No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Extreme isolation by distance in a montane frog Rana cascadae
Abstract
Given the recent interest in declining amphibian populations, it is surprising that there are so few data on genetic drift and gene flow in anuran species. We used seven microsatellite loci to investigate genetic structure and diversity at both large and small geographic scales, and to estimate gene flow in the Cascades frog, Rana cascadae. We sampled 18 sites in a hierarchical design (inter-population distances ranging from 1–670km) to test for isolation by distance and to determine the geographic scale over which substantial gene flow occurs. Eleven of these sites were sampled as three fine-scale clusters of three, three, and five sites separated by pairwise distances of 1–23km to estimate number of migrants exchanged per generation via F
ST
and by a coalescent approach. We found R. cascadae exhibits a strong pattern of isolation by distance over the entire species range, and that there is a sharp drop in migrants exchanged between sites separated by greater than 10km. These data, in conjunction with results of other recent studies, suggest that montane habitats promote unusually strong genetic isolation among frog populations. We discuss our results in light of future management and conservation of R. cascadae.
... The six major genetic groups of populations identified in this study are outlined and labeled. Sampling localities of R. cascadae from Monsen and Blouin (2004) are shown as small 'x' symbols differentiation and gene flow among populations within each of the remaining groups, and (4) compare the pattern of differentiation among R. pretiosa populations with that among populations of R. cascadae, a more continuouslydistributed and non-endangered congener that also occurs in Oregon and Washington. ...
... These loci were developed for R. pretiosa (loci with ''RP'' prefix) or for R. luteiventris (loci with ''SFC'' prefix), which is the sister species of R. pretiosa (Green et al. 1997; Hillis and Wilcox 2005; Funk et al. 2008 ). PCR amplifications (25 ll) were carried out with the components and conditions as described in Monsen and Blouin (2004), but with locus-specific annealing temperatures and fluorescently-labeled forward primers (see Appendix A for primer sequences). One locus (RP385) would not amplify cleanly in the samples from the Klamath Basin (JC, KW, KE, AR, WR, and BL populations), but gave clean, scorable bands from all other populations. ...
... The question was whether R. pretiosa shows a different pattern of IBD than R. cascadae, as one might expect given the patchier distribution of R. pretiosa populations. For this comparison we used the 18 R. cascadae populations assayed for microsatellite variation in Monsen and Blouin (2004). These R. cascadae samples were scored at 6 microsatellite loci, 4 of which were also used in this study on R. pretiosa. ...
The Oregon spotted frog (Rana pretiosa) is one of the most threatened amphibians in the Pacific Northwest. Here we analyzed data from 13 microsatellite loci and 298 bp of mitochondrial DNA in frogs collected from 23 of the remaining R. pretiosa populations in order to (1) assess levels of genetic diversity within populations of R. pretiosa, (2) identify the major genetic groups in the species, (3) estimate levels of genetic differentiation and gene flow among populations within each major group, and (4) compare the pattern of differentiation among R. pretiosa populations with that among populations of R. cascadae, a non-endangered congener that also occurs in Oregon and Washington. There is a strong, hierarchical genetic structure in R. pretiosa. That structure includes six major genetic groups, one of which is represented by a single remaining population. R. pretiosa populations have low genetic diversity (average H
e = 0.31) compared to R. cascadae (average H
e = 0.54) and to other ranid frogs. Genetic subdivision among populations is much higher in R. pretiosa than in R. cascadae, particularly over the largest geographic distances (hundreds of kilometers). A joint analysis of migration rates among populations and of effective sizes within populations (using MIGRATE) suggests that both species have extremely low migration rates, and that R. pretiosa have slightly smaller effective sizes. However, the slight difference in effective sizes between species appears insufficient to explain the large difference in genetic diversity and in large-scale genetic structure. We therefore hypothesize that low connectivity among the more widely-spaced R. pretiosa populations (owing to their patchier habitat), is the main cause of their lower genetic diversity and higher among-population differentiation. Conservation recommendations for R. pretiosa include maintaining habitat connectivity to facilitate gene flow among populations that are still potentially connected, and either expanding habitat or founding additional ‘backup’ populations to maintain diversity in the isolated populations. We recommend that special consideration be given to conservation of the Camas Prairie population in Northern Oregon. It is the most geographically isolated population, has the lowest genetic diversity (H
e = 0.14) and appears to be the only remaining representative of a major genetic group that is now almost extinct. Finally, because the six major groups within R. pretiosa are strongly differentiated, occupy different habitat types, and are geographically separate, they should be recognized as evolutionarily significant units for purposes of conservation planning.
... On the one hand, populations show a clear pattern of isolation by distance over the entire study area covering nearly its whole range within the Iberian Peninsula (Fig. 4). This effect has been previously reported in some other studies of amphibian populations (Vos et al. 2001;Monsen and Blouin 2004;Palo et al. 2004;Spear et al. 2005;Knopp and Merilä 2009) but not in others (Allentoft et al. 2009;Purrenhage et al. 2009). When the analysis is applied to the three main clusters, this pattern is not so clear. ...
... Based on the genetic structure obtained, three operational conservation units can be defined with a clear gene flow pattern within each one of them (Moritz 1994;Crandall et al. 2000). Understanding patterns of gene flow between subpopulations is important for effective conservation because species and population survival may depend on dispersal between patches of suitable habitat (Monsen and Blouin 2004). ...
The increasing fragmentation of natural habitats may strongly affect patterns of dispersal and gene flow among populations, and thus alter evolutionary dynamics. We examined genetic variation at twelve microsatellite loci in the Agile frog (Rana dalmatina) from 22 breeding ponds in the Iberian Peninsula, the southwest limit of its range, where populations of this species are severely fragmented and are of conservation concern. We investigated genetic diversity, structure and gene flow within and among populations. Diversity as observed heterozygosities ranged from 0.257 to 0.586. The mean number of alleles was 3.6. Just one population showed a significant F IS value. Four populations show evidence of recent bottlenecks. Strong pattern of structure was observed due to isolation by distance and to landscape structure. The average degree of genetic differentiation among populations was F ST = 0.185. Three operational conservation units with meta-population structure were identified. Additionally, there are some other isolated populations. The results reinforce the view that amphibian populations are highly structured even in small geographic areas. The knowledge of genetic structure pattern and gene flow is fundamental information for developing programmes for the preservation of R. dalmatina at the limits of its geographic distribution.
... Sometimes amphibians are highly genetically differentiated at moderate distances. Populations of cascade frogs (Rana cascadae) showed strong genetic differentiation separated by 50 km (Monsen and Blouin 2004). Significant genetic differentiation found between sites at a distance of only 3.8 km in tungara frogs (Engystomops pustulosus) (Lampert et al. 2003). ...
... Natural features can also act as barriers and promote genetic isolation among anuran populations (Monsen and Blouin 2004). A study on Columbia spotted frogs (Rana luteiventris) reported a positive correlation between genetic differentiation and elevation with mountain ridges that appeared to be physical barriers (Funk et al. 2005). ...
... Although clear patterns of genetic differentiation were evident across many different spatial scales, at the coarsest, range-wide level, five deeply divergent genetic groups were present across phylogenetic (Fig. 1), ordination (Fig. 2), and Bayesian clustering (Fig. 3) approaches, even when explicitly modeling admixture (Fig. 4). Fst among these groups was extraordinarily high (Table 3), and currently stands as the highest that we are aware of for any anuran (Monsen and Blouin 2004). That such variation exists and was not apparent in an earlier mtDNA analysis emphasizes the importance of resampling with genomic tools, especially for declining species that may lose important genetic variation and local adaptation without immediate conservation actions. ...
... The extraordinarily high Fst values among major clades are consistent with the interpretation that R. boylii is deeply divided taxon that demands conservation actions following a cladelevel, in addition to a watershed-level, approach. The among-clade and among-locality Fst values observed here were considerably higher than those found over similar distances in the related Rana cascadae by Monsen and Blouin (2004), which has previously served as an exemplar of extremely strong genetic differentiation in an amphibian species. While major hydrological boundaries explain a reasonable portion of the broad-scale genetic diversity of R. boylii, there are also regions where distantly related samples occur in the same HUC6-level hydrological unit. ...
Genomic data are useful for attaining high resolution in population genetic studies and have become increasingly available for answering questions in biological conservation. We analyzed RADseq data for the protected foothill yellow-legged frog ( Rana boylii ) throughout its native range in California and Oregon, including many of the same localities included in an earlier study based on mitochondrial DNA. We recovered five primary clades that correspond to geographic regions within California and Oregon, with better resolution and more spatially consistent patterns than the previous study, confirming the increased resolving power of genomic approaches compared to single-locus analyses. Bayesian clustering, PCA and population differentiation with admixture analyses all indicated that approximately half the range of R. boylii consists of a single, relatively uniform population, while regions in the Sierra Nevada and Central Coast Range of California are deeply differentiated genetically. Additionally, a major methodological challenge for large genome organisms, including many amphibians, is deciding on sequence similarity clustering thresholds for population genetic analyses using RADseq data, and we develop a novel set of metrics that allow researchers to set a sequence similarity threshold that maximizes the separation of paralogous regions while minimizing the oversplitting of naturally occurring allelic variation within loci.
... Although clear patterns of genetic differentiation were evident across many different spatial scales, at the coarsest, range-wide level, five deeply divergent genetic groups were present across phylogenetic (Fig. 1), ordination (Fig. 2), and Bayesian clustering (Fig. 3) approaches, even when explicitly modeling admixture (Fig. 4). Fst among these groups was extraordinarily high (Table 3), and currently stands as the highest that we are aware of for any anuran (Monsen and Blouin 2004). That such variation exists and was not apparent in an earlier mtDNA analysis emphasizes the importance of resampling with genomic tools, especially for declining species that may lose important genetic variation and local adaptation without immediate conservation actions. ...
... The extraordinarily high Fst values among major clades are consistent with the interpretation that R. boylii is deeply divided taxon that demands conservation actions following a cladelevel, in addition to a watershed-level, approach. The among-clade and among-locality Fst values observed here were considerably higher than those found over similar distances in the related Rana cascadae by Monsen and Blouin (2004), which has previously served as an exemplar of extremely strong genetic differentiation in an amphibian species. While major hydrological boundaries explain a reasonable portion of the broad-scale genetic diversity of R. boylii, there are also regions where distantly related samples occur in the same HUC6-level hydrological unit. ...
Genomic data have the potential to inform high resolution landscape genetic and biological conservation studies that go far beyond recent mitochondrial and microsatellite analyses. We characterize the relationships of populations of the foothill yellow-legged frog, Rana boylii, a declining, “sentinel” species for stream ecosystems throughout its range in California and Oregon. We generated RADseq data and applied phylogenetic methods, hierarchical Bayesian clustering, PCA and population differentiation with admixture analyses to characterize spatial genetic structure across the species range. To facilitate direct comparison with previous analyses, we included many localities and individuals from our earlier work based on mitochondrial DNA. The results are striking, and emphasize the power of our landscape genomic approach. We recovered five extremely differentiated primary clades that indicate that R. boylii may be the most genetically differentiated anuran yet studied. Our results provide better resolution and more spatially consistent patterns than our earlier work, confirming the increased resolving power of genomic data compared to single-locus studies. Genomic structure is not equal across the species distribution. Approximately half the range of R. boylii consists of a single, relatively uniform population, while Sierra Nevada and coastal California clades are deeply, hierarchically substructured with biogeographic breaks observed in other codistributed taxa. Our results indicate that clades should serve as management units for R. boylii rather than previously suggested watershed boundaries, and that the near-extinct population from southwestern California is particularly diverged, exhibits the lowest genetic diversity, and is a critical conservation target for species recovery.
... Sometimes amphibians are highly genetically differentiated at moderate distances. Populations of cascades frog (Rana cascadae) showed strong genetic differentiation separated by 50 kilometers (Monsen & Blouin 2004) and Lampert et al. (2003) found significant genetic differentiation between sites at a distance of only 3.8 kilometers in túngara frogs (Physalaemus pustulosus). Not all anuran species are great dispersers and the saffron frog (Geocrinia lutea) is even more extreme and has shown genetic differentiation between populations that were separated by only 1.25 kilometers (Driscoll 1998). ...
... Barriers can also be natural and mountain habitats promote genetic isolation among Anuran populations (Monsen & Blouin 2004). In a study of the Columbia spotted frog there was a positive correlation between genetic differentiation and elevation, and mountain ridges seem to be physical barriers . ...
Dispersal is an important factor in animal ecology. Anurans (frogs and toads) are often philopatric (home loving) but some specimens in a population usually have the capacity to disperse relatively long distances. In this study I investigated the colonization of newly constructed ponds in the southwest of Sweden by three anuran species: The common toad (Bufo bufo), the moor frog (Rana arvalis) and the common frog (Rana temporaria). The ponds were constructed between two and five years ago and were now as frequently occupied as older source ponds in the area. For the common toad and the common frog there was no correlation between distance to source populations and degree of colonization. The moor frog was more common in ponds that were situated in the vicinity of older source ponds with ample populations. The main impression was that these species rapidly colonize newly constructed ponds, at least within moderate distances from source populations. There were some differences between the species though and it seems like the moor frog have more limited dispersal abilities than the other two species.
... cascadae in Oregon and Washington also found gene flow sharply dropped at distances greater than 10 km suggesting strong genetic isolation among populations (Monsen and Blouin 2004). ...
... This hypothesized "mountain-island" model suggests that gene flow occurs often among high-elevation populations that are not separated by deep lowelevation canyons, below the species lower elevational limits. This hypothesis is also supported by the findings of Monsen and Blouin (2004) who found a sharp drop in gene flow among R. cascadae populations in Oregon and Washington separated by distances greater than 10 km. However, future studies using molecular techniques could assess the degree to which low-elevation canyons influence gene flow. ...
... On the one hand, populations show a clear pattern of isolation by distance over the entire study area covering nearly its whole range within the Iberian Peninsula (Fig. 4). This effect has been previously reported in some other studies of amphibian populations (Vos et al. 2001;Monsen and Blouin 2004;Palo et al. 2004;Spear et al. 2005;Knopp and Merilä 2009) but not in others (Allentoft et al. 2009;Purrenhage et al. 2009). When the analysis is applied to the three main clusters, this pattern is not so clear. ...
... Based on the genetic structure obtained, three operational conservation units can be defined with a clear gene flow pattern within each one of them (Moritz 1994;Crandall et al. 2000). Understanding patterns of gene flow between subpopulations is important for effective conservation because species and population survival may depend on dispersal between patches of suitable habitat (Monsen and Blouin 2004). ...
The increasing fragmentation of natural habitats may strongly affect patterns of dispersal and gene flow among populations, and thus alter evolutionary dynamics. We examined genetic variation at twelve microsatellite loci in the Agile frog (Rana dalmatina) from 22 breeding ponds in the Iberian Peninsula, the southwest limit of its range, where populations of this species are severely fragmented and are of conservation concern. We investigated genetic diversity, structure and gene flow within and among populations. Diversity as observed heterozygosities ranged from 0.257 to 0.586. The mean number of alleles was 3.6. Just one population showed a significant F
IS value. Four populations show evidence of recent bottlenecks. Strong pattern of structure was observed due to isolation by distance and to landscape structure. The average degree of genetic differentiation among populations was F
ST = 0.185. Three operational conservation units with metapopulation structure were identified. Additionally, there are some other isolated populations. The results reinforce the view that amphibian populations are highly structured even in small geographic areas. The knowledge of genetic structure pattern and gene flow is fundamental information for developing programmes for the preservation of R. dalmatina at the limits of its geographic distribution.
... Private alleles 3 to 20, and the average expected heterozygosities within populations ranged from 0.25 to 0.87 (Monsen & Blouin 2004). In addition, Monsen & Blouin (2004) indicated that the number of alleles per locus ranged from 1 to 11 per population, while the average expected heterozygosity per population ranged from 0.45 to 0.73, and the average observed heterozygosities per population ranged from 0.45 to 0.78 in Rana cascadae. The observed heterozygosity was found to be lower than in R. cascadae. ...
Anatolian mountain frogs consist of two admitted species (Rana macrocnemis and Rana tavasensis), and
this group is famous for its high land distribution throughout the Anatolian mountain chain. Despite the
unique features of these groups (cold-adapted and highland species), their population genetics have yet to
be revealed. In this study, the allelic variation and genetic structure of Anatolian mountain frogs were inve-
stigated using six microsatellite markers across its natural distribution area in Türkiye. We evaluated 138
samples from 31 locations and clustered them based on a Structure analysis. The microsatellite markers
suggested a high level of diversity in the East Anatolia cluster, while we found limited genetic diversity
in the Central Taurus and West Anatolia clusters. We found a significant bottleneck in the Central Taurus
cluster, with no genetic differentiation between R. macrocnemis and R. tavasensis. Our results show that
the Anatolian mountain frogs exhibit underlying inbreeding signs for macro and microclimatic reasons.
... In this study, we tested for gene flow between individuals of the tropical frog Mantidactylus bellyi in the Montagne d'Ambre National Park (MANP), a site where the species is broadly distributed across heterogeneous environmental conditions. We know that montane habitats promote genetic isolation through elevational gradients and/or isolation by distance among vertebrates [4,[97][98][99]. Although we were able to confirm low mitochondrial differentiation within this species in our study area, microsatellite data yielded an optimal cluster solution of three subpopulations on the massif in three of our four STRUC-TURE models (Fig 1 and S2 Table in S3 File). ...
In the processes that give rise to new species, changes first occur at the population level. But with the continuous nature of the divergence process, change in biological properties delimiting the shift from “individuals of divergent populations” towards “individuals of distinct species”, as well as abiotic factors driving the change, remain largely ambivalent. Here we study diversification processes at the population level in a semi-aquatic frog, Mantidactylus ( Brygoomantis ) bellyi , across the diverse vegetation types of Montagne d’Ambre National Park (MANP), Madagascar. Genetic diversity was assessed with seven newly developed microsatellite markers as well as mitochondrial DNA sequences and concordance with patterns of ecological, morphological, and bioacoustic divergence evaluated. We found M . bellyi lacking mitochondrial differentiation within MANP, while microsatellite datasets partitioned them into three highly differentiated, geographically separated subpopulations (with indications for up to five subpopulations). The molecular grouping–primarily clustering individuals by geographic proximity–was coincident with differences in mean depth and width of waters, suggesting a possible role of fluvial characteristics in genetic exchange in this stream-breeding species. Genetic clustering not consistent with differences in call properties, except for dominant call frequencies under the two-subpopulations model. Morphological divergence was mostly consistent with the genetic clustering; subpopulations strongly differed by their snout-vent length, with individuals from high-elevation subpopulations smaller than those from populations below 1000 m above sea level. These results exemplify how mountains and environmental conditions might primarily shape genetic and morphological divergence in frog populations, without strongly affecting their calls.
... In other words, no IBD pattern was detected in A. septentrionale. While in animals and seed plants, IBD patterns occur across hundreds or thousands of kilometres (Sharbel et al. 2000;Monsen and Blouin 2004), the few studies on IBD in rock-dwelling ferns failed to detect significant IBD at scales of more than 50 km. Across distances of 20 to 800 km, Luo et al. (2018) found no IBD in Polystichum glaciale, while Kang et al. (2008) found significant IBD in Adiantum reniforme across distances of 0.8 to 21 km, and Hunt et al. (2009) found IBD in Asplenium fontanum in distance classes up to 50 km but not for larger distances up to 1000 km. ...
Erratic boulders provide habitat for rock-dwelling species and contribute to the biodiversity of landscapes. In the calcareous Swiss lowlands, siliceous erratic boulders are exclusive habitat islands for the regionally critically endangered fern Asplenium septentrionale, about 20 bryophyte species and numerous lichens. Focusing on island biogeographical processes, we analysed the conservation genomics of A. septentrionale and the moss Hedwigia ciliata on insular erratic boulders in the Swiss lowlands and the adjacent “mainland” in siliceous mountains. We genotyped both species using double digest restriction associated DNA sequencing (ddRAD). For the tetraploid A. septentrionale, abundant identical multilocus genotypes within populations suggested prevalent intragametophytic selfing, and six out of eight boulder populations consisting of a single multilocus genotype each indicated single spore founder events. The genetic structure of A. septentrionale mainland populations coincided with Pleistocene glacial refugia. Four genetic lineages of H. ciliata were identified, and populations consisting of a single multilocus genotype were less common than in A. septentrionale. For both taxa, multilocus genotype diversity on boulders was lower than in mainland populations. The absence of common genetic groups among boulder populations, and the absence of isolation by distance patterns, suggested colonisation of boulders through independent long-distance dispersal events. Successful boulder colonisation of A. septentrionale seems to be rare, while colonisation by H. ciliata appears to be more frequent. We conclude that pivotal principles of conservation biology, such as connectivity and genetic diversity, are of less importance for the studied cryptogams on insular erratic boulders because of long-distance dispersal, intragametophytic selfing and polyploidy.
... Genetic differences among populations in advertisement calls may also be the result of neutral forces Amézquita et al. 2009;Klymus et al. 2012), such as random genetic drift. When populations become isolated by geographic distance barriers, gene flow among them decreases, and more distant populations accumulate greater differences than less distant populations (Hutchison et al. 1999;Monsen and Blouin 2004;Jang et al. 2011;Lin et al. 2014). Isolation by distance can lead to drift in mate-choice preferences, which can result in mate recognition only among nearby populations, thereby reinforcing genetic isolation (Pröhl et al. 2006;Funk et al. 2009;Wilkins et al. 2013) and increasing geographic variation. ...
... Reduced genetic variation may further increase vulnerability of amphibian populations and enhance the risk of decline (Allentoft and O'Brien 2010;Chen et al. 2012). Isolation of populations and bottleneck effects, great intraspecific variation of genetic diversity and distinct effective population sizes were observed among amphibian populations (Funk et al. 2005; Monsen and Blouin 2004;Razpet et al. 2016). In European amphibians, continental-scale decrease of genetic diversity is not only caused by anthropogenic habitat deterioration, but also associated with recolonization histories following the last glaciation (Dufresnes and Perrin 2015). ...
Amphibian populations worldwide are threatened by declines and extinctions mainly due to habitat loss and fragmentation. Habitat fragmentation threatens the yellow-bellied toad Bombina variegata in the northern and western regions of its distribution where it is strictly protected. We studied the genetic structure and diversity of populations at three geographical scales using microsatellite loci to detect potential threats for population persistence. At the local scale, we sampled four neighbouring localities at 1-2.6 km distance to detect effects of short-term (decades) fragmentation on connectivity. At the regional scale, five additional localities in the mountains of the Westerwald (Rhineland-Palatinate, Germany) were studied at up to 50.1 km distance to analyse genetic diversity and population structure. At the continental scale, we included data from regions in the northern distribution with fragmented populations (Hesse and Lower Saxony, Germany) and more continuous populations in the South (Alsace, France; Geneva, Switzerland; Trentino, Italy) to evaluate variation of genetic diversity. At the local scale, short-term fragmentation caused significant genetic differentiation between breeding assemblages only 1.4 km apart from each other. At the regional scale, we found notable genetic distance among localities. At the continental scale, we identified Alsace, Trentino and Geneva in the South as regions with low genetic structuring and high allelic richness, and the northern remaining regions in Germany as deeply structured with reduced allelic richness. We suggest that reduced genetic diversity and habitat fragmentation in northern regions makes these populations particularly vulnerable to decline. In conclusion, informed conservation management of B. variegata should focus on measures maintaining or improving con-nectivity among neighbouring populations.
... Genetic differences among populations in advertisement calls may also be the result of neutral forces Amézquita et al. 2009;Klymus et al. 2012), such as random genetic drift. When populations become isolated by geographic distance barriers, gene flow among them decreases, and more distant populations accumulate greater differences than less distant populations (Hutchison et al. 1999;Monsen and Blouin 2004;Jang et al. 2011;Lin et al. 2014). Isolation by distance can lead to drift in mate-choice preferences, which can result in mate recognition only among nearby populations, thereby reinforcing genetic isolation (Pröhl et al. 2006;Funk et al. 2009;Wilkins et al. 2013) and increasing geographic variation. ...
Anurans communicate information during breeding activity to conspecifics mainly through acoustic signals, and different evolutionary forces may produce geographic variation in such communication systems. To understand which variables influenced geographic variation in the advertisement call of Dendropsophus nanus, a generalist species with a broad distribution in South America, we tested three nonexclusive hypotheses: geographic distance, environmental temperature, and body size. The advertisement call of this species consists of two note types: Type A, which functions in spacing among males in aggregations, and Type B, which may influence female choice. To determine the effect of the three explanatory variables on each note, we sampled nine populations in central and southern Brazil. We found that geographic distance and temperature were the main variables explaining variation in both notes. An exploratory analysis revealed differences in the advertisement call between populations in western and eastern localities. Because temperature was spatially structured, geographic distance may have produced variation in temperature along the longitudinal gradient, resulting in the observed variation in bioacoustic parameters among populations. Also, we observed that individuals in warmer localities were smaller than those from colder localities, and this difference in body size was correlated to the note repetition rate of Type A notes. Our findings indicate that variation in acoustic parameters may be an indirect result of temperature acting on body size. Thus, geographic variation in the advertisement call of D. nanus may be due to both neutral and selective processes.
... Regional genetic differentiation among G. molossus candidate populations was relatively high between these two clades and each pairwise population comparison between the two regions showed significant genetic differentiation (p < 0.05; Table 4). The divergence between these two major lineages could be explained by the increased geographical distance and possibly other factors such as large rivers (Chi River and Mun River), which might obstruct gene flow (Monsen and Blouin 2004;Pröhl et al. 2010) between these two clades as is often observed in other amphibians (Pröhl et al. 2010). However, future studies should obtain new specimens from this geographic gap and re-do the phylogenetic and morphological analyses in order to determine the actual zones of contact for the morphological populations and the clades A and B populations. ...
Glyphoglossus molossus, is one of the most economically important amphibians in the Khorat Plateau, north-eastern Thailand. It is categorised as a near-threatened species by IUCN due to over-exploitation. Here, we examined the genetic structure of G. molossus using partial mitochondrial cytochrome-b gene sequences from specimens collected at 11 localities. The sequence analysis revealed the presence of 15 haplotypes, 5 of which are shared by 2 or more populations, and 10 haplotypes that are confined to a single population. The relatively low haplotype (h) and nucleotide (π) diversities suggest that the Phu Phan Mountain Range is not high enough to act as an effective dispersal barrier between the Sakon Nakhon and Khorat Basins. However, AMOVA and phylogenetic analyses based on Maximum likelihood (ML) and Bayesian inference (BI) strongly supported the presence of two genetically divergent clades, Sakon Nakhon Basin and the northern part of the Khorat Basin (clade A) and the southern part of the Khorat Basin (clade B). These two lineages are separated by substantial geographical distance, which has putatively resulted in a reduction of gene flow. Further studies, with more extensive genetic sampling, especially from throughout the species range will aid in better interpreting our results.
... . Isolation by distance is a common pattern seen in amphibian populations(Bani et al., 2015;Monsen & Blouin, 2004;Peterman, Feist, Semlitsch, & Eggert, 2013;Scribner, Arntzen, Cruddace, Oldham, & Burke, 2001), as even comparatively vagile amphibians like the northern leopard frog are dispersal limited ...
Prehistoric climate and landscape features play large roles structuring wildlife populations. The amphibians of the northern Great Plains of North America present an opportunity to investigate how these factors affect colonization, migration, and current population genetic structure. This study used 11 microsatellite loci to genotype 1,230 northern leopard frogs (Rana pipiens) from 41 wetlands (30 samples/wetland) across North Dakota. Genetic structure of the sampled frogs was evaluated using Bayesian and multivariate clustering methods. All analyses produced concordant results, identifying a major east–west split between two R. pipiens population clusters separated by the Missouri River. Substructuring within the two major identified population clusters was also found. Spatial principal component analysis (sPCA) and variance partitioning analysis identified distance, river basins, and the Missouri River as the most important landscape factors differentiating R. pipiens populations across the state. Bayesian reconstruction of coalescence times suggested the major east–west split occurred ~13–18 kya during a period of glacial retreat in the northern Great Plains and substructuring largely occurred ~5–11 kya during a period of extreme drought cycles. A range‐wide species distribution model (SDM) for R. pipiens was developed and applied to prehistoric climate conditions during the Last Glacial Maximum (21 kya) and the mid‐Holocene (6 kya) from the CCSM4 climate model to identify potential refugia. The SDM indicated potential refugia existed in South Dakota or further south in Nebraska. The ancestral populations of R. pipiens in North Dakota may have inhabited these refugia, but more sampling outside the state is needed to reconstruct the route of colonization. Using microsatellite genotype data, this study determined that colonization from glacial refugia, drought dynamics in the northern Great Plains, and major rivers acting as barriers to gene flow were the defining forces shaping the regional population structure of R. pipiens in North Dakota.
... Widespread species endemic to the DOF are ideal subjects for phylogeographic studies in the Chaco, Caatinga, and Cerrado biomes. Frogs are excellent model organisms (Nuñez, Wood, Rabanal, Fontanella, & Sites, 2011;Zeisset & Beebee, 2008) because of their limited dispersal abilities, high habitat specificity, and tendency to have high levels of population genetic structure (Johns & Avise, 1998;Monsen & Blouin, 2004 This species is fossorial and is an explosive breeder, which is strongly associated with heavy rainfall events (Fabrezi, Quinzio, Goldberg, & de Sá, 2012;Nomura, Rossa-Feres, & Langeani, 2009). ...
Aim
To test three different scenarios to account for the geographic distribution of genetic variation in Dermatonotus muelleri, a fossorial frog endemic of the South American diagonal of open formations (DOF) formed by Chaco, Cerrado, and Caatinga biomes: (a) The pan‐DOF hypothesis, where these biomes behave as a single biogeographical unit and DOF species lack population structure; (b) the southwest‐northeast (SW‐NE) hypothesis, where structured populations along the DOF have either asymmetric or unidirectional gene flow in the northeast direction; (c) the vicariance hypothesis, where a pattern of population structure with no or reduced gene flow is observed.
Location
Caatinga, Cerrado, and Chaco in South America.
Methods
We sampled 179 individuals across the species distribution and sequenced one mitochondrial and two nuclear markers. We evaluated population structure, the presence, direction, and asymmetry of gene flow, and demographic changes to test three different phylogeographic hypotheses for D. muelleri using a model‐based simulation approach.
Results
We found two geographically structured lineages with no gene flow, refuting pan‐DOF hypothesis. The Southwest lineage occurs in Chaco and western Cerrado and the Northeast lineage in eastern Cerrado and Caatinga. Our results support the model with demographic change for the Northeast lineage and constant size for Southwest lineage. The vicariance model with divergence time estimated around 4 Ma was preferred.
Main conclusions
Vicariance was the best explanation for the geographic distribution of genetic variation in Dermatonotus. Divergence time supports the role of Neogene orogeny in central Brazil for the splitting of Dermatonotus lineages. The influence of Pleistocene climatic fluctuations seems restricted to changes in one lineage's population size. Therefore, both ancient and recent events shaped the phylogeography of Dermatonotus. Genetic divergence, lack of gene flow, and the presence of a geographic barrier between lineages indicate the existence of a cryptic, undescribed species in northeastern Brazil.
... Consequently, assessing the population genetics of a species can provide valuable information for conservation much more quickly than longitudinal demographic studies [15]. Such studies have already been widely used to inform management strategies to halt or slow down amphibian decline [10,[16][17][18][19][20][21][22]. ...
Amphibians are the vertebrate group with the highest number of species threatened with extinction, and habitat loss and fragmentation are considered to be among the leading causes of their declines and extinctions. Little is known of the population biology of amphibian species inhabiting montane forests in Central and West Africa, where anthropogenic activities such as farming and cattle raising are major threats to native biodiversity. We used Amplified Fragment Length Polymorphisms (AFLPs) to assess the population genetic structure of two poorly known species, Cardioglossa schioetzi and Leptodactylodon bicolor (both in the Arthroleptidae), in and around Ngel Nyaki Forest Reserve on the Mambilla Plateau in eastern Nigeria. The landscape comprises continuous forest on steep slopes and small riparian forest fragments in a grassland matrix. While increased fragmentation is well documented for these and other forests in the mountains of Cameroon and Nigeria over the past century, there are no previous assessments of the impact of forest fragmentation on mon-tane amphibian populations in this region. Our estimates of genetic diversity are similar across populations within each species with levels of heterozygosity values consistent with local population declines. Except for a pair of populations (C. schioetzi) we did not observe genetic differentiation between forest and riparian forest fragment populations, nor across sites within continuous forest (L. bicolor). Our results demonstrate recent gene flow between forest fragments and the adjacent protected forests and suggest that small forest corridors connecting these may lessen the genetic consequences of at least 30 years of intense and severe fragmentation in Ngel Nyaki.
... Should the destruction of elephants cease while habitats remain, populations could expand from multiple locations. Should active management become necessary for recolonization, the best source populations for translocations would be those that are geographically close, as these would be most similar to any extirpated population (Monsen & Blouin, 2004). ...
The past processes that have shaped geographic patterns of genetic diversity may be difficult to infer from current patterns. However, in species with sex differences in dispersal, differing phylogeographic patterns between mitochondrial (mt) and nuclear (nu) DNA may provide contrasting insights into past events. Forest elephants (Loxodonta cyclotis) were impacted by climate and habitat change during the Pleistocene, which likely shaped phylogeographic patterns in mitochondrial (mt) DNA that have persisted due to limited female dispersal. By contrast, the nuclear (nu) DNA phylogeography of forest elephants in Central Africa has not been determined. We therefore examined the population structure of Central African forest elephants by genotyping 94 individuals from six localities at 21 microsatellite loci. Between forest elephants in western and eastern Congolian forests, there was only modest genetic differentiation, a pattern highly discordant with that of mtDNA. Nuclear genetic patterns are consistent with isolation by distance. Alternatively, male‐mediated gene flow may have reduced the previous regional differentiation in Central Africa suggested by mtDNA patterns, which likely reflect forest fragmentation during the Pleistocene. In species like elephants, male‐mediated gene flow erases the nuclear genetic signatures of past climate and habitat changes, but these continue to persist as patterns in mtDNA because females do not disperse. Conservation implications of these results are discussed.
... Knowing, when, where, and how far an animal moves is also critical to identifying the appropriate spatial scale and design of conservation areas (Brown et al., 2005). Thus, ecologists have devoted considerable effort to quantify the spatial ecology of a diverse variety of taxa (Milton and May, 1976;Rolando, 2002). ...
Southeast Asian amphibians are threatened by population declines and extinction, but little is known about their movement patterns and habitat use. This study examines the spatial ecology of the giant river frog, Limnonectes leporinus, a stream-breeding frog endemic to Borneo that is hunted for food. Radiotelemetry was evaluated as a means of tracking frogs and was found to be highly effective even in rugged terrain. Preliminary data on four individuals tracked over 22 days indicated that L. leporinus is strictly riparian spending most of its time in restricted core activity areas between 450-1910 m2 within 20m of the stream bed. Both males and females performed long distance migrations associated with reproductive activity within the stream. Home range sizes ranged between 2050-8250 m2. Although widespread in lowland primary forests, L. leporinus may be vulnerable to population declines due to its narrow habitat tolerance and migratory activity.
... Likewise, the neighbor-joining tree of pairwise Fst values shows the sampling locations in an approximate stepping-stone pattern (Fig. 7) and therefore supports the semi-continuous nature of differentiation (Kalinowski 2009). The signature of isolation by distance was also detected in the North American congener montane species Rana cascadae (Monsen and Blouin 2004) and among some populations of Rana pretiosa (Blouin et al. 2010), indicating some propensity for low levels of gene flow across larger geographic distances for related species. ...
The mountain yellow-legged species complex (Rana sierrae and Rana muscosa) has declined precipitously in distribution and abundance during the last century. The two primary threats are chytrid epidemic-associated population collapses and predation from the introduction of non-native trout. Widespread declines have occurred throughout the ranges of these species, including populations of R. sierrae in Yosemite National Park. A clear picture of genetic structure of remaining Yosemite R. sierrae populations is critical to short-term management and conservation. We conducted a population genetics study that included samples from 23 geographic sites distributed throughout the range of R. sierrae in Yosemite NP. We used minimally-invasive swab samples to collect genetic data from mitochondrial and nuclear DNA via sequencing (43 transcriptome-derived markers) and analyzed the distribution of genetic variation in a geographic context. Our mtDNA analysis partially confirmed previous results suggesting that two haplotype groups occur in Yosemite: one haplotype group contained high bootstrap support for monophyly while the other did not. However, increased geographic sampling demonstrated that the two haplotypes are not completely geographically partitioned into the two main drainages (Merced drainage and Tuolumne drainage) as previously postulated. Our nuclear DNA analysis revealed a general pattern of genetic isolation by distance, where genetic differentiation was correlated with geographic distance between sites. In addition, our analyses suggested that three clusters of genetically cohesive sites occur in the study area. Understanding population genetic patterns of variability will inform management strategies such as translocations, reintroductions, and monitoring for this endangered frog. Lastly, our next generation sequencing enabled approach allowed us to obtain multi-locus data from minimally-invasive swab samples. Thus researchers can now leverage extensive archives of swab samples (initially collected for pathogen testing) to study host genetics in previously surveyed amphibian populations.
... Although there exists several studies of species with very limited distribution ranges (for example, Sunny et al., 2014), as well as of amphibians with highly structured populations (Monsen and Blouin, 2004;Blouin et al., 2010;Savage et al., 2010;Blank et al., 2013), C. arnoldi represents an exceptional example of a critically endangered amphibian species with limited dispersal capabilities inhabiting a very small fragmented habitat. Here we present an analysis of the genetic diversity and evolutionary history of C. arnoldi, which provides general insights into management priorities of species with a very limited distribution range. ...
Endemic species with restricted geographic ranges potentially suffer the highest risk of extinction. If these species are further fragmented into genetically isolated subpopulations, the risk of extinction is elevated. Habitat fragmentation is generally considered to have negative effects on species survival, despite some evidence for neutral or even positive effects. Typically, non-negative effects are ignored by conservation biology. The Montseny brook newt (Calotriton arnoldi) has one of the smallest distribution ranges of any European amphibian (8 km(2)) and is considered critically endangered by the International Union for Conservation of Nature. Here we apply molecular markers to analyze its population structure and find that habitat fragmentation owing to a natural barrier has resulted in strong genetic division of populations into two sectors, with no detectable migration between sites. Although effective population size estimates suggest low values for all populations, we found low levels of inbreeding and relatedness between individuals within populations. Moreover, C. arnoldi displays similar levels of genetic diversity to its sister species Calotriton asper, from which it separated around 1.5 million years ago and which has a much larger distribution range. Our extensive study shows that natural habitat fragmentation does not result in negative genetic effects, such as the loss of genetic diversity and inbreeding on an evolutionary timescale. We hypothesize that species in such conditions may evolve strategies (for example, special mating preferences) to mitigate the effects of small population sizes. However, it should be stressed that the influence of natural habitat fragmentation on an evolutionary timescale should not be conflated with anthropogenic habitat loss or degradation when considering conservation strategies.Heredity advance online publication, 11 January 2017; doi:10.1038/hdy.2016.123.
... Of course these data are inadequate to represent the complicated geonemy of the morphotypes occurring in austria, nevertheless they point out the relevant effects produced by a limited gene-flow on the high morphological plasticity of A. parallelepipedus. It is generally accepted that organisms with low dispersal capacity would be more sensitive to IBD and show stronger effects of geographical barriers on their morphologies (Monsen & Blouin, 2004). The strong impact of physical barriers on the genetics of A. parallelepipedus was also detected for modest interruptions of the environmental continuity (Keller et al., 2003a(Keller et al., , 2004. ...
Morphological variation of central-western European populations of Abax parallelepipedus was studied in order to revise the microsystematics of this species. Original descriptions and systematic revisions published since the second half of the 18th century are discussed. Biometric variables and morphometric indexes were evaluated on 792 specimens sampled from several European countries. The data were statistically analysed in order to discriminate the populations significantly differentiated from the nominotypical form. Features of male genitalia are also discussed. The results attest that the morphological variation becomes more relevant among populations inhabiting alpine environments and the Italian ones show the most distinctive modifications of somatic and/or aedeagic traits. On the basis of these results, A. p. euganensis Schatzmayr, 1944 is resurrected from synonymy with A. p. inferior, whereas the following new synonymies are proposed:Abax parallelepipedus parallelepipedus (Piller & Mitterpacher, 1783) = A. p. subpunctatus (Dejean, 1828) syn. nov. = A. p. audouini (L. Dufour, 1851) syn. nov. = A. p. germanus Schauberger, 1927 syn. nov.Abax parallelepipedus inferior (Seidlitz, 1887) = A. p. alpigradus Schauberger, 1927 (sensu Schatzmayr, 1944) syn. nov.A phylogeographical scenario is hypothesized and discussed in the light of the collected data.
... Amphibians are known for their low vagility and are easily separated by geographic barriers (Monsen and Blouin 2004;Funk et al. 2005;Guarnizo et al. 2009). Advertisement calls of frogs, playing a critical role in sexual selection and species recognition, are one of the best models to study divergent evolution in acoustic signals. ...
Acoustic signals for mating are important traits that could drive population differentiation and speciation. Ecology may play a role in acoustic divergence through direct selection (e.g., local adaptation to abiotic environment), constraint of correlated traits (e.g., acoustic traits linked to another trait under selection), and/or interspecific competition (e.g., character displacement). However, genetic drift alone can also drive acoustic divergence. It is not always easy to differentiate the role of ecology versus drift in acoustic divergence. In this study, we tested the role of ecology and drift in shaping geographic variation in the advertisement calls of Microhyla fissipes. We examined three predictions based on ecological processes: (1) the correlation between temperature and call properties across M. fissipes populations; (2) the correlation between call properties and body size across M. fissipes populations; and (3) reproductive character displacement (RCD) in call properties between M. fissipes populations that are sympatric with and allopatric to a congener M. heymonsi. To test genetic drift, we examined correlations among call divergence, geographic distance, and genetic distance across M. fissipes populations. We recorded the advertisement calls from 11 populations of M. fissipes in Taiwan, five of which are sympatrically distributed with M. heymonsi. We found geographic variation in both temporal and spectral properties of the advertisement calls of M. fissipes. However, the call properties were not correlated with local temperature or the callers' body size. Furthermore, we did not detect RCD. By contrast, call divergence, geographic distance, and genetic distance between M. fissipes populations were all positively correlated. The comparisons between phenotypic Q st (P st) and F st values did not show significant differences, suggesting a role of drift. We concluded that genetic drift, rather than ecological processes, is the more likely driver for the geographic variation in the advertisement calls of M. fissipes.
... Distance, Relationship between linearized genetic heterogeneity with distance and log body mass for various vertebrate classes and locomotory modes. Values are individual species mean slope values calculated from the following references: (1) amphibians(Newman and Squire, 2001;Vos et al., 2001; Lampert et al., 2003; Austin et al., 2004; Burns et al., 2004;Monsen and Blouin, 2004;Palo et al., 2004;Spear et al., 2005; Arens et al., 2006; Johansson et al., 2006;Manier and Arnold, 2006; Arens et al., 2007;Zamudio and Wieczorek, 2007;Spear and Storfer, 2008; Chan et al., 2009; Chan and Zamudio, 2009;Wang, 2009;Blouin et al., 2010; Arruda et al., 2011); (2) reptiles(Gibbs et al., 1997;Prior et al., 1997; Bushar et al., 1998; Hutchison and Templeton, 1999; Cunningham et al., 2002;Manier and Arnold, 2005; Böhme et al., 2007; Hedtke et al., 2007; Hoehn et al., 2007; Jansen et al., 2008; Johansson et al., 2008; Chan et al., 2009;Marshall et al., 2009;Prosser et al., 1999;Urquhart et al., 2009;Row et al., 2010; Klug et al., 2011;Pernetta et al., 2011); (3) flying mammals(Burland et al., 1999; Castella et al., 2000; Castella et al., 2001; Campbell et al., 2006;Racey et al., 2007;Rossiter et al., 2007;Ngamprasertwong et al., 2008;Salgueiro et al., 2008; Chen et al., 2010; Floyd et al., 2010; Chinnasamy et al., 2011); (4) terrestrial mammals(Forbes and Hogg, 1999; Gerlach and Musolf, 2000; Girman et al., 2001; Comstock et al., 2002;Yu and Peng, 2002;Møller et al., 2004; Cronin et al., 2005;Trizio et al., 2005; Lampila et al., 2009;McDevitt et al., 2009;Schmidt et al., 2009; Floyd et al., 2011; Frantz et al., 2012;Thimmayya and Buskirk, 2012); (5) marine mammals(Valsecchi et al., 1997; Escorza-Treviño and Dizon, 2000; Hoelzel et al., 2002; Larson et al., 2002; Krützen et al., 2004;Trujillo et al., 2004; Adams and Rosel, 2006;Quérouil et al., 2007; Graves et al., 2008; González-Suárez et al., 2009; Herreman et al., 2009; Dickerson et al., 2010;Mendez et al., 2010); and (6) birds(Gibbs et al., 2000; Lee et al., 2001;Williams et al., 2002;Tiedemann et al., 2004; Burg et al., 2005; Davis et al., 2006; Johnsen et al., 2006; Funk et al., 2007; Koopman et al., 2007;Nittinger et al., 2007; Barr et al., 2008; Hull et al., 2008; Lindsay et al., 2008;Pavlacky et al., 2009; Bicknell et al., 2012). ...
Vagility is the inherent power of movement by individuals. Vagility and the available duration of movement determine the dispersal distance individuals can move to interbreed which affects the fine-scale genetic structure of vertebrate populations. Vagility and variation in population genetic structure are normally explained by geographic variation and not by the inherent power of movement by individuals. We present a new, quantitative definition for physiological vagility that incorporates aerobic capacity, body size, body temperature, and the metabolic cost of transport, variables that are independent of the physical environment. Physiological vagility is the speed at which an animal can move sustainably based on these parameters. This meta-analysis tests whether this definition of physiological vagility correlates with empirical data for maximal dispersal distances and measured microsatellite genetic differentiation with distance ((FST/1-FST)/ ln km) for amphibians, reptiles, birds and mammals utilizing three locomotor modes (running, flying, swimming). Maximal dispersal distance and physiological vagility increased with body mass for amphibians, reptiles and mammals utilizing terrestrial movement. The relative slopes of these relationships indicate that larger individuals require longer movement durations to achieve maximal dispersal distances. Both physiological vagility and maximal dispersal distance were independent of body mass for flying vertebrates. Genetic differentiation with distance was greatest for terrestrial locomotion, with amphibians showing the greatest mean and variance in differentiation. Flying birds, flying mammals, and swimming marine mammals showed the least differentiation. Mean physiological vagility of different groups (class and locomotor mode) accounted for 98% of the mean variation in genetic differentiation with distance in each group. Genetic differentiation with distance was not related to body mass. The physiological capacity for movement (physiological vagility) quantitatively predicts genetic isolation by distance in the vertebrates examined.
... Our fine-scale analysis of the montane frog specialist, Amietia wittei, revealed relatively high rates of gene flow (F ST = 0.01-0.16). Greater population differentiation and isolation across smaller geographic scales have been reported for other high-elevation amphibian species, such as the cascades frog, Rana cascadae(Monsen & Blouin 2004), the long-toed salamander, Ambystoma macrodactylum(Tallmon et al. 2000;Giordano et al. 2007;Savage et al. 2010), the spotted frog, Rana luteiventris ...
Estimating population connectivity and species’ abilities to disperse across the landscape is crucial for understanding the long-term persistence of species in changing environments. Surprisingly, few landscape genetics studies focused on tropical regions despite the alarming extinction rates within these ecosystems. Here, we compared the influence of landscape features on the distribution of genetic variation of an Afromontane frog, Amietia wittei, with that of its more broadly distributed lowland congener, A. angolensis, on Mt. Kilimanjaro, Tanzania. We predicted high gene flow in the montane species with movements enhanced through terrestrial habitats of the continuous rainforest. In contrast, dispersal might be restricted to aquatic corridors and reduced by anthropogenic disturbance in the lowland species. We found high gene flow in A. wittei relative to other montane amphibians. Nonetheless, gene flow was lower than in the lowland species which showed little population structure. Least-cost path analysis suggested that dispersal is facilitated by stream networks in both species, but different landscape features were identified to influence connectivity among populations. Contrary to a previous study, gene flow in the lowland species was negatively correlated with the presence of human settlements. Also, genetic subdivision in A. wittei did not coincide with specific physical barriers as in other landscape genetics studies, suggesting that factors other than topography may contribute to population divergence. Overall these results highlight the importance of a comparative landscape genetics approach for assessing the influence of the landscape matrix on population connectivity, particularly because non-intuitive results can alter the course of conservation and management.This article is protected by copyright. All rights reserved.
... For example, researchers at Western Washington University found a sharp decline in gene flow among Cascade frog populations separated by more than 6 miles (10 kilometers) [261]. In urban areas, effective isolation distances may be much shorter for many species because roads, buildings, and paved areas between habitat patches may be difficult or impossible to cross. ...
The purpose of this paper is to review the science of how and why wildlife species need to move across a landscape, including suggested methods to map and improve connectivity. The information will be used to create a regional wildlife connectivity map and strategy for the greater Portland-Vancouver metropolitan region, and will be incorporated into a regional conservation framework.
Connectivity can be difficult or impossible to regain after urbanization, yet it is critically important to the Portland-Vancouver region’s wildlife. Habitat loss and fragmentation have partially or fully isolated many of the remaining habitat patches, and the matrix between patches may be too harsh for many species to navigate. Over time, isolated habitat patches tend to lose wildlife species, and without connectivity, these species cannot repopulate an area. Improving connectivity will help maintain the region’s biodiversity by allowing species to move as needed to fulfill their life history requirements.
The amount and placement of a few key landscape features, especially trees, shrubs and hard surfaces, significantly influence the types of wildlife that can survive in urban areas. The size and shape of a habitat patch, as well as the relationship with surrounding habitats, play key roles in habitat quality and wildlife communities. Disturbance also plays a key role, and impacts may be species-specific. Roads, trails and development impose a variety of disturbances deriving from noise, sound, light, and human and pet impacts. However, the overall amount of habitat and the degree to which it is interconnected likely exert the most profound influence on urban wildlife.
This literature review consists of four sections plus appendices. The first section, “Fundamental Concepts in Wildlife Connectivity,” presents concepts and information about the ecology of connectivity, including the consequences of habitat fragmentation, ecological issues relating to urbanization and disturbance, invasive species and climate change. The second section, “Overview of the Region’s Habitat and Wildlife,” describes historic and current habitat and discusses species groups and specific issues relating to each group. The third section, “More about Corridors,” reviews connectivity issues such as corridor shape, risks and spatial scale. The final section, “Connecting habitats: How it’s Done,” provides a practical approach to creating a regional wildlife corridors map. The appendices include tables reviewing literature recommendations on corridor widths, patch size requirements and gap-crossing abilities for selected species, and a review of models and assessment techniques to identify wildlife connectivity. A regional vertebrate species list and literature cited are also provided in appendices.
Creating a wildlife connectivity strategy may range from relatively simple drawings on a map to complex modeling processes. At its best, it is a collaborative and iterative process. At its worst, the process becomes mired in arguments about specifics and takes too long, perhaps forever, to complete, even as population increases and more houses and roads are built. The movement strategy can identify opportunities to strategically invest in connectivity and initiate a process relying on long-range planning, restoration, acquisition, easements and other tools. Monitoring and adaptive management approaches, along with leadership, collaboration and public support, will be needed to ensure the strategy is effective. The long-term benefits for the region’s biodiversity will be worth the effort.
... We suspect that elevation may be the most likely explanation for this pattern as (i) we found evidence of hybridization in ESUs occupying adjacent high elevational strata (ESUs 8 and 9; Fig. 5A), yet not between ESUs occupying adjacent intermediate and high elevational strata (e.g. ESUs 4 and 5; Table 4; Fig. 5B) and (ii) previous work suggests that elevation strongly influences genetic structure in frogs (Monson & Blouin 2004;Gonzalez-Voyer et al. 2011). ...
Young species complexes that are widespread across ecologically disparate regions offer important insights into the process of speciation because of their relevance to how local adaptation and gene flow influence diversification. We used mitochondrial DNA and up to 28,152 genome-wide SNPs from polytypic barking frogs (Craugastor augusti complex) to infer phylogenetic relationships and test for the signature of introgressive hybridization among diverging lineages. Our phylogenetic reconstructions suggest (1) a rapid Pliocene-Pleistocene radiation that produced at least nine distinct lineages and (2) that geographic features of the arid Central Mexican Plateau contributed to two independent northward expansions. Despite clear lineage differentiation (many private alleles and high between-lineage Fst scores), D-statistic tests, which differentiate introgression from ancestral polymorphism, allowed us to identify two putative instances of reticulate gene flow. Partitioned D-statistics provided evidence that these events occurred in the same direction between clades but at different points in time. After correcting for geographic distance, we found that lineages involved in hybrid gene flow interactions had higher levels of genetic variation than independently evolving lineages. These findings suggest that the nature of hybrid compatibility can be conserved over long periods of evolutionary time and that hybridization between diverging lineages may contribute to standing levels of genetic variation.This article is protected by copyright. All rights reserved.
... Variation in microsatellite loci with ln geographic distance has been used to infer low gene flow and the existence of a metapopulation structure for amphibians (Jehle and Arntzen 2002;Neigel 2002). We used genetic studies of various species of amphibians (Newman and Squire 2001;Scribner et al. 2001;Vos et al. 2001;Curtis and Taylor 2003;Lampert et al. 2003;Austin et al. 2004;Burns et al. 2004;Monsen and Blouin 2004;Palo et al. 2004;Jehle et al. 2005;Johansson et al. 2005Johansson et al. , 2006Kraaijeveld-Smit et al. 2005;Spear et al. 2005;Arens et al. 2006Arens et al. , 2007Manier and Arnold 2006;Cabe et al. 2007;Zamudio and Wieczorek 2007;Spear and Storfer 2008;Chan and Zamudio 2009;Wang 2009;Blouin et al. 2010;Arruda et al. 2011). The majority of the microsatellite studies suggest that genetic heterogeneity increases with distance; however, it is difficult to interpret F ST directly, because different studies almost always use a single species, report their results over different geographic distances, and have inherently different levels of polymorphisms in the microsatellite loci measured. ...
Abstract Physiological vagility represents the capacity to move sustainably and is central to fully explaining the processes involved in creating fine-scale genetic structure of amphibian populations, because movement (vagility) and the duration of movement determine the dispersal distance individuals can move to interbreed. The tendency for amphibians to maintain genetic differentiation over relatively short distances (isolation by distance) has been attributed to their limited dispersal capacity (low vagility) compared with other vertebrates. Earlier studies analyzing genetic isolation and population differentiation with distance treat all amphibians as equally vagile and attempt to explain genetic differentiation only in terms of physical environmental characteristics. We introduce a new quantitative metric for vagility that incorporates aerobic capacity, body size, body temperature, and the cost of transport and is independent of the physical characteristics of the environment. We test our metric for vagility with data for dispersal distance and body mass in amphibians and correlate vagility with data for genetic differentiation ([Formula: see text]). Both dispersal distance and vagility increase with body size. Differentiation ([Formula: see text]) of neutral microsatellite markers with distance was inversely and significantly ([Formula: see text]) related to ln vagility. Genetic differentiation with distance was not significantly related to body mass alone. Generalized observations are validated with several specific amphibian studies. These results suggest that interspecific differences in physiological capacity for movement (vagility) can contribute to genetic differentiation and metapopulation structure in amphibians.
... The scaling was performed dividing each genetic distance by the great-circle distance (the shortest distance between two points on the surface of a sphere) connecting each haplotype pair (Martin and McKay 2004). This scaling yielded comparable genetic distances across pairwise comparisons, as organisms with low vagility such as frogs generally display isolation-by-distance (Slatkin 1993;Monsen and Blouin 2004;Fouquet et al. 2007). ...
Most global hotspots of biodiversity and endemism are in montane regions. One explanation is that montane regions have intrinsically higher specia-tion rates than lowland regions because complex mountain topography and climate variation facilitate genetic isolation among populations. Here, we ask from an intraspecific perspective whether frog species whose haplotypes are connected by topographically/climatically complex regions display strong genetic isolation (greater scaled genetic distances), compared with species whose haplotypes are connected by less complex regions. We analy-sed published DNA sequences of several frog species from tropical Central and South America for the mitochondrial cob, cox1 and 16S rRNA genes. Pairwise genetic distances among haplotypes within each species were scaled to the geographic distances between each pair of haplotypes. Topo-graphic complexity was positively correlated with scaled genetic distances, and isolation-by-resistance was supported only in species from more topo-graphically complex regions. This suggests that heterogeneous topographies increase landscape resistance, which in turn favours the appearance of isolation-by-resistance. Moreover, we found that the potential barriers that restrict gene flow within species are more closely related to factors associ-ated with temperature and topography than to precipitation.
... Genetic differentiation may be affected by environmental variables such as agriculture (Johansson et al., 2005), mountain ridges (Monsen and Blouin, 2004; Funk et al., 2005), headwater sources (Castric et al., 2001; Pritchard et al., 2007), urban areas (Hitchings and Beebee, 1997; Rowe et al., 2000), river crossings (Spear et al., 2005), large bodies of water (Lee-Yaw et al., 2009), plant communities (Keyghobadi et al., 1999; Spear et al., 2005), community structure (Spear and Storfer, 2008), roads (Lesbarreres et al., 2006), and other anthropogenic barriers (Pritchard et al., 2009). Amphibians have historically been assumed to have low dispersal distances (,1 km) and high fidelity to discreet breeding sites, although current views are now bringing these assumptions into question (Smith and Green, 2005). ...
BioOne (www.bioone.org) is an electronic aggregator of bioscience research content, and the online home to over 160 journals and books published by not-for-profit societies, associations, museums, institutions, and presses. We examined the genetic population structure for the Great Plains Toad (Bufo cognatus) in the Chihuahuan Desert of southern New Mexico in order to discern at what spatial scale genetic differentiation is apparent. In addition, we tested whether habitats in the Chihuahuan Desert of southern New Mexico differed in their resistance to gene flow in B. cognatus. We used microsatellites to estimate genetic differentiation in populations that varied in distance from 1 to 60 km. Of 120 pairwise tests of genetic differentiation, 44 were significant. However, differentiation was low between all sites (F ST = 0.0–0.087), almost all of the genetic variation being within populations (96.3%). Compared to published studies of other anuran species, populations of B. cognatus in southern New Mexico are among the most genetically homogenous anuran species. Significant isolation by distance did occur over all populations despite the genetic similarity, suggesting that differentiation does occur at a broader scale. In addition, several landscape-based models of gene flow were produced and tested against the allelic data. A community model assigned each plant community a different level of resistance to gene flow. This model was not found to describe the estimated genetic variation between populations better than simple Euclidean distance. However, the river model, which assigned low resistance to the aquatic habitats including the Rio Grande, described the estimated genetic variation better than Euclidean distance, suggesting that the Rio Grande, and potentially other rivers throughout the toad's range, may act as a route of dispersal for B. cognatus, reducing genetic differentiation among distant populations.
... Consequently, they have to rely on land-bridges for dispersal (Veith et al., 2003). Roads, mountain ridges and open or dry habitats apparently reduce gene flow between populations (Lougheed et al., 1999;Monsen & Blouin, 2004;Spear et al., 2005;Crawford et al., 2007) while forests, wetlands and rivers are associated with increased gene flow (Spear et al., 2005). Hyla savignyi the Lemon-Yellow Tree Frog (Audouin, 1827) is a species of frog in the Hylidae family and is found throughout the most of West Asia (Tarkhnishvili & Gokhelashvili, 1999;Gvozdik et al., 2008;Stöck et al., 2008;Gvozdik et al., 2010;IUCN, 2011;Gül et al., 2012). ...
Most of Turkey’s land area is covered by one of three biodiversity hotspots (Caucasus, Irano-Anatolian, and Mediterranean). Anatolia is one of the main corridors for postglacial colonization of Europe. Uncovering how populations of a species differ genetically and ecologically is important for understanding evolutionary processes. Here, I examined ecological information to define ecological divergence between two lineages of Hyla savignyi. Using ecological niche modeling, I determined whether the two genetically divergent lineages of H. savignyi are geographically isolated and addressed the effect of the geographical distribution in the Anatolian Diagonal on the lineages. Separate analysis of the lineages showed no overlap of their predicted ranges based on climatic data of their respective habitats. This suggests that the lineages were formed as a result of range fragmentation during the Ice Age, and were consequently adapted to different climatic conditions.
... Amphibians with widespread geographic ranges, such as H. substriatus, often consist of multiple evolutionary lineages with a marked history of diversifying forces (Lemmon et al. 2007;Rissler & Apodaca 2007;Newman & Rissler 2011 Five features of the landscape are known to impact amphibian population genetic structure: distance between populations (e.g. Monsen & Blouin 2004;Funk et al. 2005;Spear et al. 2005;Manier & Arnold 2006), degree of incline between populations (e.g. Funk et al. 2005;Lowe et al. 2006;Richards-Zawacki 2009), the effect of hydrologic basins (e.g. ...
The Eastern Afromontane Biodiversity Hotspot is known for microendemism and exceptional population genetic structure. The region's landscape heterogeneity is thought to limit gene flow between fragmented populations and create opportunities for regional adaptation, but the processes involved are poorly understood. Using a combination of phylogeographic analyses and circuit theory, I investigate how characteristics of landscape heterogeneity including regional distributions of slope, rivers and streams, habitat and hydrological basins (drainages) impact genetic distance among populations of the endemic spotted reed frog (Hyperolius substriatus), identifying corridors of connectivity as well as barriers to dispersal. Results show that genetic distance among populations is most strongly correlated to regional and local hydrologic structure and the distribution of suitable habitat corridors, not isolation by distance. Contrary to expectations, phylogeographic structure is not coincident with the two montane systems, but instead corresponds to the split between the region's two major hydrological basins (Zambezi and East Central Coastal). This results in a paraphyletic relationship for the Malawian Highlands populations with respect to the Eastern Arc Mountains and implies that the northern Malawian Highlands are the diversity centre for H. substriatus. Although the Malawian Highlands collectively hold the greatest genetic diversity, individual populations have lower diversity than their Eastern Arc counterparts, with an overall pattern of decreasing population diversity from north to south. Through the study of intraspecific differentiation across a mosaic of ecosystem and geographic heterogeneity, we gain insight into the processes of diversification and a broader understanding of the role of landscape in evolution.
... Genetic diversity within these populations, as measured by the mean number of alleles per microsatellite locus and expected heterozygosity, is quite low compared to other montane Rana (Monsen and Blouin, 2004;Zhan et al., 2009;Zhao et al., 2009). While these studies were conducted with different microsatellite loci, it is noteworthy that only a few threatened or endangered ranids show similar low levels of microsatellite variation, including Rana luteiventris (Funk et al., 2005), Rana latastei (Ficetola et al., 2007), and Rana pipiens (Wilson et al., 2008). ...
... A similar pattern of weak isolation by distance has been seen in a number of other anurans (Seppa and Laurila 1999; Monsen and Blouin 2003). Isolation by distance may occur in northern leopard frogs at a finer geographic scale than used in this study, as has been seen in the montane frog (Monsen and Blouin 2004). We also used modern methods based on genotypic frequencies to examine population structure (Pritchard et al. 2000; Guillot et al. 2005; Corander and Marttinen 2006). ...
The northern leopard frog (Rana pipiens Schreber, 1782) underwent I large decline in the western portion of its range and only Occurs in 20% of historically occupied sites in Alberta. Its absence may reflect all inability to disperse to these sites because of habitat fragmentation, and human-mediated translocation has been proposed. In this Study, we used three criteria to examine the genetic suitability of potential translocation sources: diversity, similarity to area of reintroduction, and evolutionary history. We genotyped 197 samples and sequenced 812 bp of the mitochondrial NADH dehydrogenase I gene from 14 Canadian northern leopard frog populations. Nuclear and mitochondrial diversity were highest in Manitoba and western Ontario and declined westward. There was no significant relationship between genetic and geographic distance, suggesting that genetic drift is a driving force affecting the genetic relationships between populations. Regions separated by more than similar to 50 kin were quite differentiated. Therefore, Source Populations similar to the original inhabitants of an area for reintroduction may be uncommon.. Mitochondrial analyses revealed that all populations share 11 close evolutionary history, belonging to the western haplotype group. While genetic criteria Support the use Of Manitoba and Ontario as sources, the desirability of environmental similarity to the reintroduction site suggests that ecologically exchangeable Alberta Populations should also be considered.
... Genetic population structure data are currently unavailable for most amphibian species in the Pacific Northwest, but a few data are beginning to emerge. For example, the spatial scale of the genetic neighborhood of the stillwater-breeding Cascades frog (Rana cascadae), sampled across a broad range of populations, was about 10 km (Monsen and Blouin, 2004). As previously mentioned, a 20-30 km estimate was recently obtained from preliminary data on coastal tailed frogs (S. ...
Stream–riparian areas represent a nexus of biodiversity, with disproportionate numbers of species tied to and interacting within this key habitat. New research in Pacific Northwest headwater forests, especially the characterization of microclimates and amphibian distributions, is expanding our perspective of riparian zones, and suggests the need for alternative designs to manage stream–riparian zones and their adjacent uplands. High biodiversity in riparian areas can be attributed to cool moist conditions, high productivity and complex habitat. All 47 northwestern amphibian species have stream–riparian associations, with a third being obligate forms to general stream–riparian areas, and a quarter with life histories reliant on headwater landscapes in particular. Recent recognition that stream-breeding amphibians can disperse hundreds of meters into uplands implies that connectivity among neighboring drainages may be important to their population structures and dynamics. Microclimate studies substantiate a “stream effect” of cool moist conditions permeating upslope into warmer, drier forests. We review forest management approaches relative to headwater riparian areas in the U.S. Pacific Northwest, and we propose scenarios designed to retain all habitats used by amphibians with complex life histories. These include a mix of riparian and upslope management approaches to address the breeding, foraging, overwintering, and dispersal functions of these animals. We speculate that the stream microclimate effect can partly counterbalance edge effects imposed by upslope forest disturbances, hence appropriately sized and managed riparian buffers can protect suitable microclimates at streams and within riparian forests. We propose one approach that focuses habitat conservation in headwater areas – where present management allows extensive logging – on sensitive target species, such as tailed frogs and torrent salamanders that often occur patchily. Assuming both high patchiness and some concordance among the distribution of sensitive species, protecting areas with higher abundances of these animals could justify less protection of currently unoccupied or low-density habitats, where more intensive forest management for timber production could occur. Also, we outline an approach that protects juxtaposed headwater patches, retaining connectivity among sub-drainages using a 6th-field watershed spatial scale for assuring well-distributed protected areas across forested landscapes. However, research is needed to test this approach and to determine whether it is sufficient to buffer downstream water quality and habitat from impacts of headwater management. Offering too-sparse protection everywhere is likely insufficient to conserve headwater habitats and biodiversity, while our alternative targeted protection of selected headwaters does not bind the entire forest landscape into a biodiversity reserve.
Shared selection pressures often explain convergent trait loss, yet anurans (frogs and toads) have lost their middle ears at least 38 times with no obvious shared selection pressures unifying ‘earless’ taxa. Anuran tympanic middle ear loss is especially perplexing because acoustic communication is dominant within Anura and tympanic middle ears enhance airborne hearing in most tetrapods. Here we examine whether particular geographic ranges, microhabitats, activity patterns, or aspects of acoustic communication are associated with anuran tympanic middle ear loss. Although we find modest differences between the geographic ranges of eared and earless species and increased diurnality in earless species, we find no universal adaptive explanation for the many instances of anuran tympanic middle ear loss. The puzzling lack of shared selection pressures motivates discussion of alternative hypotheses, including genetic or developmental constraints, and the possibility that tympanic middle ear loss is maladaptive.
Mountainous regions play a crucial role in shaping genetic differentiation among organisms. Climate change and topographical complexity are considered as the most important processes influencing the diversification of these areas. We used two tree frog species, Boana polytaenia and Boana bandeirantes to access how such biogeographical factors shaped their evolutionary history in the highly biodiverse Brazilian mountain range Serra do Espinhaço, that comprises two main mountain chains (Serra do Mar and Serra da Mantiqueira). We investigate whether the patterns of genetic diversity and differentiation were related to Pleistocene climate shifts and/or climate dynamics through elevational gradients in the mountains. We used a multilocus dataset comprising mitochondrial and nuclear DNA sequences from both species. We assessed the genealogical relationships of lineages, population structure, changes in effective population sizes over time, time of divergence of lineages, climatic suitability through time with ecological niche modeling and whether niche of linegaes are more or less similar than expected. Both species exhibited well-structured lineages in each of the mountain chains, B. polytaenia for Serra da Mantiqueira and B. bandeirantes for Serra do Mar. Diversification primarily occurred during the Middle Pleistocene, with glacial periods influencing B. polytaenia and interglacial periods favoring B. bandeirantes . The combination of Pleistocene climate changes and mountain topography influenced spatial distribution, leading to genetic variation among B. polytaenia complex species.
Catastrophic population declines due to disease often lead to fragmented remnant populations and loss of gene flow. Managers are left to determine appropriate conservation actions to recover and maintain population persistence. The recent utilization of genomic data to assist in species recovery now allows us to combine genome‐wide surveys of differentiation and diversity with the identification of potentially adaptive regions to develop conservation plans that incorporate ecological and evolutionary processes. The unprecedented global decline of amphibian populations due to the pathogen Batrachochytrium dendrobatidis has increased the need to apply genomic tools to amphibian conservation practices. We show here how understanding genetic characteristics of remnant frog populations affected by disease can be applied directly to restoration efforts. Cascades frogs (Rana cascadae) occur in the mountainous regions of the Pacific northwestern United States and have declined dramatically at the southern edge of their range in California. We conducted genome‐wide surveys within this region to inform conservation and reintroduction efforts. We found strong north‐south genetic differentiation between Oregon and California and novel spatial structure within California. Genetic diversity was lower in California than Oregon and genetic drift was the most important driver of genetic diversity and population structure in California, making conservation efforts aimed at boosting overall genetic diversity most urgent. Spatial genetic structure of populations within California suggests that reintroductions to Lassen Volcanic National Park, where they were recently extirpated, should use remaining source populations south of the park. Our findings support the treatment of California's R. cascadae populations separately from the rest of their range and highlight the importance of conservation genomics in applied species conservation.
We investigated the effects of three hydroelectric dams and their associated lakes on the population structure and connectivity of the coastal tailed frog, Ascaphus truei, in the North Cascades National Park Service Complex. Three dams were erected on the Skagit River in northern-central Washington state between 1924 and 1953 and subsequently changed the natural shape and movement of the Skagit River and its tributaries. We collected 183 individuals from 13 tributaries and generated a dataset of >2,500 loci (unlinked SNPs) using double digestion restriction site-associated DNA sequencing (ddRADseq). An analysis of molecular variance (AMOVA) identified ~99% of the genetic variation within groups, and the remaining variation among groups separated by dams, or the Skagit River. All populations exhibited low F ST values with a maximum of 0.03474. A ‘de novo’ discriminant analysis of principal components revealed two populations with no geographic cohesiveness. However, testing groups that were partitioned a priori by the dams revealed distinctiveness of populations down-river of the lowest dam. Coalescent-based analyses of recent migration suggest that up to 17.3% of each population is composed of migrants from other populations, and an estimation of effective migration rates revealed high levels of migration heterogeneity and population connectivity in this area. Our results suggest that although the populations down-river from the lowest dam are distinguishable, a high level of A . truei population connectivity exists throughout the North Cascades National Park Service Complex.
Contact zones between species provide a unique opportunity to test whether taxa can hybridize or not. Cross‐breeding or hybridization between closely related taxa can promote gene flow (introgression) between species, adaptation, or even speciation. Though hybridization events may be short‐lived and difficult to detect in the field, genetic data can provide information about the level of introgression between closely related taxa. Hybridization can promote introgression between species, which may be an important evolutionary mechanism for either homogenization (reversing initial divergence between species) or reproductive isolation (potentially leading to speciation). Here, we used thousands of genetic markers from nuclear DNA to detect hybridization between two parapatric frog species (Rana boylii and Rana sierrae) in the Sierra Nevada of California. Based on principal components analysis, admixture, and analysis of heterozygosity at species diagnostic SNPs, we detected two F1 hybrid individuals in the Feather River basin, as well as a weak signal of introgression and gene flow between the frog species compared with frog populations from two other adjacent watersheds. This study provides the first documentation of hybridization and introgression between these two species, which are of conservation concern.
Mountain chains and rivers are often found to represent barriers promoting vicariant differentiation in terrestrial vertebrates. Previous studies have supported the idea that the Cordillera de Mérida (CM), the easternmost branch of the Northern Andes, represents a geographic barrier for vertebrates, including frogs. Previous studies have also suggested that the Orinoco River (OR), the biggest river in Venezuela, also represents a geographic barrier for terrestrial vertebrates. Boana pugnax and B. xerophylla are two Neotropical hylids, members of the B. faber species group, that are distributed on either side of the CM, and whose ranges extend up to 605 and 2450 m in elevation, respectively. In addition, B. xerophylla occurs on either side of the OR. Herein, we assess the genetic, acoustic, and morphological differentiation within B. pugnax and within B. xerophylla across the CM and within B. xerophylla across the OR, and test if genetic differentiation is correlated with geographic distance. We also evaluated the acoustic differentiation between the recently recognized B. xerophylla and its sister species, B. crepitans, and found marked differences between advertisement calls, corroborating their status as distinct species. Genetic and morphometric analyses of populations from opposite sides of the CM revealed differentiation in B. pugnax but not in B. xerophylla. Within the latter species, we found molecular, acoustic, and morphometric differentiation among samples of B. xerophylla from western Venezuela versus the Guiana Shield. Genetic variation within B. pugnax and within B. xerophylla was not explained by geographic distance. Thus, our data show conspecific population structure across the CM in B. pugnax, plus the possible existence of two species within what today is considered B. xerophylla, yet the CM apparently is not involved in this divergence. These results suggest that even for closely related species with shared ecology and distribution, genetic and phenotypic differentiation respond differently to common ecological or historical factors.
Increasingly, endangered vertebrate species are being maintained in captive breeding programs as a method of ensuring their survival. Despite these increasing numbers of captive breeding colonies, there have been few studies designed to examine the long-term success of these programs at maintaining genetic diversity. To elucidate the effectiveness of a captive breeding colony of the endangered species Sauromalus varius (the San Esteban Chuckwalla) at maintaining genetic variation over time, we employed seven polymorphic microsatellite loci. F-statistics and analysis of molecular variance strongly suggest that the colony is exhibiting genetic signs of inbreeding. Genetic variation within the colony has decreased by an average of 12.2% within the colony between the 2 y sampled with an average loss of 30.5% of genetic variation within offspring. This study provides an important test of the effectiveness of captive breeding colonies at maintaining genetic variation within a vertebrate group over time.
Population connectivity is an important source of information for planning conservation strategy. The degree of connectivity implies using alternative conservation prioritizations based on the appropriate spatial scale for management units. In species with low population connectivity, it is important to preserve local populations in order to maintain the species throughout its range. In contrast, species with high connectivity require extensive management aiming at preserving gene flow through the entire species range. Here we examine at the continental scale the relationship between inter-population/inter-individual genetic and geographical distances to study the isolation-by-distance (IBD) pattern within the European range of nine wild bee species. We then assess the suitability of multi-local or extensive conservation to ensure their long-term survival. Results based on inter-population differences show only two out of nine species with significant IBD. European bee populations seem quite connected when their IBD is compared to IBD of other phyla. However, our results based on inter-individual distances show that eight out of nine species display significant IBD. These different results are presumably a consequence of potential limitations of the inter-population approach. Therefore, we speculate that the inter-population approach could result in inaccurate IBD estimations. This approach should therefore be replaced by the inter-individual approach in order to provide strong supported conservation guidelines. We support multi-local conservation programs based on our analysis of inter-individual distances.
Abstract Although studies of population genetic structure are very common, whether genetic structure is stable over time has been assessed for very few taxa. The question of stability over time is particularly interesting for frogs because it is not clear to what extent frogs exist in dynamic metapopulations with frequent extinction and recolonization, or in stable patches at equilibrium between drift and gene flow. In this study we collected tissue samples from the same five populations of leopard frogs, Rana pipens, over a 22–30 year time interval (11–15 generations). Genetic structure among the populations was very stable, suggesting that these population were not undergoing frequent extinction and colonization. We also estimated the effective size of each population from the change in allele frequencies over time. There exist few estimates of effective size for frog populations, but the data available suggest that ranid frogs may have much larger ratios of effective size (Ne) to census size (Nc) that toads (bufonidae). Our results indicate that R. pipiens populations have effective sizes on the order of hundreds to at most a few thousand frogs, and Nee/Nc ratios in the range of 0.1–1.0. These estimates of Ne/Nc are consistent with those estimated for other Rana species. Finally, we compared the results of three temporal methods for estimating Ne. Moment and pseudolikelihood methods that assume a closed population gave the most similar point estimates, although the moment estimates were consistently two to four times larger. Wang and Whitlock's new method that jointly estimates Ne and the rate of immigration into a population (m) gave much smaller estimates of Ne and implausibly large estimates of m. This method requires knowing allele frequencies in the source of immigrants, but was thought to be insensitive to inexact estimates. In our case the method may have failed because we did not know the true source of immigrants for each population. The method may be more sensitive to choice of source frequencies than was previously appreciated, and so should be used with caution if the most likely source of immigrants cannot be identified clearly.
Aim Understanding the patterns and processes underlying phenotype in a polytypic species provides key insights into microevolutionary mechanisms of diversification. The red-eyed treefrog, Agalychnis callidryas, exhibits strong regional differentiation in colour pattern, corresponding to five admixed mitochondrial DNA clades. We evaluated spatial diversity patterns across multiple, putative barriers to examine the fine-scale processes that mediate phenotypic divergence between some regions while maintaining homogeneity between others. Location We examined patterns of phenotypic diversification among 17 sites that span five putative biogeographic barriers in lower Central America (Costa Rica and Panama). Methods We tested the extent to which genetic distance (F(ST)) derived from six multilocus nuclear genotypes covaried with measures of phenotypic distance (leg coloration) within and between biogeographic regions. We used linear regression analyses to determine the role of geographic and genetic factors in structuring spatial patterns of phenotypic diversity. Results The factors that best explained patterns of phenotypic diversity varied among biogeographic regions. We identified one geographic barrier that impeded gene exchange and resulted in concordant phenotypic divergence across the Continental Divide, isolating Caribbean and Pacific populations. Across Caribbean Costa Rican populations, one barrier structured phenotypic but not genetic diversity patterns, indicating a role for selection. In other regions, the putative barriers had no determining effect on either genetic or leg colour structure. Main conclusions The processes mediating the distribution and diversification of colour pattern in this polytypic, wide-ranging treefrog varied among biogeographic regions. Spatially varying selection combined with the isolating effects of geographic factors probably resulted in the patchy distribution of colour diversity across Costa Rican and Panamanian populations.
Both postglacial colonization and habitat fragmentation can reduce the genetic diversity of populations, which in turn can affect fitness. However, since these processes occur at different spatial and temporal scales, the consequences of either process may differ. To disentangle the relative role of isolation and postglacial colonization in determining genetic diversity and fitness, we studied microsatellite diversity of 295 individuals from 10 populations and measured the hatch rate of 218 clutches from eight populations of a threatened frog, R. latastei. The populations that were affected by fragmentation to a greater extent suffered higher embryo mortality and reduced hatch rate, while no effects of distance from glacial refugium on hatch rate were detected. Altogether, distance from glacial refugium and isolation explained > 90% of variation in genetic diversity. We found that the genetic diversity was lowest in populations both isolated and far from the glacial refugium, and that distance from refugium seems to have the primary role in determining genetic diversity. The relationship between genetic diversity and hatch rate was not significant. However, the proportion of genetic diversity lost through recent isolation had a significant, negative effect on fitness. It is possible that selection at least partially purged the negative effects of the ancestral loss of genetic diversity.
It has recently become practicable to estimate the effective sizes (N(e) ) of multiple populations within species. Such efforts are valuable for estimating N(e) in evolutionary modeling and conservation planning. We used microsatellite loci to estimate N(e) of 90 populations of four ranid frog species (20-26 populations per species, mean n per population = 29). Our objectives were to determine typical values of N(e) for populations of each species, compare N(e) estimates among the species, and test for correlations between several geographic variables and N(e) within species. We used single-sample linkage disequilibrium (LD), approximate Bayesian computation (ABC), and sibship assignment (SA) methods to estimate contemporary N(e) for each population. Three of the species-Rana pretiosa, R. luteiventris, and R. cascadae- have consistently small effective population sizes (<50). N(e) in Lithobates pipiens spans a wider range, with some values in the hundreds or thousands. There is a strong east-to-west trend of decreasing N(e) in L. pipiens. The smaller effective sizes of western populations of this species may be related to habitat fragmentation and population bottlenecking.
In just the last few years, behavioral ecologists have begun to address issues in conservation biology. This volume is the first attempt to link these disciplines formally. Here leading researchers explore current topics in conservation biology and discuss how behavioral ecology can contribute to a greater understanding of conservation problems and conservation intervention programs. In each chapter, the authors identify a conservation issue, review the ways it has been addressed, review behavioral ecological data related to it, including their own, evaluate the strengths and weaknesses of the behavioral ecological approach, and put forward specific conservation recommendations. The chapters juxtapose different studies on a wide variety of taxonomic groups. A number of common themes emerge, including the ways in which animal mating systems affect population persistence, the roles of dispersal and inbreeding avoidance for topics such as reserve design and effective population size, the key role of humans in conservation issues, and the importance of baseline data for conservation monitoring and modeling attempts. Each chapter sheds new light on conservation problems, generates innovative avenues of interdisciplinary research, and shows how conservation-minded behavioral ecologists can apply their expertise to some of the most important questions we face today.
A 4 yr mark and recapture study of Fowler's toad, Bufo woodhousei fowleri, determined the rate of post-metamorphic dispersal among seven breeding areas distributed linearly within a 2 km section of the Indiana Dunes National Lakeshore. Of more than 17,000 1 wk old tadpoles carrying a unique electromorph and introduced into the population and 8539 toads marked at metamorphosis, 37 animals were recaptured as breeding adults. Of these, 73% bred for the first time in natal ponds, most migrants moved only one or two breeding areas from the natal pond (24%), and one individual was observed migrating the maximum distance across the study site. These data combined with estimates of further dispersal in the adult stage and adult mortality yielded a per-generation migration rate among breeding areas of 49%. A Lincoln-Petersen estimate of the number of breeding adults and a direct count of egg masses produced upper and lower bounds on effective population size in each area of 152 and 38. These population sizes and migration rates were used in a computer simulation to estimate the standardized equilibrium genetic variance among populations. This analysis showed that local breeding aggregations of amphibians following similar patterns of migration are not closed genetic units and would not be expected to exhibit much genetic differentiation.
Extinctions are normal biological phenomena. Both mass extinctions in geological time and local extinctions in ecological time are well documented, but rates of extinction have increased in recent years—especially in vertebrates, including amphibians—as illustrated by recent reports of their population declines and range reductions. We suggest that long-term population data are necessary for rigorously evaluating the significance of the amphibian declines. Due to the physiological constraints, relatively low mobility, and site fidelity of amphibians, we suggest that many amphibian populations may be unable to recolonize areas after local extinction.
Las extinciones son un fenómeno biológico normal. Extinciones en masa en una escala temporal geológica y extinciones locales en una escala temporal ecológica, están bien documentadas, pero en años recientes las tasas de exinción han incrementado, especialmente en vertebrados, incluyendo a los anfibios tal como ha sido ejemplificado en reportes recientes sobre la declinación de su población y la reducción de su área de distribución. Nosotros sugerimos que datos poblacionales a largo plozo son necesarios para evaluar rigurosamente la significancia de la declinación en anfibios. Nosotros sugerimos que muchas de las poblaciones de anfibios son incapaces de recolonizar áreas después de extinciones locales debido a las restricciones fisiológicas, la relativamente baja movilidad y la filopatría de los anfibios.
Formulae are given for estimators for the parameters F, θ, f (FIT, FST, FIS) of population structure. As with all such estimators, ratios are used so that their properties are not known exactly, but they have been found to perform satisfactorily in simulations. Unlike the estimators in general use, the formulae do not make assumptions concerning numbers of populations, sample sizes, or heterozygote frequencies. As such, they are suited to small data sets and will aid the comparisons of results of different investigators. A simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure.
To elucidate the evolutionary relationships of Papua New Guinean hylid frogs, we conducted an allozyme analysis using a total of 70 individuals from nine species of Litoria and two species of Nyctimystes. Fourteen enzymes extracted from skeletal muscles and livers were analyzed by starch-gel electrophoresis. These enzymes were encoded by genes at 20 presumptive loci. There were 3-11 phenotypes produced by 3-9 alleles at these loci. The mean proportion of heterozygous loci per individual, mean proportion of polymorphic loci per population, and mean number of alleles per locus in 11 species were 4.5%, 12.5%, and 1.14 on average, respectively. Genetic distances were 0.036 between two populations of L. infrafrenata; 0.248-1.849 (x=1.135) between nine species of the genus Litoria; and 1.703 between two species from the genus Nyctimystes. The intergeneric genetic distances were 1.551-2.877 (x=1.944) between Litoria and Nyctimystes. The UPGMA dendrogram and NJ tree showed the primary dichotomy of the Papua New Guinean hylids Nyctimystes and Litoria. Our distance data confirmed the presence of several sibling species of Litoria, which are similar to each other in external morphology; i. e., L. arfakiana and L. wollastoni, and L. contrastens and L. bicolor group sp.
Several estimators of population differentiation have been proposed in the recent past to deal with various types of genetic markers (i.e., allozymes, nucleotide sequences, restriction fragment length polymorphisms, or microsatellites). We discuss the relationships among these estimators and show how a single analysis of variance framework can accomodate these qualitatively different data types.
A new measure of the extent of population subdivision as inferred from allele frequencies at microsatellite loci is proposed and tested with computer simulations. This measure, called R(ST), is analogous to Wright's F(ST) in representing the proportion of variation between populations. It differs in taking explicit account of the mutation process at microsatellite loci, for which a generalized stepwise mutation model appears appropriate. Simulations of subdivided populations were carried out to test the performance of R(ST) and F(ST). It was found that, under the generalized stepwise mutation model, R(ST) provides relatively unbiased estimates of migration rates and times of population divergence while F(ST) tends to show too much population similarity, particularly when migration rates are low or divergence times are long [corrected].
It is shown that for allele frequency data a useful measure of the extent of gene flow between a pair of populations is M∘=(1/FST-1)/4, which is the estimated level of gene flow in an island model at equilibrium. For DNA sequence data, the same formula can be used if FST is replaced by NST . In a population with restricted dispersal, analytic theory shows that there is a simple relationship between M̂ and geographic distance in both equilibrium and non-equilibrium populations and that this relationship is approximately independent of mutation rate when the mutation rate is small. Simulation results show that with reasonable sample sizes, isolation by distance can indeed be detected and that, at least in some cases, non-equilibrium patterns can be distinguished. This approach to analyzing isolation by distance is used for two allozyme data sets, one from gulls and one from pocket gophers.
I describe the genetic structure of two frog species, Geocrinia rosea and Geocrinia lutea, using allozyme electrophoresis to understand population structure and thereby possible mechanisms of divergence and speciation. The sampling regimes represented the entire range of both species and provided replicated tests of the impact of ridges, rivers, and dry forest on gene flow. Geocrinia rosea and G. lutea were highly genetically subdivided (FST = 0.69, 0.64, respectively). In the extreme, there were fixed allelic differences between populations that were only 4 km (G. rosea) or 1.25 km (G. lutea) apart. In addition to localized divergence, two-dimensional scaling of genetic distance allowed the recognition of broad-scale genetic groups, each consisting of several sample sites. Patterns of divergence were unrelated to the presence of ridges, rivers, or dry forest. I argue that range contraction and expansion, combined with extreme genetic divergence in single, isolated populations, best accounts for the genetic structure of these species.
Attempts to relate estimates of regional FST to gene flow and drift via Wright's (1931) equation FST ≈ 1/ (4Nm + 1) are often inappropriate because most natural sets of populations probably are not at equilibrium (McCauley 1993), as assumed by the island model upon which the equation is based, or ineffective because the influences of gene flow and drift are confounded in the product Nm. Evaluations of the association between genetic (FST ) and geographic distances separating all pairwise populations combinations in a region allows one to test for regional equilibrium, to evaluate the relative influences of gene flow and drift on population structure both within and between regions, and to visualize the behavior of the association across all degrees of geographic separation. Tests of the model using microsatellite data from 51 populations of eastern collared lizards (Crotaphytus collaris collaris) collected from four distinct geographical regions gave results highly consistent with predicted patterns of association based on regional differences in various historical and ecological factors that affect the amount of drift and gene flow. The model provides a prerequisite for and an alternative to regional FST analyses, which often simply assume regional equilibrium, thus potentially leading to erroneous and misleading inferences regarding regional population structure.
Recapture of marked juvenile and adult wood frogs in five Appalachian Mountain ponds showed adults to be 100% faithful to the ponds in which they first bred, but approximately 18% of the juveniles dispersed to breed in ponds other than the one of origin. Effective population sizes were generally smaller than the population censuses and genetic neighborhoods had an average radius of 1,126 meters. Values of standardized genetic variance based on effective population size and mating success were relatively small. Genetic population structure estimated from the dispersal data suggested that ponds within about a 1,000 meter radius should show little genetic differentiation; ponds separated by a distance greater than 1,000 meters should experience little gene flow and show higher genetic differentiation. Wood frogs in these ponds do not show a meta-population structure as suggested for newts.
A study of dispersal movements of newly metamorphosed leopard frogs from their natal ponds was made in two ecologically distinct areas. Movements of young emerging from a small marsh in a pasture appeared to be radial, approximately equal numbers moving in all directions, but the travel of many young leaving two beach pools tended to be funneled in one direction along a lake shore. At least a few animals appeared to leave the ponds on almost every night after emergence, but mass emigrations were generally associated with warm, rainy weather. The young frogs traveled commonly up to 800 m in 2-3 days. A few were known to have established their adult residences as much as 5 km from their pond of origin.
Gene flow is an important determinant of population genetic structure, and understanding patterns of gene flow is especially meaningful in amphibians to estimate their dispersal capabilities in the face of current wetland destruction. In this study, I investigated gene flow using nine polymorphic allozyme loci in samples from 15 stream sites inhabited by the streamside salamander, Ambystoma barbouri. Among all 15 sites considered together, gene flow was generally low and populations were subdivided genetically. However, on a local level, gene flow was significantly higher between some pairs of streams and within some neighborhoods (groups of populations within 5 km of each other). Samples from all sites showed sufficient genetic subdivision to warrant salamander populations from each site to be considered as separate genetic populations. Sunfish that are major predators of larval streamside salamanders appear to act as a barrier to gene flow. This result was supported by significant genetic subdivision between two sites sampled within the same stream and separated by fish pools and two adjacent streams separated by areas with high fish densities but a geographic distance of less than a kilometer. As predicted by isolation-by-distance models, gene flow was significantly negatively correlated with geographic distance.
Attempts to relate estimates of regional FST to gene flow and drift via Wright's (1931) equation F $_{ST} \backsimeq$ 1/(4Nm + 1) are often inappropriate because most natural sets of populations probably are not at equilibrium (McCauley 1993), as assumed by the island model upon which the equation is based, or ineffective because the influences of gene flow and drift are confounded in the product Nm. Evaluations of the association between genetic (FST) and geographic distances separating all pairwise populations combinations in a region allows one to test for regional equilibrium, to evaluate the relative influences of gene flow and drift on population structure both within and between regions, and to visualize the behavior of the association across all degrees of geographic separation. Tests of the model using microsatellite data from 51 populations of eastern collared lizards (Crotaphytus collaris collaris) collected from four distinct geographical regions gave results highly consistent with predicted patterns of association based on regional differences in various historical and ecological factors that affect the amount of drift and gene flow. The model provides a prerequisite for and an alternative to regional FST analyses, which often simply assume regional equilibrium, thus potentially leading to erroneous and misleading inferences regarding regional population structure.
The population dynamics and ecology of the red-spotted newt were studied from 1974 to the present in a series of mountain ponds in the Shenandoah Mountains, Virginia. Adult and juvenile newts were censused using a combination of methods, including drift fences and dip-netting. A technique of individual recognition was developed utilizing the number and pattern of dorsal red spots. Assisted by a simple system of toeclips, designating pond and year of first capture, these methods provided records of age, survival, and movements of >8,500 individuals. The results revealed 2 migratory peaks of adults each year: a breeding migration to ponds in March, and an August-September emigration to terrestrial hibernacula. Breeding population size, ranging from 6 to >2,600 adults per pond was stationary during the study but was significantly correlated with pond age. Annual turnover of breeding populations to new adults exceeded 50%. Sex ratios were consistently 2 @M @M: 1 @V in the breeding populations but tended toward 1:1 in the cohorts of new recruits. Annual adult @V survival was density dependent and significantly less than that of @M @M. The average @V expected to breed only 1.3 times, whereas @M @M had an expectancy of 1.9 breeding seasons. Faithfully homing to the same pond year after year, adults never migrated to new ponds between breeding seasons. Juvenile production at most ponds was poor over the 3 yr. Only 1 pond had a reproductive output consistently above a calculated replacement rate. It is inferred from the combination of poor reproduction and high immigration rates that breeding adults were not replaced by their own progeny but rather by foreign-born individuals. The red-spotted newt is basically a colonizing species responding to pond habitats that rapidly shift in time and space. It is suggested that beaver ponds have the necessary attributes of small size and temporal instability to which the life-history patterns of newts seems adapted. The majority of ponds in this area functioned as reproductive sinks in a larger, metapopulational structure. Adults in such ponds were reproductive failures or most of their lives. Only a small number of adults accounted for the regional reproduction in 1974 and 1975, but I very populous pond produced >91% of the young in 1976. Because reproductive success is pond dependent, interdemal selection may play an important role in newt evolution. It is hypothesized that homing behavior evolved as a consequence of natural selection within metapopulation centers and that the eft stage is the mechanism of dispersibility to new ponds. A new model of metapopulational dynamics is presented.
I describe the genetic structure of two frog species, Geocrinia rosea and Geocrinia lutea, using allozyme electrophoresis to understand population structure and thereby possible mechanisms of divergence and speciation. The sampling regimes represented the entire range of both species and provided replicated tests of the impact of ridges, rivers, and dry forest on gene flow. Geocrinia rosea and G. lutea were highly genetically subdivided (FST = 0.69, 0.64, respectively). In the extreme, there were fixed allelic differences between populations that were only 4 km (G. rosea) or 1.25 km (G. lutea) apart. In addition to localized divergence, two-dimensional scaling of genetic distance allowed the recognition of broad-scale genetic groups, each consisting of several sample sites. Patterns of divergence were unrelated to the presence of ridges, rivers, or dry forest. I argue that range contraction and expansion, combined with extreme genetic divergence in single, isolated populations, best accounts for the genetic structure of these species.
Dispersal rates can have an important impact on many population processes. Dispersal can lead to population regulation and regional stability in the face of local instability through the formation of a metapopulation. This may be particularly true for frogs because they often have patchy distributions. In this paper I investigate dispersal by male Geocrinia alba and Geocrinia vitellina, using a mark-recapture study. Pit traps were used to determine whether frogs move out of their breeding habitat. I found that both species were very philopatric. Between the 1993 and 1994 breeding seasons, 76–86% of individuals were displaced less than 10m and 90–97% were displaced less than 20m. Dispersal was even lower within each breeding season, with 92–95% of individuals being displaced less than 5 m. Pit trapping indicated that some individuals of both species move out of the swamps in late autumn and return at the beginning of the breeding season, in late winter and early spring. Therefore, although displacement may be very restricted, the frogs are likely to move greater distances. The extreme breeding-site philopatry exhibited by G. alba and G. vitellina suggests that movement between disjunct populations is unlikely and that populations in continuous habitat may be relatively isolated from one another by distance alone. This is consistent with previous predictions based on genetic studies, which suggested there was very little migration between populations. These data support the contention that neither species is likely to exist as a metapopulation because recolonization of vacant habitat is improbable.
Although it is widely recognised that spatial subdivision of populations is common in nature, there is no consensus as to how metapopulation dynamics affect genetic diversity. We investigated the genetic differentiation of natterjack toads, Bufo calamita, in three regions of Britain where habitat continuity indicated the likely occurrence of extensive metapopulations. Our intention was to determine whether genetic analysis supported the existence of metapopulation structures, if so of what type, and to identify barriers to migration between subpopulations. Allele frequencies were determined across eight polymorphic microsatellite loci for a total of 24 toad subpopulations at three separate sites. Genetic differentiation was assessed using five measures of genetic distance, notably FST, RST, Nei's standard distance Ds,Δ2 and the Cavalli-Sforza chord distance Dc. B. calamita exhibited small but significant levels of genetic differentiation between subpopulations in all three study areas, and genetic and geographic distance correlations indicated isolation-by-distance effects in all three cases. The effects on correlation strengths of compensation for positive (sea, rivers, urban development) and negative (pond clusters) barriers to toad migration between the subpopulations in each area were also determined. Dc, a measure which assumes that differentiation is caused by drift with negligible mutation effect, yielded the most plausible interpretation of metapopulation structures. Overall the patterns of genetic variation suggested the existence of a mixed metapopulation model for this species, with high levels of gene flow compatible with one version of the classical model but often supported by particularly stable subpopulations as in the mainland-island model.
The difficulty of directly measuring gene flow has lead to the common use of indirect measures extrapolated from genetic frequency data. These measures are variants of FST, a standardized measure of the genetic variance among populations, and are used to solve for Nm, the number of migrants successfully entering a population per generation. Unfortunately, the mathematical model underlying this translation makes many biologically unrealistic assumptions; real populations are very likely to violate these assumptions, such that there is often limited quantitative information to be gained about dispersal from using gene frequency data. While studies of genetic structure per se are often worthwhile, and FST is an excellent measure of the extent of this population structure, it is rare that FST can be translated into an accurate estimate of Nm.
It is shown that for allele frequency data a useful measure of the extent of gene flow between a pair of populations is M = (1/F(ST) - 1)/4, which is the estimated level of gene flow in an island model at equilibrium. For DNA sequence data, the same formula can be used if F(ST) is replaced by N(ST). In a population with restricted dispersal, analytic theory shows that there is a simple relationship between M and geographic distance in both equilibrium and non-equilibrium populations and that this relationship is approximately independent of mutation rate when the mutation rate is small. Simulation results show that with reasonable sample sizes, isolation by distance can indeed be detected and that, at least in some cases, non-equilibrium patterns can be distinguished. This approach to analyzing isolation by distance is used for two allozyme data sets, one from gulls and one from pocket gophers.
We introduce a new genetic distance for microsatellite loci, incorporating features of the stepwise mutation model, and test its performance on microsatellite polymorphisms in humans, chimpanzees, and gorillas. We find that it performs well in determining the relations among the primates, but less well than other distance measures (not based on the stepwise mutation model) in determining the relations among closely related human populations. However, the deepest split in the human phylogeny seems to be accurately reconstructed by the new distance and separates African and non-African populations. The new distance is independent of population size and therefore allows direct estimation of divergence times if the mutation rate is known. Based on 30 microsatellite polymorphisms and a recently reported average mutation rate of 5.6 x 10(-4) at 15 dinucleotide microsatellites, we estimate that the deepest split in the human phylogeny occurred about 156,000 years ago. Unlike most previous estimates, ours requires no external calibration of the rate of molecular evolution. We can use such calibrations, however, to test our estimate.
The distribution and extinction patterns within a northern metapopulation of the pool frog (Rana lessonae) were analyzed with reference to metapopulation theory. Occupied ponds were permanent and differed from unoccupied ones in terms of higher water temperature during May-June and a closer proximity to neighboring pool-frog lo- calities. but local climate was not spatially autocorrelated. Two types of population ex- tinctions occurred (average rate = 2% per population and year): (I) deterministic extinctions due to succession or draining of pool-frog ponds, and (2) extinctions of populations whose isolation had increased to a critical degree because of Type 1 extinctions of neighboring populations. increasing their susceptibility to predation and combined demographiden- vironmental stochasticity. The Type 2 extinctions were spatially correlated to a moderate degree, which may reflect the great impact of environmental stochasticity in the system. The results confirm and emphasize the importance of interpopulation proximity and con- nectivity for metapopulation persistence.
In order to find out the influence of land use and topographic distance on the genetic structure of populations of the common frog Rana temporaria L. in the Saar-Palatinate lowlands (Federal Republic of Germany), tissue of larvae was examined by means of horizontal starch gel electrophoresis. A total of 24 loci coding for 14 different enzymes were studied. Genotype frequencies, allele frequencies and mean heterozygosity were calculated, and genetic distances using Nei's formula. Strong deviations from the Hardy-Weinberg equilibrium were found; the degree of homozygosity was higher than expected.Separation by highways reduced average heterozygosity as well as genetic polymorphism of local populations.One area surrounded by roads had high genetic distances to other sampling stations. A multiple regression analysis showed that motorways and railways have a significant (p = 0·03) barrier effect on frog populations within 3–4 km. Meadowland apparently enabled individual exchange in a range between 2 and 7 km. Consequences for the design of biotope systems are discussed.
A new Markov chain is introduced which can be used to describe the family relationships among n individuals drawn from a particular generation of a large haploid population. The properties of this process can be studied, simultaneously for all n, by coupling techniques. Recent results in neutral mutation theory are seen as consequences of the genealogy described by the chain.
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.
The natterjack toad Bufo calamita is rare in Britain, which is at the northwestern edge of its biogeographical range. We investigated the level of genetic differentiation amongst almost all (34 out of 38) of the surviving British populations of this species, and among six new populations established by translocations during the 1980s. For eight microsatellite loci, allele sizes and frequencies were analysed using samples from each of these populations. The populations clustered into three robustly differentiated groups, each of which corresponded with a geographical region (east/southeast England, Merseyside and Cumbria). The Cumbrian populations showed a further weak geographical substructuring into northern and southern clades. The populations in south Cumbria were genetically more diverse than those in any of the other regions, as judged by the mean numbers of alleles per locus and the mean heterozygosity estimates. The translocated populations clustered close to their founders and, with one exception, did not differ significantly with respect to mean allele numbers, heterozygosity or polymorphism level. However, significant genetic differentiation (as measured by unbiased RST) was found between all but one of the founder-translocation pairs. The implications of this phylogeographic study for the future conservation of B. calamita in Britain are discussed.
It has recently become evident that amphibian species in many areas of the world have suffered serious declines. Healthy, seemingly well-protected populations have disappeared for no obvious reason. Data from historic accounts and museum records indicate that the Cascades frog, Rana cascadae, was once abundant at the southern end of its range in the vicinity of Lassen Volcanic National Park, California, USA. We conducted intensive searches at all 16 sites where R. cascadae had previously been recorded in the Lassen area, plus 34 additional sites with suitable habitat. Whereas earlier biologists could sometimes find 40 or more frogs at some of these sites, we were only able to locate two frogs at a single locality. This represents a precipitous decline over a period of <15 years. The decline seems to have been caused by a combination of local factors, including (1) the presence of non-native, predatory fish which have restricted habitat and limited dispersal of frogs; (2) loss of breeding habitat due to a five-year drought; and (3) the gradual loss of open meadows and associated aquatic habitats. The loss of frogs suggests that some common management practices in parks and wilderness areas may be endangering some of the species these areas are intended to protect. Similar local factors may account for amphibian declines reported elsewhere and should be carefully evaluated along with possible global effects.
Phylogenetic relationships among Tibetan populations of theBufo bufospecies group are investigated using 1063 bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNAIle, tRNAGln, tRNAMet, and ND2. The aligned sequences contain 181 phylogenetically informative characters across all taxa sampled. Two hypotheses for colonization of the Tibetan Plateau are tested. A vicariant hypothesis predicts monophyly of populations from high elevations. A dispersalist hypothesis predicts monophyly of populations in each of two river drainages (Yangtze and Yellow rivers), which requires nonmonophyly of populations from high elevations. Both hypotheses are rejected in favor of a third hypothesis that combines elements of vicariance and dispersal. The most parsimonious phylogenetic tree places the high-elevation species,B. andrewsi,as the sister taxon to the other AsianBufopopulations; these high-elevation populations are postulated to have had a vicariant origin approximately 5 million years before present. The high-elevation population recognized asB. minshanicusis nested within low-elevation populations ofB. gargarizansand is suggested to have dispersed onto the Tibetan Plateau more recently.
An attempt has been made to establish a procedure for estimating the course taken by evolution. The model used is that of a branching random walk, which is strictly valid only when the causes of divergence between populations are random genetic drift and variable selection. With suitable transformations of the data, evolution can then be considered as a branching Brownian-motion process. To keep the model as simple as possible it was supposed that no population becomes extinct and that each population splits, at a random time, into two daughter populations each identical to its parent. The problem was to estimate the form and dimensions of the most probable tree uniting the presently living populations. The ideal method of estimation, maximum likelihood, proved difficult and had to be replaced in part by alternative procedures. In addition to describing the available procedures in detail, a simple example is worked out fully, and the logical content and limitations of the methods are considered in depth.
The n-coalescent is a continuous-time Markov chain on a finite set of states, which describes the family relationships among a sample of n members drawn from a large haploid population. Its transition probabilities can be calculated from a factorization of the chain into two independent components, a pure death process and a discrete-time jump chain. For a deeper study, it is useful to construct a more complicated Markov process in which n-coalescents for all values of n are embedded in a natural way.
The survival and continued evolution of a species is a pivotal tenet of conservation biology. Therefore, we need to understand the factors affecting survival and evolution of species to conserve them adequately. In this study I use allozyme electrophoresis to investigate the metapopulation structure and evolutionary processes that operate within the endangered frog species Geocrinia alba and G. vitellina. Genetically, G. alba and G. vitellina are highly subdivided. A number of intraspecific genetic groups can be recognised, although even within these groups there are significant differences in allele frequencies among populations. These differences imply that migration between populations is likely to be extremely restricted, if it occurs at all. The intraspecific genetic patterns suggest an evolutionary history of population bottlenecks followed by range expansion. Therefore, in the short term neither species exists as a metapopulation. However, at a larger time scale, migration, extinction and recolonisation may be central to the evolution and survival of both species. Maintenance of these processes is a challenge to which conservation managers must rise for the criteria of long-term survival and evolution to be met.
Recapture of wood frogs in 5 Appalachian Mountain (Shenandoah Mts) ponds showed adults to be 100% faithful to the ponds in which they first bred, but 18% of the juveniles dispersed to breed in ponds other than the one of origin. Effective population sizes were generally smaller than the population censuses and genetic neighborhoods had an average radius of 1126 m. Ponds within about a 1000 m radius should show little genetic differentiation; ponds separated by a distance >1000 m should experience little gene flow and show higher genetic differentiation. -from Authors
We review the early development of metapopulation ideas, which culminated in the well-known model by Levins in 1969. We present a survey of metapopulation terminology and outline the kinds of studies that have been conducted on single-species and multispecies metapopulations. Metapopulation studies have important conceptual links with the equilibrium theory of island biogeography and with studies on the dynamics of species living in patchy environments. Metapopulation ideas play an increasingly important role in landscape ecology and conservation biology.
A measure of genetic distance (D) based on the identity of genes between populations is formulated. It is defined as D = -logeI, where I is the normalized identity of genes between two populations. This genetic distance measures the accumulated allele differences per locus. If the rate of gene substitution per year is constant, it is linearly related to the divergence time between populations under sexual isolation. It is also linearly related to geographical distance or area in some migration models. Since D is a measure of the accumulated number of codon differences per locus, it can also be estimated from data on amino acid sequences in proteins even for a distantly related species. Thus, if enough data are available, genetic distance between any pair of organisms can be measured in terms of D. This measure is applicable to any kind of organism without regard to ploidy or mating scheme.