pacific populations of Black-legged Kittiwake (Rissa t. tridactyla and R. t. pollicaris, respectively). We predicted that genetic divergence of these populations, as in other northern hemisphere seabird species, might have been caused by glacial vicariance in the late Pleistocene. Further, because of regional differences in the morphology of kittiwakes, and the hypothesized historical vicariance, we predicted that genetic structure would exist within Atlantic, but not Pacific, populations. Population genetic and phylogenetic analyses of 756 base pairs of control region sequence for 398 kittiwakes indicated that Atlantic and Pacific populations are genetically differentiated from one another. Phylogenetic analyses indicated historical divergence of two mtDNA clades within the Pacific population and four mtDNA clades within the Atlantic population. Population genetic analyses indicated that colonies within the Atlantic were strongly differentiated from one another, which could be explained by restrictions in contemporary gene flow and historical fragmentation in historical refugia. Population genetic analyses provided little evidence for genetic structure in the Pacific population, which we attributed to longer time since vicariance allowing more migration between colonies. Results agree with current subspecies designations of Atlantic and Pacific populations.

High genetic diversity and low differentiation retained in the European fragmented and declining Greater Spotted Eagle (Clanga clanga) population

Article

Full-text available

Feb 2019

Characterising genetic diversity and structure of populations is essential for effective conservation of threatened species. The Greater Spotted Eagle (Clanga clanga), a large and globally vulnerable raptor, is extinct or in severe decline in most of its previous range in Europe. We assessed whether the remnants of European population are genetically impoverished, and isolated from each other. We evaluated levels of genetic diversity and population structuring by sequencing mitochondrial pseudo-control region and 10 introns from various nuclear genes, and estimated length diversity in 23 microsatellite markers. The European population has expanded since the late Pleistocene, and does not exhibit signs of a recent population bottleneck. The global genetic diversity in Europe was rather similar to that detected in other similar species. Microsatellites suggested shallow but significant differentiation between the four extant populations in Estonia, Poland, Belarus and Russia (Upper Volga region) populations, but introns and mtDNA showed that only the Estonian population differed from the others. Mitochondrial diversity was highest in the northernmost Estonian population, introns suggested lower diversity in Upper Volga, microsatellites indicated equal diversity among populations. A recent bottleneck was detected in Poland, which is consistent with the observed repopulation of the region. We conclude that significant gene flow and high genetic diversity are retained in the fragmented Greater Spotted Eagle populations; there is currently no need for genetic augmentation in Europe.

Unravelling population processes over the Late Pleistocene driving contemporary genetic divergence in Palearctic Buzzards

Article

Full-text available

Feb 2019

Trophic niche differentiation, sex ratio and phylogeography of European Collembola Publications resulting from this dissertation

Thesis

Full-text available

Jan 1996

Masoumeh Shayanmehr

Collembola are important soil-dwelling animals reaching high diversity and density. For understanding driving factors for Collembola density and diversity this study investigated (1) trophic niche differentiation of Collembola species using stable isotope analysis, (2) mode of reproduction and sex ratios in the field, (3) colonization of new habitats by parthenogenetic and sexual species and (4) the genetic variation in parthenogenetic and sexual species in Europe. To evaluate trophic niche differentiation the natural variation in nitrogen isotopes was assessed in 20 Collembola taxa from three deciduous forests stands. The 􀁇15N gradient spanned over 9 􀁇 units, which implies a wide range in food sources used. Assuming a shift in 15N of about 3 ‰ per trophic level, the results indicate a range of three trophic levels. The 􀁇15N signature formed a continuum from phycophages/herbivores to primary and secondary decomposers, reflecting a gradual shift from more detrital to more microbial diets. These results suggest that trophic niche differentiation is an important mechanism for the maintenance of the high number of Collembola species in forst ecosystems.....

HISTORICAL DEMOGRAPHY AND PRESENT DAY POPULATION STRUCTURE OF THE GREENFINCH, CARDUEUS CHLORIS-AN ANALYSIS OF mtDNA CONTROL-REGION SEQUENCES

Article

Jun 1997
EVOLUTION

Genetic variability within and among 10 geographically distinct populations of Greenfinches (Carduelis chloris) was assayed by directly sequencing a 637 BP part of the mtDNA control region from 194 individuals. Thirteen variable positions defined 18 haplotypes with a maximum sequence divergence of 0.8%. Haplotype (h = 0.28-0.77) and nucleotide (π = 0.058-0.17%) diversities within populations were low, and decreased with increasing latitude (h:rs = -0.81; π: rs = -0.89). The distribution of pairwise nucleotide differences fit better with expectations of a "sudden expansion" than of an "equilibrium" model, and the estimates of long term effective population sizes were considerably lower than current census estimates, especially in northern European samples. Selection is an unlikely cause of observed patterns because the distribution of variability conformed to expectations of neutral infinite alleles model and haplotype diversity across populations was positively correlated with heterozygosity (HE ) in nuclear genes (rs = 0.74, P < 0.05). Hence, a recent bottleneck, followed by serial bottlenecking during the process of post-Pleistocene recolonization of northern Europe, together with recent population expansion provide a plausible explanation for the low genetic diversity in the north. Genetic distances among populations showed a clear pattern of isolation-by-distance, and 14% of the haplotypic variation was among populations, the rest being distributed among individuals within populations. In accordance with allozyme and morphological data, a hierarchical analysis of nucleotide diversity recognized southern European populations as distinct from northern European ones. However, the magnitude of divergence in mtDNA, allozymes and morphology were highly dissimilar (morphology > mtDNA > allozymes).

NORTH AMERICAN BLACK BEAR mtDNA PHYLOGEOGRAPHY: IMPLICATIONS FOR MORPHOLOGY AND THE HAIDA GWAII GLACIAL REFUGIUM CONTROVERSY

Article

Oct 1997
EVOLUTION

The controversial role of Haida Gwaii (Queen Charlotte Islands) as a biological refugium on the northwestern coast of North America has been widely discussed for more than fifty years. The presence of morphologically divergent subspecies on Haida Gwaii is one of the major lines of evidence suggesting this archipelago's role as a refugium during the Wisconsin. However, since morphological distinction can be derived postglacially as well as in extended isolation, such evidence is ambiguous. To examine this question, we did a phylogenetic analysis of cytochrome b sequences (719 bp) of black bear (Ursus americanus), one of the distinctive endemics of Haida Gwaii, and compared these with conspecifics from across North America, focusing primarily on the northwestern coast. We found that the Haida Gwaii bear are indistinguishable from coastal bear of British Columbia and Vancouver Island, but are highly distinct from continental bear. Coastal and continental bears differ by 24 synapomorphies and an average sequence divergence of 3.6%. The coastal mitochondrial lineage occurs in each of the three recognized coastal subspecies suggesting that the morphological characteristics differentiating these taxa may be postglacially derived. The data are consistent with recent suggestions that a glacial refugium existed on the now submerged continental shelf connecting Haida Gwaii, Vancouver Island, and the coastal fringe of mainland British Columbia. This refugium would have been an additional source for postglacial recolonization of northwestern North America.

MORPHOLOGICAL AND MOLECULAR VARIATION ACROSS A MIGRATORY DIVIDE IN WILLOW WARBLERS, PHYLLOSCOPUS TROCHILUS

Article

Full-text available

Dec 1999
EVOLUTION

A migratory divide is a narrow region in which two populations showing different migratory directions meet arid presumably also mate and hybridize. Banding of willow warblers, Phylloscopus trochilus, in Europe has demonstrated a migratory divide latitudinally across central Scandinavia. In autumn, southern birds migrate southwest to tropical West Africa, whereas northern birds migrate southeast to East and South Africa. The migratory divide is associated with concordant differences in size and plumage coloration. Based on morphology, we estimate the width of the transition zone between northern and southern willow warblers to be less than 350 km. We found indication of linkage disequilibria around the migratory divide, in that measures of body size were correlated with plumage coloration within the contact zone, but uncorrelated within the populations south or north of the contact zone. The presence of linkage disequilibria and the fact that several morphological clines occur together suggest that the hybrid zone is a result of secondary contact between populations that have differentiated in allopatry. This interpretation is in accord with the knowledge of the recolonization pattern of the Scandinavian peninsula after the last glaciation; animals and plants appeared to have colonized either from the south or from the north around the northern bay of the Baltic Sea. If northern and southern willow warblers resided in allopatric populations during late Pleistocene glaciations and the hybrid zone is a result of postglacial range expansions, we would expect some degree of genetic differentiation accumulated during the period in isolation. In contrast, northern and southern willow warblers are near panmictic in the frequencies of alleles of mitochondrial DNA and at two microsatellite loci. The observed pattern, clear morphological and behavioral differentiation without genetic differentiation at neutral loci, suggests either that the differences are maintained by strong selection on the expressed genes in combination with high levels of current gene flow or, in the case of weak gene flow, that the divergence in morphology and behavior is very recent.

Population structure of Purple Sandpipers (Calidris maritima) as revealed by mitochondrial DNA and microsatellites

Article

Full-text available

Apr 2017

The Purple Sandpiper (Calidris maritima) is a medium-sized shorebird that breeds in the Arctic and winters along northern Atlantic coastlines. Migration routes and affiliations between breeding grounds and wintering grounds are incompletely understood. Some populations appear to be declining, and future management policies for this species will benefit from understanding their migration patterns. This study used two mitochondrial DNA markers and 10 microsatellite loci to analyze current population structure and historical demographic trends. Samples were obtained from breeding locations in Nunavut (Canada), Iceland, and Svalbard (Norway) and from wintering locations along the coast of Maine (USA), Nova Scotia, New Brunswick, and Newfoundland (Canada), and Scotland (UK). Mitochondrial haplotypes displayed low genetic diversity, and a shallow phylogeny indicating recent divergence. With the exception of the two Canadian breeding populations from Nunavut, there was significant genetic differentiation among samples from all breeding locations; however, none of the breeding populations was a monophyletic group. We also found differentiation between both Iceland and Svalbard breeding populations and North American wintering populations. This pattern of divergence is consistent with a previously proposed migratory pathway between Canadian breeding locations and wintering grounds in the United Kingdom, but argues against migration between breeding grounds in Iceland and Svalbard and wintering grounds in North America. Breeding birds from Svalbard also showed a genetic signature intermediate between Canadian breeders and Icelandic breeders. Our results extend current knowledge of Purple Sandpiper population genetic structure and present new information regarding migration routes to wintering grounds in North America.

Final results published in Molecular Ecology (2005) 14, 2645–2657

Data

Dec 2016

Population genetic structure in migratory sandhill cranes

Data

Dec 2016

DIFERENCIACIÓN GENÉTICA DE LAS AGREGACIONES INVERNANTES DEL PLAYERITO OCCIDENTAL EN MÉXICO

Thesis

Full-text available

Jul 2011

Ana Ruth Alvarez Sánchez

The Western Sandpiper Calidris mauri is a migratory shorebird that breeds during the summer in the East Siberian tundra and the coast of Alaska. Most individuals of this species migrates along the Pacific Flyway to spend the winter in temperate and tropical latitudes, some use the Atlantic Flyway. Near 30% of the western Sandpiper global population spend their winter in the northwest of Mexico. In order to understand this population dynamics, a detailed knowledge of the individuals that occupy this zone is required. Genetic markers have been used to determine the migratory connectivity, to identify the migrant geographic origin and to indirectly consider the relative importance of the wintering sites. The objective of the present study was to establish the identity and the genetic structure of the western Sandpiper in some of the most important nonbreeding aggregations of Mexico. To achieve this goal, genotypes of 168 adult individuals were identified using 10 nuclear markers microsatellites in 7 winter aggregations located in the Peninsula of Baja California, Sinaloa and the Yucatan Peninsula, coasts (México). Although the genetic diversity was moderately high (Ho=0.713, Na=14 and Ne=5.1), the alleles distribution was homogenous between localities. Consequently, structure population analysis was similar for the different estimators of genetic differentiation used (FST = ‐0.0008, RST= 0.004, DST= ‐0.002). The estimations were also similar when considering separately males and females. These results were congruent with those obtained through a Bayesiana approach (STRUCTURE k=1). Our data suggest that individuals wintering in México belong to the same reproductive group, sustaining the monotypical character of Calidris mauri. Previous studies based on RAPDs markers and mtDNA sequences have demonstrated subtle differences when comparing the individuals from the migratory Pacific Flyway and those from the Atlantic. Although our results indicate a lack of differentiation, the highest divergence was observed between the Yucatan Peninsula (in the Atlantic coast) and Santa Maria Bay (in the Pacific); therefore to incorporate samples from reproduction zones to clarify if it exists certain level of genetic segregation whiting this

Waterbirds of Lake Baikal, Eastern Siberia, Russia

Article

Full-text available

Aug 2009

Jiří Mlíkovský

Lake Baikal lies in eastern Siberia, Russia. Due to its huge size, its waterbird fauna is still insufficiently known in spite of a long history of relevant research and the efforts of local and visiting ornithologists and birdwatchers. Overall, 137 waterbird species have been recorded at Lake Baikal since 1800, with records of five further species considered not acceptable, and one species recorded only prior to 1800. Only 50 species currently breed at Lake Baikal, while another 11 species bred there in the past or were recorded as occasional breeders. Only three species of conservation importance (all Near Threatened) currently breed or regularly migrate at Lake Baikal : Asian Dowitcher Limnodromus semipalmatus, Black-tailed Godwit Limosa limosa and Eurasian Curlew Numenius arquata.

Conservation Genetics of Great Bustard in the Ponto- Caspian Steppes (Ukraine and the Lower Volga Basin)

Article

Full-text available

Dec 2007

Bustard Studies 6 2007 pp 99-110 Publisher: Society for the Protection of Great Bustard e.V. & Zoological Society Frankfurt 1858 e.V. (Germany) The great bustard is a key species in conservation of the European lowland dry grassland ecosystem, especially in the Ponto-Caspian steppes.We have investigated the genetic diversity, population structure and demographic history of great bustards in a regional scale by analysing mitochondrial (mt)DNA sequences (a 662 bp fragment of control region I and II) in 84 individuals sampled from the Ukraine and the Lower Volga basin. This marker revealed moderate nucleotide (pi = 0.0068) and haplotype (h = 0.924) diversity that could be partitioned into three matrilineage clusters scattered throughout the study area. Consequently, the amount of variation between populations was relatively low (FST = 0.11) indicating a weak, but significant geographical genetic subdivision in great bustard mtDNA. Spatial analysis suggested that genetic isolation by distance has a small, but not negligible effect in the studied population. A history of allopatric population fragmentation around 10,0000 years (100 kyr BP) ago followed by secondary genetic contact and past population growth (60 -48 kyr BP) accompanied by range expansion is the most likely demographic scenario. These findings have important implications for currrent conservation of great bustards. Published by: The Society for the protection of Great Bustard e.V. and the Zoological Society Frankfurt 1858 e.V. Germany ISBN-13: 9783000219276

Genetic structure and diversity of breeding Montagu`s harrier (Circus pygargus) in Europe

Article

Full-text available

Jul 2015
EUR J WILDLIFE RES

The Montagu’s harrier (Circus pygargus) is a long-distance migratory raptor, breeding in Europe and Western Asia and wintering in sub-Saharan Africa. The population of the species has declined in Europe during the twentieth century, and Montagu’s harrier is red-listed in many European countries as declining or threatened. The main aims of the study were to evaluate the genetic diversity of European breeding populations and estimate the genetic differentiation among them, using polymorphism in the hypervariable domain of the mitochondrial control region. We analysed 158 individuals from central Spain, Germany, the Czech Republic and Poland. The results indicated high genetic diversity in the European breeding population, probably reflecting the large population size of the species. However, we found decreased genetic variability in the breeding population of Germany. Among the 18 identified haplotypes, 2 were of high frequency. There was no clear connection between the position of the haplotype in the genealogy and its geographical distribution. Genetic structure was weakly pronounced (H ST = 0.053, P < 0.001). SAMOVA indicated the presence of three genetic groups: The first group consisted of samples from central Spain and northeastern Poland, the second from southern Poland and the Czech Republic, and the third group separated samples from Germany from the other regions. Genetic differentiation between pairs of groups was low, suggesting a low level of philopatry and a high dispersal ability of Montagu’s harrier.

Population Genetic Structure in Migratory Sandhill Cranes and the Role of Pleistocene Glaciations

Data

Full-text available

Feb 2015

Previous studies of migratory sandhill cranes (Grus Canadensis) have made significant progress explaining evolution of this group at the species scale, but have been unsuccessful in explaining the geographically partitioned variation in morphology seen on the population scale. The objectives of this study were to assess the population structure and gene flow patterns among migratory sandhill cranes using microsatellite DNA genotypes and mitochondrial DNA haplotypes of a large sample of individuals across three populations. In particular, we were interested in evaluating the roles of Pleistocene glaciation events and postglaciation gene flow in shaping the present-day population structure. Our results indicate substantial gene flow across regions of the Midcontinental population that are geographically adjacent, suggesting that gene flow for most of the region follows an isolation by- distance model. Male-mediated gene flow and strong female philopatry may explain the differing patterns of nuclear and mitochondrial variation. Taken in context with precise geographical information on breeding locations, the morphologic and microsatellite DNA variation shows a gradation from the Arctic-nesting subspecies G. c. canadensis to the non- Arctic subspecies G. c. tabida. Analogous to other Arctic-nesting birds, it is probable that the population structure seen in Midcontinental sandhill cranes reflects the result of postglacial secondary contact. Our data suggest that subspecies of migratory sandhills experience significant gene flow and therefore do not represent distinct and independent genetic entities.

Trophic niche differentiation, sex ratio and phylogeography of European Collembola

Article

Full-text available

Jan 2007

Masoumeh Shayanmehr

Egg characteristics vary longitudinally in Arctic shorebirds

Article

Full-text available

May 2023

Arctic environments are changing rapidly and if we are to understand the resilience of species to future changes, we need to investigate alterations in their life histories. Egg size and egg shape are key life-history traits, reflecting parental investment as well as influencing future reproductive success. Here we focus on egg characteristics in two Arctic shorebirds, the Dunlin (Calidris alpina) and the Temminck’s stint (Calidris temminckii). Using egg photos that encompass their full breeding ranges, we show that egg characteristics exhibit significant longitudinal variations, and the variation in the monogamous species (Dunlin) is significantly greater than the polygamous species (Temminck’s stint). Our finding is consistent with the recent “disperse-to-mate” hypothesis which asserts that polygamous species disperse further to find mates than monogamous species, and by doing so they create panmictic populations. Taken together, Arctic shorebirds offer excellent opportunities to understand evolutionary patterns in life history traits.

Contrasting patterns of genetic diversity and lack of population structure in the lesser spotted eagle Clanga pomarina (Aves: Accipitriformes) across its breeding range

Article

Full-text available

Jun 2022

Characterizing the genetic diversity and structure of populations is essential for understanding their evolutionary history and planning species conservation. The lesser spotted eagle (Clanga pomarina) is a large migratory raptor with a relatively small breeding range concentrated in Eastern Europe. We evaluated the level of genetic diversity and population structuring by estimating the length diversity of 23 microsatellite markers in 306 individuals and sequencing 473 nucleotides from the mitochondrial pseudo-control region in 265 individuals across the distribution range. The microsatellite data suggested shallow differentiation between geographical regions and moderate genetic diversity across the range; no recent population bottlenecks were detected. Mitochondrial diversity was relatively low; however, high values were recorded at the southern edge of the distribution range. This, in combination with the star-like distribution of mitochondrial haplotypes, suggests the expansion of the European population from a single (Balkan) refugium during the late Pleistocene or early Holocene after the glacial population bottleneck. However, the Caucasian population may have survived in a separate refugium. We conclude that the lack of clear population structuring and ongoing gene flow across Europe support the treatment of the geographically restricted global population of the lesser spotted eagle as a single evolutionary and conservation unit.

Eastern-breeding Lesser Yellowlegs are more likely than western-breeding birds to visit areas with high shorebird hunting during southward migration

Article

Full-text available

Dec 2021

Shorebirds have experienced a precipitous reduction in abundance over the past four decades. While some threats to shorebirds are widespread (e.g., habitat alteration), others are regional and may affect specific populations. Lesser Yellowlegs (Tringa flavipes) are long-distance migrants that breed across the North American boreal biome and have declined in abundance by 60–80% since the 1970s. The documented harvest of Lesser Yellowlegs in the Caribbean and northeastern South America during southward migration is a possible limiting factor for the species, but it is unknown to what extent birds from different breeding origins may be affected. To address the question of differential occurrence in harvest zones during southward migration, we used PinPoint GPS Argos transmitters to track the southward migrations of 85 adult Lesser Yellowlegs from across the species’ breeding range and 80° of longitude from Anchorage, Alaska, USA, to the Mingan Archipelago, Quebec, Canada. We classified migratory locations as inside or outside three zones with high levels of harvest (Caribbean, coastal Guianas, and coastal Brazil) and then fit generalized additive mixed models to estimate the probability of occurrence of Lesser Yellowlegs in harvest zones according to their breeding origin. Individuals from the Eastern Canada population had a higher probability of occurrence within one or more harvest zones and remained in those zones longer than individuals breeding in Alaska and western Canada. Linear regressions also suggested that longitude of the breeding origin is an important predictor of occurrence in harvest zones during southward migration. Lastly, our findings, combined with other sources of evidence, suggest that current estimated harvest rates may exceed sustainable limits for Lesser Yellowlegs, which warrants further investigation.

Use of Band Resightings, Molecular Markers and Stable Isotopes to Understand the Migratory Connectivity of Dunlin Breeding in Beringia and Wintering in the East Asian-Australasian Flyway

Conference Paper

Full-text available

Jun 2020

We used resightings of banded adults and hatch year birds, molecular markers and stable isotopes to document the migratory connectivity of five subspecies of Dunlin (Calidris alpina) that breed in Beringia and migrate either along the East Asian-Australasian Flyway or the Pacific Flyway of North America. Of more than 4000 Dunlin banded in the past decade, roughly 230 (~6%) have been resighted away from their capture site. Most resightings were of arcticola Dunlin seen in Japan and Taiwan, although a smaller number of 2 kistchinski and sakhalina Dunlin have also been resighted along the East Asian-Australasian flyway. Few resightings have occurred in mainland China despite this being the major nonbreeding area for Dunlin. Due to potential biases associated with resighting marked Dunlin, we also employed molecular and stable isotope markers to indirectly assess migratory connectivity. In order to use molecular markers, which rely on the relatedness of individuals to establish linkages, it must be shown that individuals belonging to the five subspecies can be differentiated from one another. Preliminary results from variable microsatellite DNA markers indicated this was not possible among individuals of the sakhalina, pacifica and arcticola subspecies. However, we still need to test two more Russian-breeding subspecies and conduct mitochondrial DNA analysis on all five subspecies before we can determine the value of this technique. Should either the microsatellite or mitochondrial DNA reveal significant population structure, we can then use samples collected from birds on the nonbreeding grounds and try to link them to breeding areas. We also used stable isotope signatures of particular feathers grown by Dunlin on their breeding and nonbreeding grounds to determine if individuals from the five subspecies could be differentiated. Use of stable isotope markers to establish migration connectivity relies on the fact that feathers carry chemical markers that reflect the chemical composition of the resources used by birds as they grow the feathers, and that these chemical markers vary spatially across the surface of the earth. Preliminary results indicate that isotope markers from feathers acquired on the breeding grounds can distinguish among individuals from three subspecies (arcticola, pacifica, sakhalina) with some certainty. Additional analysis involving more individuals of all five subspecies is needed to fully evaluate this technique, although several classification procedures yielded low mis-classification rates. Like the molecular technique, we need to first determine whether this technique can differentiate the five Dunlin subspecies before attempting to connect individuals sampled on the staging and nonbreeding grounds to breeding areas. Dunlin exhibit a number of features that make them especially vulnerable to degradation or loss of habitats required during their migration and nonbreeding period. These features include a tendency to aggregate in a limited number of locations, a migration schedule timed to seasonally abundant food resources, and use of wetland habitats that are affected by a wide variety of human activities and developments. Because of this, it is essential that we understand how the various subspecies use the landscape so we can identify areas in need of recognition or protection, and promote their conservation.

Low Genetic Variability in the Geographically Widespread Andean Condor

Article

Full-text available

Feb 2003

We characterized DNA sequence variation in the mitochondrial control region and 12S ribosomal subunit for a sample of Andean Condors (Vultur gryphus) representing populations distributed throughout the species' extensive geographic range (Colombia to central Argentina and Chile). Domains II and III of the control region along with part of the 12S gene were sequenced from 38 individuals (956 base pairs in 30 individuals and 430–824 base pairs for an additional 8 individuals sampled from museum specimens), and Domain I was sequenced from five of these birds (400 base pairs). We identified a total of five haplotypes based on four variable sites distributed over Domains II and III of the control region and the 12S gene. An additional variable site was identified in Domain I. All changes were transitions and no more than three sites differed between any two individuals. Variation in the control region of condors was lower than for most other birds analyzed for these loci. Although low genetic variability is often associated with endangered megafauna, the condor example is notable because the species still maintains a substantial geographic range. Thus, low genetic variability may occur even in megafauna whose ranges have not been severely reduced over recent centuries. Our results therefore suggest that genetic data from geographically widespread megafauna provide important baseline data for assessing the relationship between genetic variability and its causes in other endangered species. Baja Variabilidad Genética en Poblaciones de Vultur gryphus con Amplia Distribución Geográfica Resumen. Caracterizamos la variación de la secuencia de ADN en la región de control mitocondrial y la subunidad ribosomal 12S en una muestra de Vultur gryphus representativa de poblaciones distribuidas a lo largo del extenso rango geográfico de la especie (Colombia, hasta el centro de Argentina y Chile). Los dominios II y III de la región de control, junto con parte del gen 12S, fueron secuenciados en 38 individuos (956 pares de base en 30 individuos y 430–824 pares de base para una muestra adicional de 8 especímenes de museo), y el dominio I fue secuenciado en 5 de estas aves (400 pares de base). Identificamos un total de cinco haplotipos basados en cuatro sitios variables en los dominios II y III de la región de control y el gen 12S. Un sitio variable adicional fue identificado en el dominio I. Todos los cambios fueron transiciones y entre dos individuos cualesquiera no variaron más de 3 sitios. La variación en la región de control de los cóndores fue más baja que para la mayoría de las aves analizadas para estos mismos loci. Aunque la baja variabilidad genética es a menudo asociada con megafauna en peligro de extinción, el ejemplo del cóndor es notable porque la especie aún mantiene un rango geográfico substancial. Así, la baja variabilidad genética se puede dar incluso en la megafauna cuya dispersión no haya sido sujeta a severas reducciones en los ultimos siglos. Por lo tanto, nuestros resultados sugieren que los datos genéticos de rapaces con amplia distribución geográfica y de otra megafauna proveen de importante información de base para evaluar la relación existente entre la variabilidad genética y sus causas en otra megafauna en peligro.

Population Divergence Times and Historical Demography in red Knots and Dunlins

Article

Aug 2005

We employed Bayesian coalescent modeling of samples of mitochondrial control region sequences in two species of shorebird, Red Knots (Calidris canutus) and Dunlins (Calidris alpina) to estimate evolutionary effective population size, population divergence times, and time to most recent common ancestor of genes in the samples. The gene trees for the two species contrast sharply: knot haplotypes were connected in a shallow, star phylogeny whereas Dunlin haplotypes were related in a deeper bifurcating genealogy. Divergence times of populations representing all six subspecies of knots are estimated to have occurred within the last 20 000 (95% CI: 5600–58 000) years, and evolutionary effective population sizes of females are small (Nef = 2000–14 000). We hypothesized that breeding knots were restricted to unglaciated regions of Eurasia during the last glacial maximum, and gradually expanded eastwards into Alaska, the high Canadian Arctic and Greenland as the ice melted. Population divergence times in Dunlins are much older (58 000–194 000 ybp) and effective population size has historically been higher in major lineages (Nef = 12 000–44 000). We conclude that Dunlin populations were not severely reduced in size in the last 200 000 years, and major lineages have differentiated under restricted gene flow for a much longer time than knots. Knots present a snapshot of genetic evolution in the last 20 000 years, whereas Dunlins display patterns of genetic evolution over an order of magnitude longer time frame. Tiempos de Divergencia Poblacional e Historia Demográfica en Calidris canutus y C. alpina Resumen. Aplicamos modelos Bayesianos de coalescencia en una muestra de secuencias de la región de control mitocondrial de dos especies de playeros, Calidris canutus y C. alpina, para estimar el tamaño efectivo de la población, los tiempos de divergencia entre poblaciones y la distancia cronológica al antepasado común más reciente de los genes muestreados. Los árboles genealógicos de las dos especies contrastan fuertemente: los haplotipos de C. canutus están conectados superficialmente siguiendo un patrón filogenético en forma de estrella, mientras que los haplotipos de C. alpina se relacionan de manera más profunda, mostrando patrones de genealogía bifurcados. Se estima que la divergencia poblacional de las seis subespecies de C. canutus tuvo lugar durante los últimos 20 000 años aproximadamente, y los tamaños efectivos de la población de hembras son pequeños (Nef = 2000–14 000). Presumimos que la reproducción de C. canutus estuvo restringida sólo a regiones de Eurasia que estuvieron libres de hielo durante el último máximo glacial y se expandieron gradualmente hacia el este de Alaska, el Ártico canadiense y Groenlandia cuando el hielo se derritió. Los tiempos de divergencia poblacional en C. alpina son más antiguos (58 000–194 000), y el tamaño efectivo de la población ha sido históricamente más alto en los linajes principales (Nef = 12 000–44 000). Concluimos que las poblaciones de C. alpina no mostraron reducciones serias en los últimos 200 000 años, y que sus linajes se han diferenciado por un período de tiempo mucho más prolongado que los de C. canutus. Los patrones encontrados para C. canutus representan una imagen de evolución genética ocurrida durante los últimos 20 000 años, mientras que los patrones de C. alpina indican la ocurrencia de evolución genética durante un período de tiempo diez veces más largo.

Genotyping-by-sequencing reveals genomic homogeneity among overwintering Pacific Dunlin (Calidris alpina pacifica) aggregations along the Pacific coast of North America

Article

Aug 2019

Information on how migratory populations are genetically structured during the overwintering season of the annual cycle can improve our understanding of the strength of migratory connectivity and help identify populations as units for management. Here, we use a genotype-by-sequencing approach to investigate whether population genetic structure exists among overwintering aggregations of the Pacific Dunlin subspecies (Calidris alpina pacifica) sampled at 2 spatial scales (within and among overwintering sites) in the eastern Pacific Flyway. Genome-wide analyses of 874 single nucleotide polymorphisms across 80 sampled individuals revealed no evidence for genetic differentiation among aggregations overwintering at 3 locations within the Fraser River Estuary (FRE) of British Columbia. Similarly, comparisons of aggregations in the FRE and those overwintering in southern sites in California and Mexico indicated no genetic segregation between northern and southern overwintering areas. These results suggest that Pacific Dunlin within the FRE, Sacramento Valley (California), and Guerrero Negro (Mexico) are genetically homogeneous, with no evident genetic structure between sampled sites or regions across the overwintering range. Despite no evidence for differentiation among aggregations, we identified a significant effect of geographical distance between sites on the distribution of individual genotypes in a redundancy analysis. A small proportion of the total genotypic variance (R 2 = 0.036, P = 0.011) was explained by the combined effect of latitude and longitude, suggesting weak genomic patterns of isolation-by-distance that are consistent with chain-like migratory connectivity between breeding and overwintering areas. Our study represents the first genome-scale investigation of population structure for a Dunlin subspecies and provides essential baseline estimates of genomic diversity and differentiation within the Pacific Dunlin.

Unexpected distribution patterns of Carduiceps feather lice (Phthiraptera: Ischnocera: Philopteridae) on sandpipers (Aves: Charadriiformes: Scolopacidae)

Article

Full-text available

Feb 2017
SYST ENTOMOL

The louse genus Carduiceps Clay & Meinertzhagen, 1939 is widely distributed on sandpipers and stints (Calidrinae). The current taxonomy includes three species on the Calidrinae (Carduiceps meinertzhageni, Carduiceps scalaris, Carduiceps zonarius) and four species on noncalidrine hosts. We estimated a phylogeny of four of the seven species of Carduiceps (the three mentioned above and Carduiceps fulvofasciatus) from 13 of the 29 hosts based on three mitochondrial loci, and evaluated the relative importance of flyway differentiation (same host species has different lice along different flyways) and flyway homogenization (different host species have the same lice along the same flyway). We found no evidence for either process. Instead, the present, morphology-based, taxonomy of the genus corresponds exactly to the gene-based phylogeny, with all four included species monophyletic. Carduiceps zonarius is found both to inhabit a wider range of hosts than wing lice of the genus Lunaceps occurring on the same group of birds, and to occur on Calidris sandpipers of all sizes, both of which are unexpected for a body louse. The previously proposed family Esthiopteridae is found to be monophyletic with good support. The concatenated dataset suggests that the pigeon louse genus Columbicola may be closely related to the auk and diver louse genus Craspedonirmus. These two genera share some morphological characters with Carduiceps, but no support was obtained for grouping these three genera together. Based on mitochondrial data alone, the relationships among genera within this proposed family cannot be properly assessed, but some previously suggested relationships within this proposed family are confirmed.

References

Chapter

Jan 1998

Phylogeography and subspecies taxonomy of dunlins (Calidris alpina) in western Palearctic analysed by DNA microsatellites and amplified fragment length polymorphism markers

Article

Dec 2007

In a circumpolar wader, the dunlin (Calidris alpina), there are 11 named subspecies, but only five mitochondrial DNA (mtDNA) lineages have been found. In the present study, we investigated the genetic structure of dunlins in western Palearctic (from East Greenland to Taimyr peninsula) using DNA microsatellites and amplified fragment length polymorphism (AFLP) markers that may detect more recent differentiation than mtDNA. In this region, we consider four described subspecies; alpina, schinzii, arctica and centralis, together comprising two mtDNA lineages. We analyse seven polymorphic microsatellite loci and 91 AFLP markers in 287 and 152 unrelated individuals, respectively, originating from 17 populations. Neither microsatellites nor AFLPs reveal distinct groups that correspond to currently recognized subspecies. There is a clear pattern of isolation by distance in microsatellites. Our results do not contradict the former mtDNA results that there are two phylogenetic lineages (approximately corresponding to schinzii and centralis) that have met and formed a cline (alpina). We find no difference between schinzii and arctica (East Greenland). We conclude that, given the lack of distinct groups and the gradual changes in microsatellite allele frequencies, these markers provide little genetic support for the dunlin subspecies taxonomy in the western Palearctic. (c) 2007 The Linnean Society of London.

Variation in mitochondrial DNA of four species of migratory raptors

Article

Full-text available

Sep 2004

Elise Pearlstine

Four species of North American raptors, the Sharp-shinned Hawk (Accipiter strialus), Cooper's Hawk (A. cooperii), Red-tailed Hawk (Buteo jamaicensis), and American Kestrel (Falco sparverius) are migratory and utilize established flyways for summer and fall migrations. I used restriction-fragment analysis of mitochondrial DNA from individuals from each of these four species on two western and one eastern migratory flyway to test for genetic differences indicative of separation of eastern and western populations. Although the differences were small, western migratory Red-tailed Hawks possessed different mtDNA haplotypes than eastern individuals. There were no consistent differences between eastern and western individuals of the other three species. Further analyses of widespread migratory species of raptor are clearly indicated using other appropriate techniques.

Mitochondrial DNA polymorphism in populations of Siberian and European roe deer (Capreolus pygargus and C-capreolus)

Article

Apr 1998
HEREDITY

We have amplified and sequenced 679 nucleotides of the mitochondrial DNA control-region in 45 Siberian (Capreolus pygargus) and European (C. capreolus) roe deer from two localities in Russia and seven in Italy. Average interspecific sequence divergence was 4.9%. Six different haplotypes were found in Siberian roe deer, and 14 haplotypes in Alpine European roe deer. A population of the endemic Italian subspecies C. c, italicus was monomorphic bearing a single haplotype with one unique nucleotide deletion and a fixed transversion. Phylogenetic relationships among haplotypes indicated that the two species were separated with 100% bootstrap support, and there were two distinct population clusters within each species. These clusters correspond to different geographical locations of the samples: Siberian roe deer were subdivided into west Siberia (Kurgan region) and east Siberia (Amur region), and European roe deer were subdivided into an eastern and a western Alpine group. Average sequence divergence among conspecific populations was 1.2%. Calibrations of evolutionary rates of the different domains of the control-region suggest that Siberian and European roe deer speciated about 2-3 million years ago, and haplotype diversity within species was generated during the last 150 000-370 000 years. Geographical structuring of sequence variability in roe deer allows us to identify historical and recent intraspecific population differences, including the effects of human disturbance. The genetic peculiarities of the endemic Italian subspecies C. c. italicus call for careful conservation of its surviving populations.

Ecology of tundra birds: Patterns of distribution, breeding and migration along the Northeast Passage

Article

May 1999

Several different aspects of the geographical ecology of tundra birds were investigated during the Swedish-Russian Tundra Ecology -94 expedition along the Northeast Passage in 1994. Quantitative censuses of breeding bird communities and populations were made at the temporary field sites, supplemented by surveys from helicopter over wider tundra areas. The occurrence of avian predatory species-skuas, snowy owl and rough-legged buzzard-was analyzed with respect to interspecific relationships as well as to the abundance of their main prey, the lemmings. Geographical variation in color phases among skuas and of genetics in dunlins (based on mitochondrial DNA) were examined, as well as the social organization in different wader species and moult strategies among populations of dunlins. Bird migration was recorded by a tracking radar placed on the expedition ship, and by complementary visual observations. These studies demonstrated the patterns of flight directions, altitudes, speeds (also measured by optical instruments) and migratory routes of the tundra birds. Ringing results contributed to put these results into a global migratory perspective. Two important aspects of the energetics of arctic birds were investigated during the expedition: the basal metabolic rates of waders when departing on migration, and the fuel loads deposited by the migrating waders. The effect of longitudinal displacement on the migratory orientation of a long-distance passerine migrant, the wheatear, was tested by repeated orientation experiments at a number of test sites along the Northeast Passage.

Late Quaternary paleogeography and evolution of arctic breeding waders

Article

Full-text available

Jan 2000

This review links published data on mitochondrial DNA phylogeography of three wader species breeding in the Arctic to the availability of suitable breeding habitat during the past 250 000 years. We argue that the breeding ranges of arctic waders were most restricted in size during warm phases in the earth's climate (interglacials), resulting in population bottlenecks in species breeding in the high arctic zone, such as Red Knot Calidris canutus and Ruddy Turnstone Arenaria interpres, and population contraction and the initiation of genetic divergence in low arctic species, such as Dunlin Calidris alpina. When the climate cooled, all species could spread over larger areas. However, large ice-sheets fragmented tundra habitat, which resulted in more differentiation. Subspecies of Dunlin that became isolated during or before the last glacial period are genetically distinct, while those that originated after the glacial cannot be distinguished using mitochondrial DNA. The sensitivity of waders breeding in the high Arctic to increases in global temperature raises concerns over the effect of possible global warming due to anthropogenic factors on these species.

The deep roots of bird migration: Inferences from the historical record preserved in DNA

Article

Jan 2002

A.J. Baker

Coalescent analysis is a useful tool for relating the historical relationships among gene lineages to the demographic parameters of populations. In this paper I show how simulations of the coalescent process can be used in three species of migratory birds (Dunlin Calidris alpina, Yellow Warbler Dendroica petrechia, Common Chaffinch Fringilla coelebs) to detect historical migration events in these species, and thus to get at the deep roots of population structure. These analyses indicate that current faithful behavioural migration to natal breeding sites is maintaining regional population divergences that originated in the last half of the Pleistocene.

Mitochondrial Control Region Sequences as Tools for Understanding Evolution

Chapter

Dec 1997

The chapter summarizes what is known about the control region of birds in terms of its organization, the location of markers within it, and presents exemplars from laboratory observations illustrating the potential and problems of fast-evolving sequences in elucidating the population structure and molecular systematics of closely related taxa. In addition to transition and transversion substitutions and numerous small indels, length differences accumulate through variation in a number of tandem repeats, and relatively large duplication or deletion of events. Both inter- and intraspecific variations are more common in the two flanking domains than in the conserved central blocks, with tandem repeats occurring primarily in domain III and larger duplications restricted to among-species comparisons. A thorough analysis of intraspecific sequence variation leads inevitably to the consideration of the population genetic processes responsible for major phylogenetic subdivisions in gene trees and to consideration of taxonomic recognition of these discrete clades as subspecies, phylogenetic species, or biological species. A major difficulty illustrated by the knot sequences is that populations are unlikely to be in equilibrium with respect to mutation and genetic drift.

Distribution, phenology and long-term trends of Dunlin Calidris alpina in France

Article

Apr 2014

The coasts of France are known as wintering and staging areas for Dunlin, but the function and importance of the sites at which they are found remains unclear, especially during migration. This study updates information on the numbers and the distribution of Dunlin in France using International Waterbird Census data (counts in January 1977–2013, organized by Wetlands International) and monthly counts carried out at the main sites during 2000–2012. Over the past ten years, France has supported around 312,000 Dunlins in winter, which is about 23% of the wintering population of Europe. About a third were recorded at sites on the north coast (North Sea and Channel), while two-thirds were on the Atlantic coast. Numbers peaked in midwinter. The Mediterranean shore, where intertidal areas are limited, did not support many Dunlin in winter. At the national level the total number in midwinter has been more or less constant for the past 37 years, but with different trends on the Channel and Atlantic coasts. Importantly, around 50% of the midwinter population was concentrated at only eight sites. Most of the Dunlin that winter in France belong to the subspecies alpina which breeds in N Scandinavia and Russia, but significant numbers of migrant Greenlandic and Icelandic Dunlin (subspecies arctica and schinzii) occur on the central Atlantic coast in April or May. Patterns of autumn migration remained unclear. Information on the occurrence of subspecies or the different breeding populations is lacking; however, phenology at the main wintering and staging sites has varied substantially, suggesting that they are used by birds of different origin and/or age.

Population genetic relationships in the roseate tern: globally, regionally and locally

Article

Jan 2004

Anna Lashko

Population Genetics and Evaluation of Genetic Evidence for Subspecies in the Semipalmated Sandpiper ( Calidris pusilla )

Article

Full-text available

Jun 2013

Semipalmated Sandpipers (Calidris pusilla) are among the most common North American shorebirds. Breeding in Arctic North America, this species displays regional differences in migratory pathways and possesses longitudinal bill length variation. Previous investigations suggested that genetic structure may occur within Semipalmated Sandpipers and that three subspecies corresponding to western, central, and eastern breeding groups exist. In this study, mitochondrial control region sequences and nuclear microsatellite loci were used to analyze DNA of birds (microsatellites: n = 120; mtDNA: n = 114) sampled from seven North American locations. Analyses designed to quantify genetic structure and diversity patterns, evaluate genetic evidence for population size changes, and determine if genetic data support the existence of Semipalmated Sandpiper subspecies were performed. Genetic structure based only on the mtDNA data was observed, whereas the microsatellite loci provided no evidence of genetic differentiation. Differentiation among locations and regions reflected allele frequency differences rather than separate phylogenetic groups, and similar levels of genetic diversity were noted. Combined, the two data sets provided no evidence to support the existence of subspecies and were not useful for determining migratory connectivity between breeding sites and wintering grounds. Birds from western and central groups displayed signatures of population expansions, whereas the eastern group was more consistent with a stable overall population. Results of this analysis suggest that the eastern group was the source of individuals that colonized the central and western regions currently utilized by Semipalmated Sandpipers.

Sex bias in a wintering population of Dunlin Calidris alpine in central Taiwan

Article

Aug 2012

The sexes of many migratory shorebird species differ in timing and distance of their migrations, but this phenomenon has been little studied for birds in the East Asian-Australasian Flyway (EAAF). Using molecular sexing techniques (but also taking morphometric data), we compared the sex ratio of Dunlin Calidris alpina sampled on the west coast of Taiwan between September 2007 and May 2008. We found an overall sex bias (59.2%) toward females, including juveniles. A discriminant function deduced from three morphological measurements correctly identified 89.0% of Dunlin, but performed better in identifying males than females. Since Taiwan is at the southern end of the Dunlin's East Asian winter range, our results support the 'arrival-time' hypothesis whereby the sex that arrives earlier on the breeding grounds winters closer to them. To maintain stable populations, conservation must take account of this differential use of wintering grounds by the two sexes.

Phylogeographic population structure of great reed warblers: An analysis of mtDNA control region sequences

Article

Feb 1999

Staffan Bensch

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.

Population Genetics of Southeastern Wood Ducks

Article

Oct 2001

Numerous studies document nest-site philopatry in wood ducks (Aix sponsa). Such behavior should promote unique genetic structure among breeding populations. This hypothesis was tested by analyzing restriction site variation in mitochondrial DNA (mtDNA) of 218 nesting wood duck hens. We tested the utility of mtDNA variation in identifying migrants from a sample of 92 wood ducks harvested by duck hunters. Genetic variation was found only in the cytochrome b gene. Statistically significant genetic structure existed among 8 breeding populations, but was function of haplotype frequencies in 1 population that differed from the other 7. Restriction enzyme digestion revealed 2 haplotypes common to all populations and 3 rare haplotypes. Haplotype diversity within populations was low with respect to other avian studies. Direct sequence analysis of 41 wood ducks produced 2 common and 16 rare mtDNA haplotypes with no geographic structure. Hunter-harvested birds had similar haplotypes as breeding birds. For many years, wood duck managers in the southeastern United States have been interested in delineating subpopulations of wood ducks. Our data may reinforce and broaden existing efforts to manage southern wood ducks using management units determined by band returns.

A Test of the Glacial Refugium Hypothesis using Patterns of Mitochondrial and Nuclear DNA Sequence Variation in Rock Ptarmigan (Lagopus mutus)

Article

Dec 1999

Morphological and Molecular Variation across a Migratory Divide in Willow Warblers, Phylloscopus trochilus

Article

Full-text available

Dec 1999

A migratory divide is a narrow region in which two populations showing different migratory directions meet and presumably also mate and hybridize. Banding of willow warblers, Phylloscopus trochilus, in Europe has demonstrated a migratory divide latitudinally across central Scandinavia. In autumn, southern birds migrate southwest to tropical West Africa, whereas northern birds migrate southeast to East and South Africa. The migratory divide is associated with concordant differences in size and plumage coloration. Based on morphology, we estimate the width of the transition zone between northern and southern willow warblers to be less than 350 km. We found indication of linkage disequilibria around the migratory divide, in that measures of body size were correlated with plumage coloration within the contact zone, but uncorrelated within the populations south or north of the contact zone. The presence of linkage disequilibria and the fact that several morphological dines occur together suggest that the hybrid zone is a result of secondary contact between populations that have differentiated in allopatry. This interpretation is in accord with the knowledge of the recolonization pattern of the Scandinavian peninsula after the last glaciation; animals and plants appeared to have colonized either from the south or from the north around the northern bay of the Baltic Sea. If northern and southern willow warblers resided in allopatric populations during late Pleistocene glaciations and the hybrid zone is a result of postglacial range expansions, we would expect some degree of genetic differentiation accumulated during the period in isolation. In contrast, northern and southern willow warblers are near panmictic in the frequencies of alleles of mitochondrial DNA and at two microsatellite loci. The observed pattern, clear morphological and behavioral differentiation without genetic differentiation at neutral loci, suggests either that the differences are maintained by strong selection on the expressed genes in combination with high levels of current gene flow or, in the case of weak gene flow, that the divergence in morphology and behavior is very recent.

Intercontinental genetic structure and gene flow in Dunlin (Calidris alpina), a potential vector of avian influenza

Article

Full-text available

Dec 2014
EVOL APPL

Waterfowl (Anseriformes) and shorebirds (Charadriiformes) are the most common wild vectors of influenza A viruses. Due to their migratory behavior, some may transmit disease over long distances. Migratory connectivity studies can link breeding and nonbreeding grounds while illustrating potential interactions among populations that may spread diseases. We investigated Dunlin (Calidris alpina), a shorebird with a subspecies (C. a. arcticola) that migrates from nonbreeding areas endemic to avian influenza in eastern Asia to breeding grounds in northern Alaska. Using microsatellites and mitochondrial DNA, we illustrate genetic structure among six subspecies: C. a. arcticola, C. a. pacifica, C. a. hudsonia, C. a. sakhalina, C. a. kistchinski, and C. a. actites. We demonstrate that mitochondrial DNA can help distinguish C. a. arcticola on the Asian nonbreeding grounds with >70% accuracy depending on their relative abundance, indicating that genetics can help determine if C. a. arcticola occurs where they may be exposed to highly pathogenic avian influenza (HPAI) during outbreaks. Our data reveal asymmetric intercontinental gene flow, with some C. a. arcticola short-stopping migration to breed with C. a. pacifica in western Alaska. Because C. a. pacifica migrates along the Pacific Coast of North America, interactions between these subspecies and other taxa provides route for transmission of HPAI into other parts of North America.This article is protected by copyright. All rights reserved.

Numbers, midwinter distribution, and migration of wader populations using the East Atlantic flyway

Article

Full-text available

Jan 1989

Evidence of general instability of past climate from a 250-kyr ice-core record

Article

Full-text available

Jul 1993
NATURE

A detailed stable-isotope record is presented for the full length of the Greenland Ice-core Project Summit ice core covering the last 250,000 years according to a graduated timescale. It appears that the climatic stability of the Holocene is the exception rather than the rule; the last interglacial is also noted to have lasted longer than is implied by the deep-sea SPECMAP record. This discrepancy may be accounted for if the climate instability at the outset of the last interglacial delayed the melting of the Saalean ice sheets in America and Eurasia.

Mitochondrial DNA and two perspectives on evolutionary genetics

Article

Full-text available

Jun 2008
BIOL J LINN SOC

This essay reviews comparative studies of animal mitochondrial DNA (mtDNA), with emphasis on findings made and ideas developed at Berkeley. It argues that such studies are bringing together two previous paths of progress in evolutionary biology. One path is that of those who worked far above the species level and were concerned with genealogical trees, time scales and the accumulation of new mutations on surviving molecular lineages. The other path is that of those who worked at and below the species level and were concerned mainly with population structure, migration and the frequencies of alleles that existed in an ancestral population. This fusion of paths is made possible by the high rate at which mutations accumulate on mtDNA lineages and by this molecule's uniparental and apparently haploid mode of inheritance. These properties make mtDNA a superb tool for building trees and time scales relating molecular lineages at and below the species level. In addition, owing to its mode of inheritance, mtDNA is more sensitive to bottlenecks in population size and to population subdivision than are nuclear genes. Joint comparative studies of both mtDNA and nuclear DNA variability give us valuable insights into how effective population size has varied through time. Such studies also give insight into the conditions under which mtDNA from one species can colonize another species.

Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics

Article

Full-text available

Nov 1987
Annu Rev Ecol Systemat

Analysis of Molecular Variance Inferred From Metric Distances Among DNA Haplotypes: Application to Human Mitochondrial DNA Restriction Data

Article

Full-text available

Jul 1992

We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.

Slatkin M, Maddison WP. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-613

Article

Full-text available

Dec 1989

A method for estimating the average level of gene flow among populations is introduced. The method provides an estimate of Nm, where N is the size of each local population in an island model and m is the migration rate. This method depends on knowing the phylogeny of the nonrecombining segments of DNA that are sampled. Given the phylogeny, the geographic location from which each sample is drawn is treated as multistate character with one state for each geographic location. A parsimony criterion applied to the evolution of this character on the phylogeny provides the minimum number of migration events consistent with the phylogeny. Extensive simulations show that the distribution of this minimum number is a simple function of Nm. Assuming the phylogeny is accurately estimated, this method provides an estimate of Nm that is as nearly as accurate as estimates obtained using FST and other statistics when Nm is moderate. Two examples of the use of this method with mitochondrial DNA data are presented.

An Approach to Population and Evolutionary Genetic Theory for Genes in Mitochondria and Chloroplasts, and Some Results

Article

Full-text available

Apr 1983

We developed population genetic theory for organelle genes, using an infinite alleles model appropriate for molecular genetic data, and considering the effects of mutation and random drift on the frequencies of selectively neutral alleles. The effects of maternal inheritance and vegetative segregation of organelle genes are dealt with by defining new effective gene numbers and substituting these for 2N(e) in classical theory of nuclear genes for diploid organisms. We define three different effective gene numbers. The most general is N(λ), defined as a function of population size, number of organelle genomes per cell, and proportions of genes contributed by male and female gametes to the zygote. In many organisms, vegetative segregation of organelle genomes and intracellular random drift of organelle gene frequencies combine to produce a predominance of homoplasmic cells within individuals in the population. Then, the effective number of organelle genes is N(eo), a simple function of the numbers of males and females and of the maternal and paternal contributions to the zygote. Finally, when the paternal contribution is very small, N(eo) is closely approximated by the number of females, N(f). Then if the sex ratio is 1, the mean time to fixation or loss of new mutations is approximately two times longer for nuclear genes than for organelle genes, and gene diversity is approximately four times greater. The difference between nuclear and organelle genes disappears or is reversed in animals in which males have large harems.

Mitochondrial control-region sequences in two shorebird species, the turnstone and the Dunlin, and their utility in population genetic studies

Article

Full-text available

Feb 1994

We determined the mitochondrial control-region sequences of five turnstones (Arenaria interpres) and three dunlins (Calidris alpina). Comparisons revealed that the central part (part II) is conserved relative to much more variable parts at the beginning (part I) and the end (part III). This pattern of sequence conservation is also found in the control regions of other vertebrates. The average sequence divergence between turnstone and dunlin was 21.8% for part I, 7.5% for part II, and 29.5% for part III. Within-species sequence divergence over the entire control region was much lower, at 0.9% for turnstones and 2.0% for dunlins. In both shorebird species, part III contains a repetitive sequence composed only of A and C nucleotides, which has not been found in the control regions of other birds. A survey of the part I sequences of 25 turnstones and 25 dunlins sampled around the world revealed that these species have very different population genetic structures. Dunlins are not only much more differentiated in their sequences but also have a strongly subdivided population genetic structure. Pleistocene vicariant events combined with strong natal philopatry and high mutation rates of the sequences are likely responsible for this population genetic subdivision. Conversely, part I sequences of turnstones are weakly differentiated and are geographically unstructured. We argue that this is not the result of global gene flow but that, instead turnstones have recently expanded from a refugial population that was bottlenecked.

Empirical Tests of Some Predictions From Coalescent Theory With Applications to Intraspecific Phylogeny Reconstruction

Article

Full-text available

Aug 1993

Empirical data sets of intraspecific restriction site polymorphism in Drosophila have been gathered in order to test hypotheses derived from coalescent theory. Three main ideas are tested: (1) haplotype frequency in the sample contains information on the topological position of a given haplotype in a cladogram, (2) the frequency of a haplotype is related to the number of mutational connections to other haplotypes in the cladogram and (3) geographic location can be used to infer topological positioning of haplotypes in a cladogram. These relationships can then be used to better estimate intraspecific phylogenies in two ways: (1) rooting the phylogeny and (2) resolving ambiguities in a cladogram. This information will allow one to reduce the number of alternative phylogenies and incorporate the uncertainties involved in reconstructing intraspecific phylogenies into subsequent analyses that depend heavily on the topology of the tree.

Geographic variation in Dunlins, Calidris alpina, of North America

Article

Jan 1977
Can Field Nat

M. Ralph Browning

DNA Polymorphism Detectable by Restriction Endonucleases

Article

Feb 1981

Data on DNA polymorphisms detected by restriction endonucleases are rapidly accumulating. With the aim of analyzing these data, several different measures of nucleon (DNA segment) diversity within and between populations are proposed, and statistical methods for estimating these quantities are developed. These statistical methods are applicable to both nuclear and non-nuclear DNAs. When evolutionary change of nucleons occurs mainly by mutation and genetic drift, all the measures can be expressed in terms of the product of mutation rate per nucleon and effective population size. A method for estimating nucleotide diversity from nucleon diversity is also presented under certain assumptions. It is shown that DNA divergence between two populations can be studied either by the average number of restriction site differences or by the average number of nucleotide differences. In either case, a large number of different restriction enzymes should be used for studying phylogenetic relationships among related organisms, since the effect of stochastic factors on these quantities is very large. The statistical methods developed have been applied to data of Shah and Langley on mitochondrial (mt)DNA from Drosophila melanogaster, simulans and virilis. This application has suggested that the evolutionary change of mtDNA in higher animals occurs mainly by nucleotide substitution rather than by deletion and insertion. The evolutionary distances among the three species have also been estimated.

Dispersal of Dunlin Calidris alpina in relation to sites of birth and breeding

Article

ORNIS FENNICA

M. Soikkeli

Distribution, reproductive success, and population trend in the Dunlin Calidris alpina schinzii on the Swedish west coast

Article

Jan 1991

In 1989, the breeding population of dunlin in the provinces of Bohuslan and Halland was surveyed. Total population size was a maximum of 44 pairs. The number of breeding pairs has declined during the 1980s and the population has been restricted to about ten localities; 55% of the total population occurred at two sites. At two of the surveyed localities, hatching success varied considerably among years, reflecting variation in nest predation rate. On average, 0.8 and 1.0 fledglings per pair were produced at the two localities. -from Authors

Global Population Structure and Natural History of the Green Turtle (Chelonia mydas) in Terms of Matriarchal Phylogeny

Article

Aug 1992

To address aspects of the evolution and natural history of green turtles, we assayed mitochondrial (mt). DNA genotypes from 226 specimens representing 15 major rookeries around the world. Phylogenetic analyses of these data revealed (1) a comparatively low level of mtDNA variability and a slow mtDNA evolutionary rate (relative to estimates for many other vertebrates); (2) a fundamental phylogenetic split distinguishing all green turtles in the Atlantic-Mediterranean from those m the Indian-Pacific Oceans; (3) no evidence for matrilineal distinctiveness ora commonly recognized taxonomic form in the East Pacific (the black turtle C. rn. agassizi or C. agassizi); (4) in opposition to published hypotheses, a recent origin for the Ascension Island rookery, and its close genetic relationship to a geographically proximate rookery m Brazil; and (5) a geographic population substructure within each ocean basin (typically involving fixed or nearly fixed genotypic differences between nesting populations) that suggests a strong propensity for natal homing by females. Overall, the global matriarchal phylogeny of Chelonia mydas appears to have been shaped by both geography (ocean basin separations) and behavior (natal homing on regional or rookeryspecific scales). The shallow evolutionary population structure within ocean basins likely results from demographic turnover (extinction and colonization) of rookeries over time frames that are short by evolutionary standards but long by ecological standards.

Breeding and Wintering Areas of Dunlin Migrating through Southern Baltic

Article

May 1989

Jadwiga Gromadzka

Two main questions are discussed: (1) the eastern limit of Dunlin Calidris alpina populations migrating through the Baltic and (2) migration between the Baltic and the Mediterranean/Black Sea. Ringing and moult data show that some Dunlins migrating to the Baltic orignate from more easterly regions than previously presumed. Many Dunlins migrating in autumn through the Baltic are in active moult. Some of them probably start their moult while breeding and originate from areas east of the Urals. These birds show some easily recognized plumage patterns: their new median coverts (usually only some of them) are of "adult buff" type. This is characteristic of Central and Eastern Siberia populations which start moulting very early, while still on their breeding grounds. Ringing data show that these birds winter in western Europe as well as in the Mediterranean. Some Dunlins from the Baltic migrate in autumn in a SE direction - to the Mediterranean and the Black Sea regions. The origin of these birds is not known. The SE direction may be used also by Polish breeding schinzii. Some Dunlins of the sub-species alpina, ringed in the Baltic in autumn, are controlled in spring at the Black Sea; in autumn they seem to migrate along a more northern route - through the Baltic, while in spring they choose a more southern route - through the Black Sea (loop migration).

Polymerase-Chain-Reaction (PCR) Analysis of Microsatellites: A New Approach to Studies of Genetic Relationships in Birds

Article

Oct 1992

Hans Ellegren

Genomic DNA libraries of the Barn Swallow (Hirundo rustica) and the Pied Flycatcher (Ficedula hypoleuca) were screened for the presence of dinucleotide microsatellite repeats. Two thymine-guanine repeats, " $({\rm TG})_{n}$ ," and two thymine-cytosine repeats, " $({\rm TC})_{n}$ ," were isolated and sequenced from the two species, respectively. Polymerase-chain-reaction (PCR) analysis of 25 unrelated Barn Swallows and 10 unrelated Pied Flycatchers revealed 3 to 15 alleles per locus and heterozygosities in the range of 0.46 to 0.89. Mendelian inheritance was confirmed for all four loci in 10 Pied Flycatcher and 2 Barn Swallow families comprising a total of 240 meioses. The occurrence of nonparental alleles in offspring from two Barn Swallow families was consistent with extrapair fertilization as revealed by a parallel DNA-fingerprinting analysis. A DNA amount approximately corresponding to 0.01 μl blood was used for PCR analysis. DNA was also prepared from feathers and approximately 1% of a preparation from a single remex or rectrix was sufficient for PCR amplification. One of the primer pairs from the Barn Swallow also amplified a polymorphic locus in the House Martin (Delichon urbica) and in the Bank Swallow (R. riparia).

Breeding Ecology and Annual Cycle Adaptations of the Red-Backed Sandpiper (Calidris alpina) in Northern Alaska

Article

Jan 1966

Richard T. Holmes

Matriarchal Population Genetic Structure in an Avian Species with Female Natal Philopatry

Article

Aug 1992

We employ mitochondrial (mt) DNA markers to examine the matrilineal component of population genetic structure in the snow goose Chen caerulescens. From banding returns, it is known that females typically nest at their natal or prior nest site, whereas males pair with females on mixed wintering grounds and mediate considerable nuclear gene flow between geographically separate breeding colonies. Despite site philopatry documented for females, mtDNA markers show no clear distinctions between nesting populations across the species' range from Wrangel Island, USSR to Baffin Island in the eastern Canadian Arctic. Two major mtDNA clades (as well as rare haplotypes) are distributed widely and provide one of the few available examples of a phylogeographic pattern in which phylogenetic discontinuity in a gene tree exists without obvious geographic localization within a species' range. The major mtDNA clades may have differentiated in Pleistocene refugia, and colonized current nesting sites through recent range expansion via pulsed or continual low-level dispersal by females. The contrast between results of banding returns and mtDNA distributions in the snow goose raises general issues regarding population structure: direct contemporary observations on dispersal and gene flow can in some cases convey a misleading impression of phylogeographic population structure, because they fail to access the evolutionary component of population connectedness; conversely, geographic distributions of genetic markers can provide a misleading impression of contemporary dispersal and gene flow because they retain a record of evolutionary events and past demographic parameters that may differ from those of the present. An understanding of population structure requires integration of both evolutionary (genetic) and contemporary (direct observational) perspectives.

Geographical variation and taxonomy of the Dunlin Calidris alpina (L.)

Article

Jan 1986

J G Greenwood

Bill Lengths, Wintering Areas, and Taxonomy of North American Dunlins, Calidris alpina

Article

Oct 1971

The Last Great Ice Sheets

Book

Dec 1981

Late Weichselian Ice Sheets in Eurasia and Greenland (B. G. Andersen). Late Wisconsin Ice Sheets of North America (P. A. Mayewski, G. H. Denton, & T. J. Hughes). Late Wisconsin-Weichselian Mountain Glaciers and Small Ice Caps (J. T. Hollin & D. H. Schilling). Numerical Reconstruction of Valley Glaciers and Small Ice Caps (D. H. Schilling & J. T. Hollin). Numerical Reconstruction of Paleo-Ice Sheets (T. J. Hughes). The Last Great Ice Sheets: A Global View (T. J. Hughes, G. H. Denton, B. G. Andersen, D. H. Schilling, J. L. Fastook, & C. S. Lingle). The History of the Marine Ice Sheet in West Antarctica During the Last Glaciation: A Working Hypothesis (M. Stuiver, G. H. Denton, & T. J. Hughes). The Arctic Ice Sheet: An Outrageous Hypothesis (G. H. Denton & T. J. Hughes).

Principles of Genealogical Concordance in Species Concepts and Biological Taxonomy

Article

Jan 1990

Species Concepts and Speciation Analysis

Article

Jan 1983

Joel Cracraft

Systematic biologists have directed much attention to species concepts because they realize that the origin of taxonomic diversity is the fundamental problem of evolutionary biology. Questions such as, What are the units of evolution? and, How do these units originate? thus continually capture the attention of many. It is probably no exaggeration to say that most believe the “systematic” aspects of the problem have been solved to a greater or lesser extent, whereas the task before us now is to understand the “genetic” and “ecologic” components of differentiation, i. e., those aspects often perceived to constitute the “real mechanisms” of speciation: A study of speciation is, to a considerable extent, a study of the genetics and evolution of reproductive isolating mechanisms (Bush, 1975, p. 339). ... a new mechanistic taxonomy of speciation is needed before population genetics, which deals with evolutionary mechanisms, can be properly integrated with speciation theory; that is, the various modes of speciation should be characterized according to the various forces and genetic mechanisms that underly [sic] the evolution of isolating barriers (Templeton 1980, p. 720).

Association between mitochondrial DNA and morphological evolution in Canada Geese

Article

Nov 1990

Summary Variation within and between eight subspecies of Canada geese was assessed by restriction fragment analysis of mitochondrial DNA (mtDNA), electrophoresis of proteins encoded by nuclear DNA, and the morphometric analysis of skeletons. Estimates of mtDNA sequence divergence between Canada goose subspecies ranged from 0.04 to 2.54%. Pairwise comparisons of the three data matrices revealed that only mtDNA variation and body size are significantly correlated. Subspecies with northern breeding grounds are small-bodied and display small variations of one mtDNA clone, whereas those breeding further south are largebodied and show small differences in another mtDNA clone. Canada geese exhibit strong geographic differentiation with respect to mtDNA sequence, but weak structuring in protein-encoding nuclear DNA. This finding can be explained by a lower level of gene flow for the mitochondrial genome than for the nuclear genome, which in turn emanates from the maternal inheritance of mtDNA and male-biased dispersal in Canada geese. Despite male-mediated flow of nuclear genes, strong morphometric differentiation persists among Canada geese subspecies.

Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide. Molecular Ecology (3): 313-327

Article

Jan 1994

The Interpretation of Population Structure by F-Statistics with Special Regard to Systems of Mating

Article

Sep 1965
EVOLUTION

S. W. Wright

The general conclusion of part I is that the theoretical correlation between representatives of a locus in gametes, uniting or otherwise, relative to one or another array of such representatives (F-statistics), gives a broader basis for comparison of population structures, including progress in fixation, than does the alternative concept: the probability of identity of such representatives by origin. One reason is that correlations vary from -1 to +1 while probabilities vary only from 0 to +1. The probability concept gives, however, a very useful supplementary interpretation where applicable. The relation of the basic set of F-statistics, FIT, FIS, FST, to variances within populations is discussed in part II and applications to diverse patterns of population structure are reviewed (the island model with or without selective differences, isolation by distance in continuous populations under balancing of local inbreeding and dispersion, uniformly distributed clusters under a similar balance, selective clines, breeds of livestock). In part III, these F-statistics are applied to systems of mating in populations of given small size, in which consanguine mating is either avoided as much as possible, or pursued as much as is possible without any disruption of the group. The apparently paradoxical result obtained by Kimura and Crow that heterozygosis declines more rapidly under the former than under the latter is discussed from the standpoint of these statistics. These systems have been found to agree in one respect, the ultimate proportion of recombinant lines in the race between fixation and recombination among lines starting from double heterozygotes.

Migration of dunlin calidris alpina: A worldwide overview

Article

Jun 1984

Julian G. Greenwood

Ringing recoveries have been used to determine the winter quarters for the different breeding populations of Dunlin. These are Greenlandic, Icelandic, and British breeding birds to north‐west Africa; those from the Baltic to north‐west Africa, the Mediterranean and Persian Gulf; Lapplandic to the British Isles south to north‐west Africa; western Russian to the British Isles, the Mediterranean, the Caspian and Abrabian Gulf; eastern Russian and northern Alaskan to the Asian Pacific coast; western Alaskan to the North American Pacific coast; arctic Canadian to the North American Atlantic coast. Populations that breed in different areas occupy greatly overlapping regions in winter throughout much of the range.

Cytonuclear genetic architecture in mosquitofish populations and the possible roles of introgressive hybridization

Article

Jun 1993
MOL ECOL

Spatial genetic structure in populations of mosquitofish (Gambusia) sampled throughout the south-eastern United States was characterized using mitochondrial (mt) DNA and allozyme markers. Both sets of data revealed a pronounced genetic discontinuity (along a broad path extending from south-eastern Mississippi to north-eastern Georgia) that corresponds to a recently recognized distinction between the nominal forms G. affinis to the west and G. holbrooki to the east. However, several populations from the general contact region exhibited unusual allelic associations in high frequency, suggestive of evolutionary processes within a zone of introgressive hybridization. These involve: (i) cytonuclear profiles representing combinations of nuclear and mitochondrial genotypes that tended to be more nearly species-specific and concordant elsewhere; and (ii) significant nuclear gametic disequilibria, perhaps attributable to positive assortative mating and/or differential fitnesses of homospecific vs. recombinant genotypes. However, outside this suspected hybrid region, ‘heterospecific’ genetic markers also appeared in low frequency, thus complicating interpretations. These discordant alleles on a broader geographic scale may reflect: (a) the retention of polymorphisms from an ancestral gene pool; (b) occasional evolutionary convergence (especially with respect to electrophoretic mobility of allozyme alleles); (c) the ‘footprints’ of a moving hybrid zone; or (d) differential introgressive penetrance across the current hybrid region.

Variance of Gene Frequencies

Article

Mar 1969

C. Clark Cockerham

The role that inbreeding and coancestry play in the distribution of neutral genes is incorporated into the variance of a linear function to provide a simple cumulative expression of the variance among mean gene frequencies of groups of individuals. The total variance of gene frequencies is subdivided into components corresponding to genes within individuals, among individuals within groups, and among groups. Various intraclass correlations, some of which may be negative, of gene frequencies are formulated. The various types of parameters are considered for and extended to include further structuring of the population, separate sexes, systems of mating, and effective numbers. Estimators and tests of hypotheses for the parameters are developed.

Principles of Systematic Zoology

Article

Jun 1969
Syst Zool

Ernst Mayr

The science of taxonomy the species category species taxa intrapopulational variational variation and the comparison of population samples specification and taxonomic decisions the theory of classification taxonomic characters phenetics cladistics evolutionary classification numerical methods taxonomic collections and identification taxonomic collections and identification taxonomic publications principles of zoological nomenclature.

Mitochondrial DNA Lineages in Composite Flocks of Migratory and Wintering Dunlins (Calidris alpina)

Article

Oct 1996

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 genetic legacy of Mother Goose– phylogeographic patterns of lesser snow goose Chen caerulescens caerulescens maternal lineages

Article

Sep 1992

Tom W Quinn

By using the polymerase chain reaction to amplify and sequence 178 bp of a rapidly evolving region of the mtDNA genome (segment I of the control region) from 81 individuals, approximately 11% of the variation present in the lesser snow goose Chen caerulescens caerulescens L. mitochondrial genome was surveyed. The 26 types of mtDNA detected formed two distinct mitochondrial clades that differ by an average of 6.7% and are distributed across the species range. Restriction analysis of amplified fragments was then used to assign the mtDNA of an additional 29 individuals to either of these clades. Within one major clade, sequence among mtDNAs was concordant with geographic location. Within the other major clade the degree of sequence divergence among haplotypes was lower and no consistent geographic structuring was evident. The two major clades presumably result from vicariant separation of lesser snow geese during the Pleistocene.

The coalescent in two partially isolated difusion populations

Article

Jan 1989

Naoyuki Takahata

The n0 coalescent of Kingman (1982a, b) describes the family relationships among a sample of n0 individuals drawn from a panmictic species. It is a stochastic process resulting from n0 − 1 independent random events (coalescences) at each of which n (2 ≤ n ≤ n0) ancestral lineages of a sample are descended from n − 1 distinct ancestors for the first time. Here a similar genealogical process is studied for a species consisting of two populations with migration between them. The main interest is with the probability density of the time length between two successive coalescences and the spatial distribution of n − 1 ancestral lineages over two populations when n to n − 1 coalescence takes place. These are formulated based on a non-linear birth and death process with killing, and are used to derive several explicit formulae in selectively neutral population genetics models. To confirm and supplement the analytical results, a simulation method is proposed based on the underlying bivariate Markov chain. This method provides a general way for solving the present problem even when an analytical approach appears very difficult. It becomes clear that the effects of the present population structure are most conspicuous on 2 to 1 coalescence, with lesser extents on n to n − 1 (3 ≤ n) coalescence.This implies that in a more general model of population structure, the number of populations and the way in which a sample is drawn are important factors which determine the n0 coalescent.

Saitou N, Nei M.. The Neighbor-Joining Method-a New Method for Reconstructing Phylogenetic Trees. Mol Biol Evol 4: 406-425

Article

Aug 1987

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.

Mitochondrial DNA phylo-geographic differentiation among avian populations and the evo-lutionary significance of subspecies Gene flow, effective population sizes, and genetic variance components in birds

Jan 1980
626-636789

R M Ball
J C Avise

Ball, R. M., and J. C. Avise. 1992. Mitochondrial DNA phylo-geographic differentiation among avian populations and the evo-lutionary significance of subspecies. Auk 109:626-636. Barrowclough, G. F 1980. Gene flow, effective population sizes, and genetic variance components in birds. Evolution 34:789-798.

Sur les races du B6casseau cincle (ou vari-able) et du Tetras a bec noir

Jan 1932
261-270

S A Buturlin

Buturlin, S. A. 1932. Sur les races du B6casseau cincle (ou vari-able) et du Tetras a bec noir. Alauda 4:261-270.

Phylogeny inference package, version 3.41

Jan 1975

J Felsenstein
U N Glutz Von Blotzheim
K M Bauer
E Bezzel

Felsenstein, J. 1991. Phylogeny inference package, version 3.41. University of Washington, Seattle. Glutz von Blotzheim, U. N., K. M. Bauer, and E. Bezzel. 1975. Handbuch der Vogel Mitteleuropas. Band 6. Charadriiformes (Teil 1). Akademische, Wiesbaden.

Post-nuptial moult in dunlin Calidris al-pina Migration of dunlin Calidris alpina: a worldwide overview Geographical variation and taxonomy of the dunlin Calidris alpina

Jan 1983
223-22835

J G Greenwood

Greenwood, J. G. 1983. Post-nuptial moult in dunlin Calidris al-pina. Ibis 125:223-228.. 1984. Migration of dunlin Calidris alpina: a worldwide overview. Ringing and Migration 5:35-39.. 1986. Geographical variation and taxonomy of the dunlin Calidris alpina. Bulletin of the British Ornithologists' Club 106: 43-56.

Zur Brutbiologie des Alpenstrandlaufers

Jan 1966
173-188

R Heldt

Heldt, R. 1966. Zur Brutbiologie des Alpenstrandlaufers. Corax 1: 173-188.

The plovers, sandpipers, and snipes of the world

Jan 1981

P A Johnsgard

Johnsgard, P. A. 1981. The plovers, sandpipers, and snipes of the world. University of Nebraska Press, Lincoln.

Reproduction and survival in a declining pop-ulation of the southern dunlin Calidris alpina schinzii. Wader Study Group Bulletin (supplement)

Jul 1991
56-6847

P E Jonsson

Jonsson, P. E. 1991. Reproduction and survival in a declining pop-ulation of the southern dunlin Calidris alpina schinzii. Wader Study Group Bulletin (supplement). 61:56-68. This content downloaded from 91.213.220.173 on Sat, 28 Jun 2014 16:59:47 PM All use subject to JSTOR Terms and Conditions P. W. WENINK ET AL.

A new subspecies of dunlin, Calidris alpina littoralis from the Sakhalin island

Jan 1987
1110-1113

V A Nechaev
P S Tomkovich

Nechaev, V. A., and P. S. Tomkovich. 1987. A new subspecies of dunlin, Calidris alpina littoralis from the Sakhalin island. Zool-ogicheskii Zhurnal 66:1110-1113. (In Russian, with English summary).

Breeding cycle and population dynamics in the dunlin Dispersal of dunlin in relation to sites of birth and breeding

Jan 1967
158-1981

M Soikkeli

Soikkeli, M. 1967. Breeding cycle and population dynamics in the dunlin. Annales Zoologici Fennici 4:158-198.. 1970. Dispersal of dunlin in relation to sites of birth and breeding. Ornis Fennica 47:1-9.

A taxonomic study of the American dunlin (Erolia alpina subssp.)

Jan 1953
85-88

W E C Todd

Todd, W. E. C. 1953. A taxonomic study of the American dunlin (Erolia alpina subssp.). Journal of the Washington Academy of Sciences 43:85-88.

Geographical variatiability of the dunlin in the Soviet Far East. Byulletin Moskovskogo Obshchestva Is-pytateli

Jan 1986
3-15

P S Tomkovich

Tomkovich, P. S. 1986. Geographical variatiability of the dunlin in the Soviet Far East. Byulletin Moskovskogo Obshchestva Is-pytateli Prirody Otdel Biologicheskii 91:3-15. (In Russian, with English summary).

Global Mitochondrial DNA Phylogeography of Holarctic Breeding Dunlins (Calidris alpina)

Abstract

No full-text available

Recommended publications

Global mitochondrial DNA phylogeography of holarctic breeding dunlins, Calidris alpina.