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Do rivers function as genetic barriers for the plateau wood frog at high elevations?
Abstract
Using the plateau wood frog Rana kukunoris from the Hengduan Mountains as a model system, we tested whether rivers form significant genetic barriers (the riverine barrier hypothesis) to high elevation amphibians. Samples were collected from eight sites across three major river drainages, the Min, the Dadu and the Yalong Rivers, and the population genetic structure of these frogs was evaluated with data from eight microsatellite DNA loci. A large amount of genetic structure was found, and the pairwise FST ranged from 0.022 to 0.508 and a global FST was 0.215. Both analysis of molecular variance and isolation by distance analysis suggested that rivers, mountain ridges and geographic distances all contributed significantly to the population structure. However, no single landscape has prominent barrier effect to the plateau wood frog populations. An assignment analysis using the computer program Structure grouped the eight populations into four population clusters, and no single type of landscape can sufficiently explain the clustering. In conclusion, rivers do not appear to be the leading genetic barriers for the plateau wood frog. The strong population genetic structure is likely the consequence of attributes of the species, as opposed to environmental fragmentation, and the barrier effect of the landscapes is largely swamped by the large amount of intrinsic population structure.
... These effects should depend on the size of the river, increasing thus from the headwaters to the river estuary. The river barrier hypothesis has been tested using (1) molecular markers in populations (mammals: Patton et al. 1994, Peres et al. 1996birds: Aleixo 2004;frogs: Funk et al. 2007, Gascon et al. 1998, Noonan & Wray 2006, Zhao et al. 2009insects: Tantrawatpan et al. 2011), (2) distribution of geographical ranges of species (mammals: Harcourt & Wood 2012;birds: Hayes & Sewlal 2004;insects: Knopp et al. 2011), and (3) phylogeographical analysis (frogs: Symula et al. 2003;insects: Hall & Harvey 2002). While numerous studies have not found rivers acting as barriers (Gascon et al. 1998, Knopp et al. 2011, Patton et al. 1994, Symula et al. 2003, others documented an increased diversification across the river at least in some circumstances or taxa (Aleixo 2004, Hayes & Sewlal 2004, Noonan & Wray 2006, Peres et al. 1996, Tantrawatpan et al. 2011, Zhao et al. 2009). ...
... The river barrier hypothesis has been tested using (1) molecular markers in populations (mammals: Patton et al. 1994, Peres et al. 1996birds: Aleixo 2004;frogs: Funk et al. 2007, Gascon et al. 1998, Noonan & Wray 2006, Zhao et al. 2009insects: Tantrawatpan et al. 2011), (2) distribution of geographical ranges of species (mammals: Harcourt & Wood 2012;birds: Hayes & Sewlal 2004;insects: Knopp et al. 2011), and (3) phylogeographical analysis (frogs: Symula et al. 2003;insects: Hall & Harvey 2002). While numerous studies have not found rivers acting as barriers (Gascon et al. 1998, Knopp et al. 2011, Patton et al. 1994, Symula et al. 2003, others documented an increased diversification across the river at least in some circumstances or taxa (Aleixo 2004, Hayes & Sewlal 2004, Noonan & Wray 2006, Peres et al. 1996, Tantrawatpan et al. 2011, Zhao et al. 2009). As summarized by Haffer (1997) for Amazonia, rivers are not unimportant, but have been overrated as barriers. ...
... Almost all studies focused geographically on rivers in Amazonia (but see Tantrawatpan et al. 2011, Zhao et al. 2009) and considered their importance for the origin of species (Haffer 1997). Here, we broaden the analysis to examine whether rivers, acting as dispersal barriers, can also impact on the quantitative composition of communities. ...
Major tropical rivers have been suggested to be important dispersal barriers that increase the beta diversity of animal communities in lowland rain forests. We tested this hypothesis using assemblages of frogs in the floodplains of the Sepik River, a major river system in Papua New Guinea. We surveyed frogs at five sites within a continuous 150 × 500-km area of lowland rain forest bisected by the Sepik, using standardized visual and auditory survey techniques. We documented 769 frogs from 44 species. The similarity in species composition decreased with logarithm of geographical distance between the sites, which ranged from 82 to 465 km. The similarity decay did not depend on whether or not the compared sites were separated by the Sepik River or whether the species were aquatic or terrestrial breeders. Likewise, a DCA ordination of frog assemblages did not show separation of sites by the river as a significant factor explaining their composition. Our results suggest that even major rivers, such as the Sepik, may not act as dispersal barriers. Rivers may not limit the distribution of frogs and therefore have a limited effect on determining frog species abundance and assemblage structure in rain forests.
... In contrast, rivers alone failed to explain the population structure of Rana kukunoris (Zhao, Dai, & Fu, 2009) and a range-wide study of this species , which did not test specifically for river effects, also failed to discover that rivers served as barriers to dispersal. ...
... In EQTP, the impacts of rivers are different among species. Rivers in sEQTP are effective barriers for N. pleskei and S. boulengeri(Li et al., 2009), but not for R. kukunoris(Zhao et al., 2009;Zhou et al., 2013). The different impacts may be caused by different characters of these species. ...
Pleistocene glacial–interglacial climatic oscillations greatly shaped the current genetic structure of many species. However, geographic features may influence the impact of climatic cycling. Distinct geographic and environmental characters between northern and southern parts of the eastern Qinghai–Tibetan Plateau (EQTP) facilitate explorations into the impacts of geographic features on species. The northern parts of EQTP contain large areas of marsh, and the environment is rather homogeneous. In contrast, the southern EQTP harbors complex alpine valleys and a much more heterogeneous setting. We evaluate DNA sequence variation from both the mitochondrial and nuclear genomes in Nanorana pleskei, a species endemic to the EQTP. Hypothesis testing on the evolutionary history of N. pleskei indicates that northern populations can disperse freely, but alpine valleys isolate southern populations. Demographic histories between northern and southern populations also differ. Northern populations appear to have experienced population expansions, while southern frogs exhibit a far more stable demographic history. By combining climatic analyses and species' distribution models, our study suggests that geographic and environmental features drive the differences between the northern and southern EQTP.
... Chinese brown frogs (Rana chensiensis) from different sides of the Tsinling Mountains have pairwise FST from 0.0175 to 0.1625 (Zhan et al., 2009). The plateau brown frog (R. kukunoris) has pairwise FST from 0.022 to 0.508 (Zhao et al., 2009), similar to those of Asiatic toads. ...
... Mountains constitute significant barriers for gene flow among amphibians (e.g., Funk et al., 2005), and create population differentiation. Other amphibians in the same region, such as the plateau wood frog (R. kukunoris), also exhibit high diversity and high population differentiation (Zhao et al., 2009). ...
We investigated the population genetic structure of Asiatic toads (Bufo gargarizans) from the mountains of western China to determine their species status, using genotypic data of ten microsatellite DNA loci and DNA sequences from one mitochondrial gene. A total of 197 samples from eight sites were examined, which cover a large range of elevations (559-3457 m), as well as all three traditionally defined species (or subspecies). AMOVA did not reveal any particularly large among-groups structure, whether the sites were grouped by drainage, elevation, region, or species (subspecies). Individual assignment tests placed all samples into two genetic clusters, which largely corresponded to their geographic locations. An isolation-by-distance pattern was also detected when an outlier population (site 3) was excluded. Furthermore, a mitochondrial gene tree revealed deep divergence among haplotypes, sometimes within the same site. The clade patterns were partially associated with geographic distribution but had no resemblance to the traditional 2- or 3-species classification. Overall, these toad populations harbor a large amount of genetic diversity and have very high population differentiation, but taken together the evidence suggests that all populations belong to a single species. Our results are consistent with most previous molecular studies, and we recommend using Bufo gargarizans to represent all Asiatic toad populations from western China without subspecies division.
... Chinese brown frogs (Rana chensiensis) from different sides of the Tsinling Mountains have pairwise FST from 0.0175 to 0.1625 (Zhan et al., 2009). The plateau brown frog (R. kukunoris) has pairwise FST from 0.022 to 0.508 (Zhao et al., 2009), similar to those of Asiatic toads. ...
... Mountains constitute significant barriers for gene flow among amphibians (e.g., Funk et al., 2005), and create population differentiation . Other amphibians in the same region, such as the plateau wood frog (R. kukunoris), also exhibit high diversity and high population differentiation (Zhao et al., 2009). ...
Amphibians are declining at an alarming rate across the world. The species living at extreme environments are particularly vulnerable to extinction. Asiatic toad (Bufo gargarizans) is one of few amphibians at very high altitude and we have known little about their genetic diversity and conservation situations among highland populations. Using transcriptome sequencing, fourteen novel microsatellite markers were developed for Asiatic toad. To characterize these loci, two populations of Asiatic toad from Tibetan Plateau were genotyped. All loci were variable, with the number of alleles ranging from 1 to 15 within populations. The expected and observed heterozygosity per locus ranged from 0.00 to 0.87 and from 0.00 to 0.89, respectively. Two of these loci showed significant deviations from Hardy–Weinberg equilibrium and no linkage disequilibrium was detected. We expect that these markers will provide useful tools in population genetics and conservation studies for Asiatic toad.
... Most amphibians undergo a complex biphasic life cycle with larval forms that are restricted to and strongly depend on aquatic habitats, whereas the terrestrial stages are potentially more vagile and prone to dispersal. Still, rivers may serve as barriers in amphibian populations and may confine their dispersal [34][35][36] . Here we selected two endemic genera of Sumatran ranid frogs (Sumaterana and Wijayarana) to investigate whether the paleoriver systems of Sumatra played a role in structuring the distribution of their genetic diversity. ...
Rivers are known to act as biogeographic barriers in several strictly terrestrial taxa, while possibly serving as conduits of dispersal for freshwater-tolerant or -dependent species. However, the influence of river systems on genetic diversity depends on taxa-specific life history traits as well as other geographic factors. In amphibians, several studies have demonstrated that river systems have only minor influence on their divergence. Here, we assess the role of the paleodrainage systems of the Sunda region (with a focus on the island of Sumatra) in shaping the evolutionary history of two genera of frogs ( Sumaterana and Wijayarana ) whose tadpoles are highly dependent on cascading stream habitats. Our phylogenetic results show no clear association between the genetic diversification patterns of both anurans genera and the existence of paleodrainage systems. Time-calibrated phylogenies and biogeographical models suggest that these frogs colonized Sumatra and diversified on the island before the occurrence of the Pleistocene drainage systems. Both genera demonstrate phylogenetic structuring along a north–south geographic axis, the temporal dynamics of which coincide with the geological chronology of proto Sumatran and -Javan volcanic islands. Our results also highlight the chronic underestimation of Sumatran biodiversity and call for more intense sampling efforts on the island.
... In most studies, rivers have shown negative effects. For example, rivers represent significant dispersal barriers in Gephyromantis enki, a micro-endemic species of Madagascar, in Rana kukunoris, a high elevation species of the Hengduan Mountains in China, and in Engystomops pustulosus from Panama (Lampert et al., 2003;Zhao et al., 2009;Wollenberg Valero, 2015). On the contrary, streams constitute dispersal corridors in the Chihuahuan Desert for Anaxyrus cognatus (Jungels et al., 2010), in the mountains of Kilimanjaro for Amietia wittei (Zancolli et al., 2014) and in the Andes for Hypsiboas andinus (Koscinski et al., 2009). ...
Habitat loss, overexploitation, the presence of invasive species, climate change and the proliferation of diseases continue to put at risk anuran species that represent 90% of all amphibians. Biphasic life cycle, habitat specialization to oviposit and forage, low dispersal abilities, and permeable skin make anurans particularly susceptible to the effect of landscape composition and configuration on their capacity to move through the landscape (connectivity). Limited connectivity can result in reduced gene flow, low genetic variation and high genetic structuring. Therefore, identifying landscape elements that promote or limit the dispersal of anurans is fundamental to propose conservation plans that allow maintaining areas that enhance connectivity to assure the evolutionary potential of the species by preserving genetic diversity. Here, we reviewed studies evaluating the effect of natural and anthropogenic elements of the landscape on gene flow across temperate, tropical and subtropical landscapes. Our results suggest that roads have the strongest negative effect on connectivity resistance in anurans from temperate regions. Urbanization, fragmentation, and land cover change into agriculture and grasslands are other anthropogenic landscape elements that provide resistance to connectivity in anurans worldwide. In temperate and tropical regions, rivers are the most important natural element negatively affecting connectivity, having a stronger effect in the tropics. Contrary, streams and forests cover promote connectivity in all regions. We provide a review of the growing progress of landscape genetics in this group of vulnerable organisms and highlight the importance of considering this research field for the conservation of the threatened ecosystems that anurans inhabit.
... Major water bodies, such as large rivers, have been suggested to be at least partial impediments to dispersal (e.g. Zeisset & Beebee, 2008;Li et al., 2009;Zhao et al., 2009); however, the smaller, narrower mountain rivers and streams found among our sampling sites tend not to impede gene flow (Zeisset & Beebee, 2008). Furthermore, it is noteworthy that the water bodies class comprises only approximately 0.25% of cell count for the study area, thus water bodies are unlikely to contribute significantly to the population structure of R. chensinensis. ...
Amphibians are excellent model systems for studying how heterogeneous landscapes drive population differentiation. Though mountain ridges have been widely implicated as barriers to amphibian dispersal, a landscape genetic study by Zhan et al. (BMC Genet, 10, 2009, 17) indicated that the Tsinling Mountains of northwestern China did not significantly impede gene flow of the Chinese wood frog (Rana chensinensis). Using their published genetic data, we re‐assessed the impact of elevation, land cover, and roads on the Chinese wood frog using an isolation by resistance (IBR) approach, which allows for the modeling of complex and heterogeneous landscapes unavailable in classical population genetic analysis. We developed a novel method for optimization of IBR analysis using circuitscape involving initial permutation‐based optimization of the correlation coefficient obtained through partial Mantel tests, followed by subsequent sensitivity analysis to improve upon the model’s biological relevance. Our results indicated that mountain ridges indeed functioned as barriers to dispersal of Chinese wood frogs, and that previous conclusions were based on methodological limitations. Furthermore, a prominent threshold effect at elevations from 1500–2000 m was evident, with elevations below this range minimally impeding gene flow and higher elevations having a significant barrier effect. We suggest that a combination of expert opinion, sensitivity analysis, and permutation‐based optimization procedures in landscape genetic studies will likely generate models that are both highly explanatory and biologically relevant.
... Our study highlights a rapid advancement of the invasion front, with an expansion of the toad particularly towards the North-West (Fig. 2), probably due to the absence of ecological barriers (Brown et al. 2015). Conversely, the northward toad invasion has been probably slowed down by the presence of the River Ivoloina, suggesting that this river functioned as a partial barrier, as already reported in literature (Leblois et al. 2000;Li et al. 2009;Zhao et al. 2009). Contrary to this, the river Ivondro in the South does not seem to play the same role in arresting the invasion; this might be due to the presence of multiple man-made canals and waterways, primarily used for transportation and fishing, that could have further facilitated the invasion, increasing the connectivity between previously isolated biota (Crooks and Suarez 2006;Rahel 2007). ...
The Asian toad, Duttaphrynus melanostictus, was accidentally introduced to Toamasina (eastern Madagascar) around 2010, and since then has spread at a substantial rate across a larger area. This study documents the expansion of the invasive range of this species, calculates the invasion spread rate, and provides estimates of toad abundance and habitat preferences. Updates of the distribution range revealed a fivefold increase of the invaded area over 3 years, and a doubling of the rate of spread, showing a shift of the invasion towards the North-West, most probably because of the absence of ecological barriers. We used N-mixture models to estimate toad abundance on the basis of repeated count data of six areas in Toamasina and its surrounding countryside. Toad distribution shows heterogeneous density across the distribution range, with an average abundance of 184 toads ha⁻¹ (95% CI 132–263). The toad’s abundance was highest in sites with the presence of organic waste, and was negatively related to the density of road networks in the proximity of study sites. The rapid expansion of the Asian toad in the Toamasina region suggests that this toad is an increasing threat for Madagascar. We propose immediate management actions that could limit the spread of alien toads in this megadiverse country.
... Furthermore, some tributaries of the Yangtze River such as the Dadu River also play an important role in shaping species' phylogeography, for example constituting a significant genetic boundary between populations of giant panda (Ailuropoda melanoleuca) (Zhu, Zhang, Gu, & Wei, 2011). What's more, the Dadu River and the Yalong River also form significant genetic boundaries for the Xizang alpine toad (Scutiger boulengeri) (Li, Chen, Tu, & Fu, 2009), the plateau wood frog (Rana kukunoris) (Zhao, Dai, & Fu, 2009) as well as the plateau frog (Nanorana pleskei) (Zhou et al., 2017). Furthermore, historical climate oscillations in the Yangtze River basin or a combination thereof and high-density human activities have had great influence on many endemic species demographic history such as the plateau frog (Zhou et al., 2017), the tufted deer (Elaphodus cephalophus) (Sun, Pan, Wang, Pang, & Zhang, 2016) and the Yunnan spiny frog (Nanorana yunnanensis) , thereby, making this area ideal for the study of the effect of the interplay between natural barriers, historical climate fluctuations and human activities on the genetic background of natural populations. ...
Aim
The characterization of the genetic structure and demographic dynamics of a species can shed light on the impacts of natural landscapes, historical climate change and human activities, thus enabling us to develop appropriate protection and management strategies. In this study, we aimed to characterize how the above‐mentioned factors shaped the genetic structure and demographic history of the Chinese muntjac (Muntiacus reevesi).
Location
The reaches of the Yangtze River, China.
Methods
Using mtDNA control region sequences and 15 nuclear microsatellite loci as genetic markers, we analysed population genetic structure with a factorial correspondence analysis (FCA), AMOVA, FST estimates and Bayesian cluster analysis. In addition, we estimated the demographic history using Bayesian skyline plot (BSP) analysis and MSVAR simulation.
Results
High genetic diversity was detected in Chinese muntjac populations. Population structure analysis strongly suggesting three genetic clusters (QL/BA/WLS, DB and JLS/WN/WYS). The demographic analyses showed that Chinese muntjac experienced population fluctuation during the late Pleistocene, followed by bottleneck during the Holocene.
Main conclusions
The extant Chinese muntjac populations harbour a surprisingly high genetic diversity despite of the bottleneck they went through. The populations show significant population structure separating populations in the upper, middle and lower regions of the Yangtze River, supporting the presence of three independent management units (QL/BA/WLS, DB and JLS/WN/WYS). The population demography of the Chinese muntjac presents high concordance with the rotation of glacial–interglacial in late Pleistocene. In addition, our study identified that the Chinese muntjac's recent population history may have been influenced by early human activities (8,509–1,605 years ago).
... The unequal distribution of amphibian species could be also an effect of isolation of the amphibian populations that live in the northern parts of the study area in plots I, II, and III. This region contains busy roads, and rivers can be barriers that restrict free migration to and from breeding sites (Zhao et al. 2009, Fouquet et al. 2012, Canessa & Parris 2013. This prevents gene flow and can affect the structure of an amphibian population, even leading to its extinction. ...
Habitat restoration is a mitigation tool often proposed in conservation biology, however, our knowledge about
its effectiveness is still limited. Here we evaluate the effects of a large-scale drainage and habitat restoration project on the amphibian community in the Narew River Valley, Poland. We used visual encounter surveys, manual calling surveys, and dip-netting to record species presence/absence and breeding status. Data were then compared with a previous study that was conducted during the restoration process. We found a general increase in breeding activity and three species were found for the first time in the study area. Amphibians bred most frequently in ephemeral ponds on wetland meadows. Anthropogenic water bodies contained a similar number of species as natural sites did. Our results suggest that the increase in the amount of water in the river valley has had a positive effect on the local amphibian community.
... For example, the Dadu River had acted as the significant genetic boundary between the Daxiangling population and Xiaoxiangling population of the giant panda (Zhu et al., 2011). In Southwestern China, the lower reach of the Yalong River had a significant barrier effect on the plateau wood frog, Rana kukunoris (Zhao, Dai & Fu, 2009). However, for some large animals, the Yangtze River was not an insurmountable geographical barrier. ...
Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer (Elaphodus cephalophus) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River. Results indicated that there are high genetic diversity levels in the two populations, but no distinguishable haplotype group or potential genetic cluster was detected which corresponded to specific geographical population. At the same time, high gene flow was observed between Wulingshan and Dabashan populations. The tufted deer populations experienced population decrease from 0.3 to 0.09 Ma BP, then followed by a distinct population increase. A strong signal of recent population decline (T = 4,396 years) was detected in the Wulingshan population by a Markov-Switching Vector Autoregressions(MSVAR) process population demography analysis. The results indicated that the Yangtze River may not act as an effective barrier to gene flow in the tufted deer. Finally, we surmised that the population demography of the tufted deer was likely affected by Pleistocene climate fluctuations and ancient human activities.
... Although this number of migrants is low, the exchange of just a few individuals may suffice to ensure genetic exchange and counteract genetic drift among ponds (Safner et al., 2011). Thus, larger rivers do not necessarily constitute complete barriers for amphibians (Arntzen and Espregueira Themudo, 2008;Zhao et al., 2009;Gehring et al., 2012). However, the role of landscape elements in driving movement depends on the life stage of animals, that is, landscape elements may constitute a barrier for juveniles but not for adults . ...
Conservation measures to increase or maintain habitat networks in pond-dwelling amphibians often consist of new breeding ponds to supplement existing ones. We examined the effectiveness of this conservation measure in the European Treefrog (Hyla arborea) by evaluating the speed of colonization and the origin of colonizers using field surveys and genetic methods in an intensively managed agricultural area in Switzerland. One to three years after pond construction, 85 European Treefrogs were found at new ponds, and of these, 30 were identified as migrants by genetic assignment tests. We observed a negative correlation between the number of migrants and geographical distance (r = −0.33): 66% of colonizers originated from ponds nearby (up to 500 m); 30% stemmed from source ponds located at distances between 500 and 2,500 m; and 4% originated from distant ponds (2,500 to 5,400 m). Four colonizers crossed a 25-m wide river. These results show that Treefrogs rapidly colonize new ponds and that the gene pools at these new ponds contain a wide range of genetic variants of a Treefrog population that is patchily structured. Thus, maintaining high pond density is an efficient conservation measure to increase functional connectivity for Treefrogs even in an intensely managed agricultural landscape.
... As in several other amphibian species, it appears that major rivers are dispersal barriers (Vieites et al 2006, Zhao et al 2009. Within Texas, the salamanders to the east of the Neches River are all more closely related to one another than to those west of the Neches, although our specimens from central Newton County are closer in straight line distance to those salamanders from Tyler County than the ones from southern Sabine County. ...
Dusky salamanders in Texas have long been identified as Desmognathus au-riculatus (Southern Dusky Salamander). However, recent taxonomic work has challenged this notion, restricting D. auriculatus to areas east of the Apalachicola River in Florida and Georgia, while all Texas populations are now considered D. conanti. Regrettably, Texas specimens were not included in the studies upon which these proposed taxonomic changes were based. Dusky salamanders have become increasingly difficult to find in Texas and have only been observed in the state 3 times since 1980. We surveyed 18 sites of which 6 were historical localities. We found 4 extant populations of dusky salamanders at new locations in Texas, one of which was a county record. We were unable to find dusky salamanders at some historically robust populations. We also used mtDNA sequence data to verify that Texas dusky salamanders are indeed D. conanti.
... However, the genetic barrier effect of rivers is more unstable than that of mountain ridges due to changing hydrological factors like water level, width, flow rate, bed height and channel position which directly affect the effectiveness of the barrier. For example, the barrier effect on the plateau wood frog Rana kukunoris was much stronger at the downstream of the Yalong River, where the water flow was higher and the river valley steeper and drier [71]. During historical periods, these hydrological factors, especially water levels, fluctuated with climate fluctuation and so were obviously affected by the Quaternary glaciations in the Pleistocene. ...
(BZ) Ichthyophis bannanicus is the only caecilian species in China. In this study, the phylogeography and population demography of I. bannanicus were explored, based on the mitochondrial DNA genes (cyt b and ND2) and 15 polymorphic microsatellite loci. Altogether 158 individuals were collected from five populations in Yunnan province, Guangxi province, Guangdong province, and Northern Vietnam. Phylogeographical and population structure analysis identified either two groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun-Deqing) or three groups (Xishuangbanna, Northern Vietnam-Yulin-Yangchun, and Deqing), indicating that the Red River and Pearl River systems may have acted as gene-flow barriers for I. bannanicus. Historical population expansion that happened 15-17 Ka ago was detected for mtDNA data and was possibly triggered by warmer weather after the Last Glacial Maximum. However, the Bayesian simulations of population history based on microsatellite data pinpointed population decline in all populations since 19,123 to 1,029 years ago, demonstrating a significant influence of anthropogenic habitat alteration on I. bannanicus.
... Although landscape genetic analysis revealed several insights into the landscape variables affecting genetic connectivity, no specific physical barrier seemed to coincide with the observed genetic breaks in A. wittei. Comparably, Zhao et al. (2009) observed strong population structure in a high-elevation frog (Rana kukunoris) in China, but no single landscape feature seemed to explain the clustering. It appears that factors other than topography contribute to genetic isolation, such as selection against dispersal or local adaptation (Dobzhansky 1937;Nosil et al. 2005). ...
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.
... Although seven major mountains (Qionglai Mountains, Daxueshan Mountains, Shaluli Mountains, Mangkang Mountains, Nushan Mountains, Gaoligong Mountains and Boshula Mountains) and five major rivers (Dadu River, Yalong River, Jinsha River, Lancang River and Nu River.) occur at the Hengduan Mountains (Fig. 1), not all mountains acted as a barrier to separate the species into several genetic groups, which in previous studies was similar with the case of N. confucianus (Hsu, Lin & Lin, 2000;Fu & Zeng, 2008;Zhao, Dai & Fu, 2009; Chen et al., Figure 3 Parsimony network of cyt b haplotypes estimated under the 95% statistical limits of parsimony using the algorithm of Templeton, Crandall & Sing (1992). Small circles stand for missing haplotypes and symbols correspond to sample localities in Fig. 1. 2010). ...
Several studies indicated that the Hengduan Mountains acted as refugia during the Pleistocene. Complex topographic configuration in this area might have played an important role in shaping the genetic divergence. Here, we investigated the phylogeography of the Chinese white-bellied rats, Niviventer confucianus, to test the role of mountain ranges in the Hengduan Mountains. Our results revealed that N. confucianus populations were clustered into three geographic lineages, which were consistent with the geographic origin, where, the Daxueshan Mountains but not the Daocheng Ice Cap regions contributed to the genetic divergence of N. confucianus populations. The Daxueshan Mountains separated N. confucianus populations into two distinct evolutionary lineages (clade A and clade B) and Motuo population formed monophyletic group (clade C). Results from the mismatch distribution and neutrality test analysis suggested a range expansion of the two clades (clade A and clade B). Divergence time estimation indicated that all splits within each clade occurred after the mid-Pleistocene. All results revealed that the complex topographic configuration in the Hengduan Mountains contributed to the genetic divergence of N. confucianus.
... In contrast, Marsh et al. (2007) found that even streams contributed to population genetic differentiation of the low dispersal salamander Plethodon cinereus. However, other studies either provided an ambiguous outcome that the rivers are barriers to gene flow between amphibian populations (Zhao et al. 2009) or found large rivers playing an important role in a biogeographical pattern of frogs leading to the allopatric distribution of phylogenetically closely related species (Zeisset and Beebee 2008). It could be concluded that the effect of rivers on genetic differentiation of amphibian populations is not uniform across studies and most likely depends on the characteristics of the rivers (their width, current, the distance from headwaters, flood occurrence) and species-specific traits (aquatic or terrestrial mode of life, dispersal abilities). ...
Urbanization is a pervasive process causing habitat fragmentation, spatial isolation of populations, and reduction of biological diversity. In this study, we applied 11 microsatellite loci and Bayesian analyses to investigate genetic diversity and population structure in marsh frogs (Pelophylax ridibundus) living in two types of environment—highly fragmented urban landscapes, and landscapes characterized by the presence of a river and artificial canals. Our results show reduced genetic diversity, lower effective population sizes, and higher genetic differentiation for spatially isolated urban populations in comparison with populations outside intensely urbanized areas. Reduction of allelic diversity in urban localities isolated for 13–37 generations is more conspicuous than reduction of expected heterozygosity. Populations living close to the River Danube, its branches, and artificial canals are genetically more homogenous. Our results also suggest that the Danube in Bratislava is not a natural barrier to gene flow. In contrast, it acts as a natural corridor for water frog dispersal. Population structure of P. ridibundus also shows higher genetic connectivity within water paths than between them, suggesting limited overland dispersal, and reflects the historical landscape structure associated with the distribution of the lost river branches.
... 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). ...
The Tamarisk Gerbil {Meriones tamariscinus) , widely distributed in Central Asia desert, also is found in arid western Mongolia-Xinjiang region of China. In the present study, we combined the mitochondrial Cyt b gene (1 140 bp) and D-loop control regions (429 bp) , a total of 1 569 bp, as molecular markers. Based on mtDNA sequence analyses, we calculated the nucleotide diversity, haplotype diversity and phylogeographic structure of the local populations, then discussed the geographical differentiation of the species. We detected 142 variable sites (9.05% of the total sequence) from 45 samples, including 34 single-state sites and 108 parsimony informative sites. No base insertions or deletions were detected. A total of 33 haplotypes were defined. Haplotype-based phylogenetic tree and haplotype network showed the 45 tamarisk gerbils clustered into two branches, of which the Hi Basin branch was the more primitive one. The divergence time for these two branches was 0. 24 Ma years ago, about in the Lushan glaciation. The population had a rapid recession in the past 15 000 years, probably a result of the Last Glacial Maximum. Based on the phylogeographic patterns inferred from the genetic variation in mtDNA Cyt b gene and D-loop region, we suggest that the population in the Hi Basin should belong in M. t. jaxartensis, and those in Jungar Basin, Gansu, and Inner Mongolia should be regarded as M. t. salchouensis.
This work summarizes the history and progress of the studies on Chinese amphibians since they first ap-peared in the Chinese literature. A wide range of research has been carried out, including the history of the definition of amphibians, faunal surveys, systematic research, ecological research, biochemical research (isozyme and other proteins or peptides, chromosomes, DNA), anatomical research, embryological research, phylogenetic and zoogeographical re-search, and many others such as ultrastructure of organs, crossbreeding test, regeneration of organs, abnormality survey, acoustics, fossils, sperm ultrastructure and parasites. In addition, the prospects for studies on Chinese amphibians in future are proposed in this paper.
Graduation date: 2011 This dissertation focuses on the evolutionary forces of genetic drift and gene flow in frog populations. The balance of these two forces and the force of mutation largely determine the amount of neutral genetic variation within populations as well as the degree of genetic similarity among populations. The stochastic evolutionary change caused by genetic drift can be quantified through the use of the effective population size (N[subscript e]) parameter. The effective size of a population is the number of breeding individuals in a conceptual, ideal population that would evolve by genetic drift at the same rate as the real population being studied. How a population responds to mutation, selection, and gene flow depends on N[subscript e], rather than the actual census population size (N). In most natural populations, N[subscript e] is considerably smaller than N. For these reasons, N[subscript e] is a fundamental parameter in basic population genetics theory as well as in applied conservation genetics. The degree of neutral genetic similarity between populations is highly dependent upon gene flow. When gene flow between a pair of populations is low, the populations are likely to become genetically differentiated. Conversely, when gene flow between populations is high, the populations will tend to be more genetically similar. Amphibians are good model organisms for studying genetic drift and gene flow because they tend to exhibit strong population structure at small spatial scales. This is a consequence of their generally small population sizes, natal philopatry, limited dispersal capabilities, and restricted habitat requirements. They are expected to have easily-detectable signatures of spatial genetic structure and genetic drift. Amphibians can be used as models to further our understanding of evolutionary processes and that understanding can be applied to the conservation of amphibians. Equipped with knowledge of what naturally influences genetic drift and gene flow in amphibians, we can apply the principles of population genetics to mitigate the genetic consequences of amphibian declines. In Chapters 2 and 3, I used molecular genetic data from frog populations to investigate N[subscript e] and the related parameter N[subscript b] (the effective number of breeders). Chapter 2 is a study of a single population of the Oregon spotted frog (Rana pretiosa). My aim was to determine where in the life cycle of this species the greatest reduction in N[subscript b] occurs. I used genetic data from microsatellites to estimate N[subscript b] at two different life stages, eggs and metamorphs, and found that estimates of N[subscript b] were similar at both stages. This result suggests that inflated variance in family size due to egg mass mortality is not a primary cause of N[subscript e] reductions relative to N in this species. Chapter 3 is a comparison of N[subscript e] estimates within and among four species of frogs in the family Ranidae: R. pretiosa, R. luteiventris, R. cascadae, and Lithobates pipiens. I obtained N[subscript e] estimates for 90 populations across the four species, using microsatellite data and several different estimators. The first three species and the western populations of L. pipiens have very small effective sizes (< 50). Eastern populations of L. pipiens are much larger, with N[subscript e] estimates in the hundreds and thousands. I also found significant correlations between N[subscript e] estimates and latitude, longitude, or altitude in R. luteiventris and L. pipiens. Chapter 4 is a study of gene flow among populations of the Cascades frog (Rana cascadae) in the Olympic Mountains of Washington. I quantified genetic differentiation among 22 R. cascadae populations with data from microsatellite markers and used a landscape genetics approach to identify environmental features that have strong influences on gene flow in this species. I used a Random Forests statistical procedure to assess which of several structural connectivity models and 15 landscape variables explained the most variation in genetic distances among populations. I found that the best-fitting Random Forests models were based on different structural connectivity models for two datasets: 'within' and 'between' genetic clusters of populations. The landscape variables identified as the most important also differed across the two datasets, suggesting that landscape influences vary across spatial scales. The results presented in this dissertation led to an increased understanding of effective population size in ranid frogs and of the environmental factors that influence population structure in R. cascadae. These studies provide a foundation for further research on the specific factors that influence genetic drift and gene flow in these species.
Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multilocus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
Background
Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis) to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow.
Results
Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains.
Conclusion
The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high elevations, which may significantly contribute to the diminishing barrier effect of mountain ridges. Additionally, a significant decrease in genetic diversity in the peripheral populations supports Mayr's central-peripheral population hypothesis.
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.
Note that an updated reference for Genepop is Rousset (2008) genepop’007: a complete re-implementation of the genepop software for Windows and Linux (DOI: 10.1111/j.1471-8286.2007.01931.x)
Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
We describe patterns of genotypic and phenotypic variation in saddle-back tamarin (Saguinus fuscicollis) populations along the central and upper Rio Juruá, western Brazilian Amazonia. The genetic data are sequence haplotypes of the mitochondrial cytochrome b gene; phenotypic data are pelage colour variants that define sharply demarcated subspecies of this extremely variable tamarin species. We show that gene flow occurs between adjacent subspecies, but that this phenomenon is restricted to the headwater section of the river, which is consistent with expectations from the riverine barrier hypothesis. In this model, the major first-order tributaries of the Amazon form effective barriers to dispersal, with between-bank gene flow limited to the narrowed sections of headwater streams and parallel divergence increasing along both banks from the headwaters to the mouth of a given river. In meandering rivers such as the Rio Juruá, we suggest passive transfer through river channel dynamics as the main mechanism permitting genetic contact between populations on opposite banks of the river. Finally, we argue that in the case of plant and animal species that are largely restricted to unflooded (terra firme) forests, such as tamarins, seasonally flooded (várzea) forest can operate as a critical additional barrier to between-bank gene flow.
I reexamine the use of isolation by distance models as a basis for the estimation of demographic parameters from measures of population subdivision. To that aim, I first provide results for values of F-statistics in one-dimensional models and coalescence times in two-dimensional models, and make more precise earlier results for F-statistics in two-dimensional models and coalescence times in one-dimensional models. Based on these results, I propose a method of data analysis involving the regression of FST/(1-FST) estimates for pairs of subpopulations on geographic distance for populations along linear habitats or logarithm of distance for populations in two-dimensional habitats. This regression provides in principle an estimate of the product of population density and second moment of parental axial distance. In two cases where comparison to direct estimates is possible, the method proposed here is more satisfactory than previous indirect methods.
Mitochondrial DNA cytochrome b sequence data from a dart-poison frog, Epipedobates femoralis, were used to test two hypotheses of Amazonian diversification: the riverine barrier and the ridge hypotheses. Samples were derived from sites located on both banks of the Rio Juruá and on both sides of the Iquitos Arch in western Amazonia. The phylogeographic structure was inconsistent with predictions of the riverine barrier hypothesis. Haplotypes from opposite river banks did not form monophyletic clades in any of our phylogenetic analyses, nor was the topology within major clades consistent with the riverine hypothesis. Further, the greatest differentiation between paired sites on opposite banks was not at the river mouth where the strongest barrier to gene flow was predicted to occur. The results instead were consistent with the hypothesis that ancient ridges (arches), no longer evident on the landscape, have shaped the phylogeographic relationships of Amazonian taxa. Two robustly supported clades map onto opposite sides of the Iquitos Arch. The mean haplotypic divergence between the two clades, in excess of 12%, suggests that this cladogenic event dates to between five and 15 million years ago. These estimates span a period of major orogenesis in western South America and presumably the formation of these ancient ridges.
Rivers have been suggested to have played an important role in shaping present-day patterns of ecological and genetic variation among Amazonian species and communities. Recent molecular studies have provided mixed support for the hypothesis that large lowland Amazonian rivers have functioned as significant impediments to gene flow among populations of neotropical species. To date, no study has systematically evaluated the impact that riverine barriers might have on structuring whole Amazonian communities. Our analyses of the phylogeography of frogs and small mammals indicate that a putative riverine barrier (the Juruá River) does not relate to present-day patterns of community similarity and species richness. Rather, our results imply a significant impact of the Andean orogenic axis and associated thrust-and-fold lowland dynamics in shaping patterns of biotic diversity along the Juruá. Combined results of this and other studies significantly weaken the postulated role of rivers as major drivers of Amazonian diversification.
We analyzed variation in advertisement calls and allozymes in 30 populations along a 5000-km transect throughout most of the range of the túngara frog, Physalaemus pustulosus. All 12 call variables measured show significant differences among populations despite the importance of the advertisement call in species recognition. Some call variables exhibited clinal variation, whereas most others differed between the two major allozyme groups that have invaded Panama at different times, perhaps 4-4.5 million yr apart. Call variables that primarily affect discrimination among conspecifics tended to exhibit greater variation than call variables that are crucial for species recognition. The proximate mechanism of production underlying a call variable, however, is a better predictor of its variation. Contrary to predictions of some sexual selection models, call variation exhibits predictable patterns of geographical variation, although a substantial portion of variation among populations is not explained by geographic position. Although allozymes, calls, and geography usually covary, closer populations can have more similar calls independent of allozyme similarity.
We analyzed variation in advertisement calls and allozymes in 30 populations along a 5000-km transect throughout most of the range of the tungara frog, Physalaemus pustulosus. All 12 call variables measured show significant differences among populations despite the importance of the advertisement call in species recognition. Some call variables exhibited clinal variation, whereas most others differed between the two major allozyme groups that have invaded Panama at different times, perhaps 4-4.5 million yr apart. Call variables that primarily affect discrimination among conspecifics tended to exhibit greater variation than call variables that are crucial for species recognition. The proximate mechanism of production underlying a call variable, however, is a better predictor of its variation. Contrary to predictions of some sexual selection models, call variation exhibits predictable patterns of geographical variation, although a substantial portion of variation among populations is not explained by geographic position. Although allozymes, calls, and geography usually covary, closer populations can have more similar calls independent of allozyme similarity
We developed 22 microsatellite markers for the Chinese wood frog (Rana chensinensis) to study the impact of landscape features on its population structure. Thirty-four individuals from one breeding site were examined and 14 loci were polymorphic. The number of alleles, expected heterozygosity and observed heterozygosity varied from two to 14, from 0.0833 to 0.9118, and from 0.1376 to 0.8667, respectively. Cross-species amplification was tested for 15 ranid frog species. The Plateau brown frog, Rana kukunoris (n = 23), was successfully amplified at 18 loci, and 15 were polymorphic with number of alleles varying from two to 18. Ten other species were also amplified at a limited number of loci.
At high altitude, rivers may function as barriers for amphibians. We examined 21 populations of Scutiger boulengeri from the Hengduan Mountains with 1038 base pairs of mitochondrial cytochrome b gene sequences. The haplotypes of S. boulengeri formed three clades on the gene tree, and each clade was restricted to one mountain ridge separated by two major river systems, the Yalong River and the Dadu River. The vicariant pattern of the gene tree suggests that these rivers functioned as effective barriers during population differentiation. On the other hand, mountain ridges may have facilitated amphibian movement. Populations within the uninterrupted mountain ranges of clades II and III, revealed little genetic structure. The northern clade I, harboured a substantial amount of genetic variation, which might be the consequence of the rugged terrain and heterogeneous habitat of this area. Furthermore, one outgroup species, Scutiger glandulatus, formed the fourth clade and nested within S. boulengeri, suggesting that S. boulengeri is likely a paraphyletic species or a species complex.
Túngara frogs (Physalaemus pustulosus) are a model system for sexual selection and communication. Population dynamics and gene flow are of major interest in this species because they influence speciation processes and microevolution, and could consequently provide a deeper understanding of the evolutionary processes involved in mate recognition. Although earlier studies have documented genetic variation across the species' range, attempts to investigate dispersal on a local level have been limited to mark-recapture studies. These behavioural studies indicated high mobility at a scale of several hundred metres. In this study we used seven highly polymorphic microsatellite loci to investigate fine-scaled genetic variation in the túngara frog. We analysed the influence of geographical distance on observed genetic patterns, examined the influence of a river on gene flow, and tested for sex-biased dispersal. Data for 668 individuals from 17 populations ranging in distance from 0.26 to 11.8 km revealed significant levels of genetic differentiation among populations. Genetic differentiation was significantly correlated with geographic distance. A river acted as an efficient barrier to gene flow. Several tests of sex-biased dispersal were conducted. Most of them showed no difference between the sexes, but variance of Assignment Indices exhibited a statistically significant male bias in dispersal.
There is substantial debate over the criteria that should be used to group populations of a species into distinct units for conservation (e.g. evolutionarily significant units, management units, distinct population segments). However, in practice molecular genetic differentiation is often the only or main criterion used to identify such units. Most genetic studies attempting to define conservation units in animals use a single molecular marker, most often mitochondrial, and use samples from a limited number of populations throughout the species' range. Although there are many benefits to using mtDNA, certain features can cause it to show patterns of differentiation among populations that do not reflect the history of differentiation at the nuclear genome where loci controlling traits of adaptive significance presumably occur. Here we illustrate an example of such mitochondrial-nuclear discordance in a ranid frog, and show how using mtDNA or nuclear loci alone could have led to very different conservation recommendations. We also found very high genetic differentiation among populations on a local scale, and discuss the conservation implications of our results.
In general, amphibians are known to exhibit a higher degree of population subdivision than any other major animal taxa, but large-scale population genetic surveys of widely distributed species are still scarce, especially in the Eurasian continent. Using microsatellite markers and mitochondrial DNA sequences, we investigated the large-scale population genetic structure of the common frog (Rana temporaria)--one of the most widespread amphibians of the Palearctic region. Analyses of cytochrome b sequences revealed evidence for two distinct lineages inhabiting western and eastern parts of Europe. The separation of these lineages c. 700,000 years ago may have been induced by the onset of the Middle Pleistocene continental glaciations. Analyses of the variability of microsatellite loci within each of the clades revealed evidence for evolution of a high degree of population subdivision (FST approximately 0.23) even in northern Fennoscandia, colonized less than 10,000 years ago. The high level of substructuring is puzzling in the face of an apparently high dispersal capacity, as evidenced by the rather rapid recolonization of northern Europe. This suggests that processes other than restricted dispersal capacity need to be explored as explanations for the high degree of population subdivision in amphibians. The colonization of northern Europe has been accompanied by loss of genetic variability as evidenced by decreasing levels of intrapopulational genetic variability in microsatellite loci from south to north across Europe.
Landscape features such as mountains, rivers, and ecological gradients may strongly affect patterns of dispersal and gene flow among populations and thereby shape population dynamics and evolutionary trajectories. The landscape may have a particularly strong effect on patterns of dispersal and gene flow in amphibians because amphibians are thought to have poor dispersal abilities. We examined genetic variation at six microsatellite loci in Columbia spotted frogs (Rana luteiventris) from 28 breeding ponds in western Montana and Idaho, USA, in order to investigate the effects of landscape structure on patterns of gene flow. We were particularly interested in addressing three questions: (i) do ridges act as barriers to gene flow? (ii) is gene flow restricted between low and high elevation ponds? (iii) does a pond equal a 'randomly mating population' (a deme)? We found that mountain ridges and elevational differences were associated with increased genetic differentiation among sites, suggesting that gene flow is restricted by ridges and elevation in this species. We also found that populations of Columbia spotted frogs generally include more than a single pond except for very isolated ponds. There was also evidence for surprisingly high levels of gene flow among low elevation sites separated by large distances. Moreover, genetic variation within populations was strongly negatively correlated with elevation, suggesting effective population sizes are much smaller at high elevation than at low elevation. Our results show that landscape features have a profound effect on patterns of genetic variation in Columbia spotted frogs.
In species affiliated with heterogeneous habitat, we expect gene flow to be restricted due to constraints placed on individual movement by habitat boundaries. This is likely to impact both individual dispersal and connectivity between populations. In this study, a GIS-based landscape genetics approach was used, in combination with fine-scale spatial autocorrelation analysis and the estimation of recent intersubpopulation migration rates, to infer patterns of dispersal and migration in the riparian-affiliated Pacific jumping mouse (Zapus trinotatus). A total of 228 individuals were sampled from nine subpopulations across a system of three rivers and genotyped at eight microsatellite loci. Significant spatial autocorrelation among individuals revealed a pattern of fine-scale spatial genetic structure indicative of limited dispersal. Geographical distances between pairwise subpopulations were defined following four criteria: (i) Euclidean distance, and three landscape-specific distances, (ii) river distance (distance travelled along the river only), (iii) overland distance (similar to Euclidean, but includes elevation), and (iv) habitat-path distance (a least-cost path distance that models movement along habitat pathways). Pairwise Mantel tests were used to test for a correlation between genetic distance and each of the geographical distances. Significant correlations were found between genetic distance and both the overland and habitat-path distances; however, the correlation with habitat-path distance was stronger. Lastly, estimates of recent migration rates revealed that migration occurs not only within drainages but also across large topographic barriers. These results suggest that patterns of dispersal and migration in Pacific jumping mice are largely determined by habitat connectivity.
The amount of genetic variability at neutral marker loci is expected to decrease, and the degree of genetic differentiation among populations to increase, as a negative function of effective population size. We assessed the patterns of genetic variability and differentiation at seven microsatellite loci in the common frog (Rana temporaria) in a hierarchical sampling scheme involving three regions (208-885 km apart), three subregions within regions and nine populations (5-20 km apart) within subregions, and related the variability and differentiation estimates to variation in local population size estimates. Genetic variability within local populations decreased significantly with increasing latitude, as well as with decreasing population size and regional site occupancy (proportion of censured localities occupied). The positive relationship between population size and genetic variability estimates was evident also when the effect of latitude (cf. colonization history) was accounted for. Significant genetic differentiation was found at all hierarchical levels, and the degree of population differentiation tended to increase with increasing latitude. Isolation by distance was evident especially at the regional sampling level, and its strength increased significantly towards the north in concordance with decreasing census and marker-based neighbourhood size estimates. These results are in line with the conjecture that the influence of current demographic factors can override the influence of historical factors on species population genetic structure. Further, the observed reductions in genetic variability and increased degree of population differentiation towards the north are in line with theoretical and empirical treatments suggesting that effective population sizes decline towards the periphery of a species' range.
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