Catchments catch all: long-term population history of a giant springtail from the southeast Australian highlands--a multigene approach

Phylogeography can reveal evolutionary processes driving natural genetic-geographical patterns in biota, providing an empirical framework for optimizing conservation strategies. The long-term population history of a rotting-log-adapted giant springtail (Collembola) from montane southeast Australia was inferred via joint analysis of mitochondrial and multiple nuclear gene genealogies. Contemporary populations were identified using multilocus nuclear genotype clustering. Very fine-scale sampling combined with nested clade and coalescent-based analyses of sequences from mitochondrial cytochrome oxidase I and three unlinked nuclear loci uncovered marked population structure, deep molecular divergences, and abrupt phylogeographical breaks over distances on the order of tens of kilometres or less. Despite adaptations that confer low mobility, rare long-distance gene flow was implicated: novel computer simulations that jointly modelled stochasticity inherent in coalescent processes and that of DNA sequence evolution showed that incomplete lineage sorting alone was unable to explain the observed spatial-genetic patterns. Impacts of Pleistocene or earlier climatic cycles were detected on multiple timescales, and at least three putative moist forest refuges were identified. Water catchment divisions predict phylogeographical patterning and present-day population structure with high precision, and may serve as an excellent surrogate for biodiversity indication in sedentary arthropods from topographically heterogeneous montane temperate forests.     

Phylogeography of the pademelons (Marsupialia: Macropodidae: Thylogale) in New Guinea reflects both geological and climatic events during the Plio‐Pleistocene

Aim Alternative hypotheses concerning genetic structuring of the widespread endemic New Guinean forest pademelons (Thylogale) based on current taxonomy and zoogeography (northern, southern and montane species groupings) and preliminary genetic findings (western and eastern regional groupings) are investigated using mitochondrial sequence data. We examine the relationship between the observed phylogeographical structure and known or inferred geological and historical environmental change during the late Tertiary and Quaternary. Location New Guinea and associated islands. Methods We used primarily museum specimen collections to sample representatives from Thylogale populations across New Guinea and three associated islands. Mitochondrial cytochrome b and control region sequence data were used to construct phylogenies and estimate the timing of population divergence. Results Phylogenetic analyses indicated subdivision of pademelons into ‘eastern’ and ‘western’ regional clades. This was largely due to the genetic distinctiveness of north‐eastern and eastern peninsula populations, as the ‘western’ clade included samples from the northern, southern and central regions of New Guinea. Two tested island groups were closely related to populations north of the Central Cordillera; low genetic differentiation of pademelon populations between north‐eastern New Guinea and islands of the Bismarck Archipelago is consistent with late Pleistocene human‐mediated translocations, while the Aru Islands population showed divergence consistent with cessation of gene flow in the mid Pleistocene. There was relatively limited genetic divergence between currently geographically isolated populations in subalpine and nearby mid‐montane or lowland regions. Main conclusions Phylogeographical structuring does not conform to zoogeographical expectations of a north/south division across the cordillera, nor to current species designations, for this generalist forest species complex. Instead, the observed genetic structuring of Thylogale populations has probably been influenced by geological changes and Pleistocene climatic changes, in particular the recent uplift of the north‐eastern Huon Peninsula and the lowering of tree lines during glacial periods. Low sea levels during glacial maxima also allowed gene flow between the continental Aru Island group and New Guinea. More work is needed, particularly multi‐taxon comparative studies, to further develop and test phylogeographical hypotheses in New Guinea.     

Phylogeny and historical biogeography of African ground squirrels: the role of climate change in the evolution of Xerus

We used phylogenetic and phylogeographical methods to infer relationships among African ground squirrels of the genus Xerus. Using Bayesian, maximum-parsimony, nested clade and coalescent analyses of cytochrome b sequences, we inferred interspecific relationships, evaluated the specific distinctness of Cape (Xerus inauris) and mountain (Xerus princeps) ground squirrels, and tested hypotheses for historical patterns of gene flow within X. inauris. The inferred phylogeny supports the hypothesized existence of an 'arid corridor' from the Horn of Africa to the Cape region. Although doubts have been raised regarding the specific distinctness of X. inauris and X. princeps, our analyses show that each represents a distinct well-supported, monophyletic lineage. Xerus inauris includes three major clades, two of which are geographically restricted. The distributions of X. inauris populations are concordant with divergences within and disjunctions between other taxa, which have been interpreted as results of Plio-Pleistocene climate cycles. Nested clade analysis, coalescent analyses, and analyses of genetic structure support allopatric fragmentation as the cause of the deep divergences within this species.     

Phylogeographical approaches to assessing demographic connectivity between breeding and overwintering regions in a Nearctic-Neotropical warbler (Wilsonia pusilla)

We characterized the pattern and magnitude of phylogeographical variation among breeding populations of a long-distance migratory bird, the Wilson's warbler (Wilsonia pusilla), and used this information to assess the utility of mtDNA markers for assaying demographic connectivity between breeding and overwintering regions. We found a complex pattern of population differentiation in mitochondrial DNA (mtDNA) variation among populations across the breeding range. Individuals from eastern North America were differentiated from western individuals and the eastern haplotypes formed a distinct, well-supported cluster. The more diverse western group contained haplotype clusters with significant geographical structuring, but there was also broad mixing of haplotype groups such that no haplotype groups were population specific and the predominance of rare haplotypes limited the utility of frequency-based assignment techniques. Nonetheless, the existence of geographically diagnosable eastern vs. western haplotypes enabled us to characterize the distribution of these two groups across 14 overwintering locations. Western haplotypes were present at much higher frequencies than eastern haplotypes at most overwintering sites. Application of this mtDNA-based method of linking breeding and overwintering populations on a finer geographical scale was precluded by the absence of population-specific markers and by insufficient haplotype sorting among western breeding populations. Our results suggest that because migratory species such as the Wilson's warbler likely experienced extensive gene flow among regional breeding populations, molecular markers will have the greatest utility for characterizing breeding-overwintering connectivity at a broad geographical scale.     

Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms

Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority because of recent outbreaks of avian influenza. Ringing studies that trace large‐scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism markers in combination with population genetics and phylogeographical approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations worldwide. Basic population genetic and phylogenetic methods suggest no or very little population structure on continental scales. Nor could individual‐based structuring algorithms discern geographical structuring. Model‐based coalescent analyses for testing models of population structure pointed to strong genetic connectivity among the world's mallard population. These diverse approaches all support the conclusion that there is a lack of clear population structure, suggesting that the world's mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population.     

Comparative phylogeography of tenebrionid beetles in the Aegean archipelago: the effect of dispersal ability and habitat preference

Comparative phylogeographical studies in island archipelagos can reveal lineage-specific differential responses to the geological and climatic history. We analysed patterns of genetic diversity in six codistributed lineages of darkling beetles (Tenebrionidae) in the central Aegean archipelago which differ in wing development and habitat preferences. A total of 600 specimens from 30 islands and eight adjacent mainland regions were sequenced for mitochondrial cytochrome oxidase I and nuclear Muscular protein 20. Individual gene genealogies were assessed for the presence of groups that obey an independent coalescent process using a mixed Yule coalescent model. The six focal taxa differed greatly in the number of coalescent groups and depth of lineage subdivision, which was closely mirrored by the degree of geographical structuring. The most severe subdivision at both mitochondrial DNA and nuclear DNA level was found in flightless lineages associated with presumed stable compact-soil habitats (phrygana, maquis), in contrast to sand-obligate lineages inhabiting ephemeral coastal areas that displayed greater homogeneity across the archipelago. A winged lineage, although associated with stable habitats, showed no significant phylogenetic or geographical structuring. Patterns of nucleotide diversity and local genetic differentiation, as measured using Φ_ST and hierarchical amova , were consistent with high levels of ongoing gene flow in the winged taxon; frequent local extinction and island recolonisation for flightless sand-obligate taxa; and very low gene flow and geographical structure largely defined by the palaeogeographical history of the region in flightless compact-soil taxa. These results show that differences in dispersal rate, mediated by habitat persistence, greatly influence the levels of phylogeographical subdivision in lineages that are otherwise subjected to the same geological events and palaeoclimatic changes.     

Phylogeographical analysis of an estuarine fish, Salanx ariakensis (Osmeridae: Salanginae) in the north-western Pacific

This study extended the geographic coverage of a previous study to explore population genetic structure and demographic history in the Ariake icefish Salanx ariakensis from three populations of continental coastlines and one island population in the north-western Pacific based on a partial sequence of the mitochondrial cytochrome b gene. The S. ariakensis showed high genetic diversity and strong genetic structure. Phylogenetic analysis showed a shallow gene tree with no clear phylogeographical structure. Contiguous range expansion and restricted gene flow were inferred to be main population events by nested-clade analysis. Significant genetic differentiations between populations could be attributable to negligible gene flow by coalescent analysis. High nucleotide diversity of each population was due to geographic mixing of heterogenous haplotypes during lowering sea levels of the Pleistocene. These findings indicate that cycles of geographic isolation and secondary contact happened in the Pleistocene glacial–interglacial cycles shaping genetic structure and population demography of S. ariakensis .     

Contemporary patterns in a historical context: phylogeographic history of the pipevine swallowtail,Battus philenor (Papilionidae)

Abstract We examined mitochondrial DNA (mtDNA) variation in pipevine swallowtail butterflies ( Battus philenor ) from throughout its extant range to provide a historical, phylogeographical context for ecological studies of the disjunct population in California. We evaluate current hypotheses regarding host plant use, behavior, and mimetic relationships of B. philenor populations and generate alternative hypotheses. Compared to populations throughout the rest of the species' range, California populations are ecologically distinct in that they lack mimics, lay significantly larger clutches of eggs, and exclusively use a unique, endemic larval host plant. Analysis of molecular variance, tests of population differentiation, and nested clade analysis of mtDNA variation indicate that, despite low levels of population genetic structure across the species' range, there is evidence of recent range expansion from presumed Pleistocene refuge(s) in southeastern North America. Colonization of California appears to have been a recent event. This phylogeographic investigation also suggests that the evolution of life-history adaptations to a novel larval host has occurred rapidly in California and the lack of mimics in California may be attributable to the recency of colonization.     

Biogeography of the livebearing fish Poecilia gillii in Costa Rica: are phylogeographical breaks congruent with fish community boundaries?

One of the original goals of phylogeography was to use genetic data to identify historical events that might contribute to breaks among communities. In this study, we examine the phylogeography of a common livebearing fish ( Poecilia gillii ) from Costa Rica. Our goal was to determine if phylogeographical breaks in this species were congruent with previously defined boundaries among four fish community provinces. We hypothesized that if abiotic factors influence both community boundaries and genetic structuring in P. gillii then we might find four clades within our focal species that were geographically separated along community boundary lines. Similarly, we expected to find most of the genetic variation in P. gillii partitioned among these four geographical regions. We generated DNA sequence data (mitochondrial cytochrome b and nuclear S7 small ribosomal subunit) for 260 individuals from 42 populations distributed across Costa Rica. We analysed these data using phylogenetic (parsimony and likelihood) and coalescent approaches to estimate phylogenetic relationships among haplotypes, patterns of gene flow and effective population size . Contrary to our expectations, we did not find four monophyletic groups that mapped cleanly to our geographical community provinces. However, one of our clades was restricted to a single province, suggesting that common earth history events could be responsible for both genetic structuring in P. gillii and fish community composition in this area. However, our results show a complex pattern of gene flow throughout other regions in Costa Rica where genetic structuring is not predicted by community province boundaries.     

The evolution of north‐east Atlantic gadfly petrels using statistical phylogeography

Macaronesia (north‐east Atlantic archipelagos) has been host to complex patterns of colonization and differentiation in many groups of organisms including seabirds such as gadfly petrels (genus Pterodroma). Considering the subspecies of widely distributed soft‐plumaged petrel for many years, the taxonomic status of the three gadfly petrel taxa breeding in Macaronesia is not yet settled, some authors advocating the presence of three, two or one species. These birds have already been the subject of genetic studies with only one mtDNA gene and relatively modest sample sizes. In this study, using a total of five genes (two mitochondrial genes and three nuclear introns), we investigated the population and phylogeographical histories of petrel populations breeding on Madeira and Cape Verde archipelagos. Despite confirming complete lineage sorting with mtDNA, analyses with nucDNA failed to reveal any population structuring and Isolation with Migration analysis revealed the absence of gene flow during the differentiation process of these populations. It appears that the three populations diverged in the late Pleistocene in the last 150 000 years, that is 10 times more recently than previous estimates based solely on one mtDNA gene. Finally, our results suggest that the Madeira petrel population is ancestral rather than that from Cape Verde. This study strongly advocates the use of nuclear loci in addition to mtDNA in demographical and phylogeographical history studies.     

Population Graphs: the graph theoretic shape of genetic structure

Patterns of intraspecific genetic variation result from interactions among both historical and contemporary evolutionary processes. Traditionally, population geneticists have used methods such as F-statistics, pairwise isolation by distance models, spatial autocorrelation and coalescent models to analyse this variation and to gain insight about causal evolutionary processes. Here we introduce a novel approach (Population Graphs) that focuses on the analysis of marker-based population genetic data within a graph theoretic framework. This method can be used to estimate traditional population genetic summary statistics, but its primary focus is on characterizing the complex topology resulting from historical and contemporary genetic interactions among populations. We introduce the application of Population Graphs by examining the range-wide population genetic structure of a Sonoran Desert cactus (Lophocereus schottii). With this data set, we evaluate hypotheses regarding historical vicariance, isolation by distance, population-level assignment and the importance of specific populations to species-wide genetic connectivity. We close by discussing the applicability of Population Graphs for addressing a wide range of population genetic and phylogeographical problems.     

Seeing in the dark: molecular approaches to the study of bat populations

Whilst the use of molecular genetic techniques is widespread in the fields of population and evolutionary biology, their application within the mammalian order Chiroptera neither reflects the species richness nor the ecological and behavioural diversity of the order. This is despite the fact that the Chiroptera are problematic to study using more direct observational techniques. Here, we standardize and synthesise the current data, assess the contribution of molecular research to the study of bat species and highlight the importance of its continued and expanded use. At an inter-population level, molecular studies have demonstrated a great diversity of population genetic structure within the order. Among populations of migratory species, genetic structure appears universally low, and hence seasonal movement is likely to be the prevailing influence. However, for sedentary species an array of factors including dispersal ability, extrinsic barriers to gene flow and historical events may determine the extent of genetic partitioning among populations. Intrinsic factors such as wing morphology or roost requirements may also influence population genetic structure in sedentary bat species, a proposal which requires further research. Molecular studies have also made important contributions towards an understanding of social organisation in bats. Evidence indicates that in many polygynous species male mating success does not translate directly into reproductive success, perhaps as a result of multiple mating by females. Estimates of relatedness within and genetic structure among colonies are, in general, very low; a finding which has important implications regarding theories concerning the formation and persistence of bat social groups. Molecular studies have provided new and important insights into the ecology of bats, and have opened up exciting and previously unexplored avenues of research. The data from these studies suggest not only a predictive framework for future studies, but also the use of genetic data in the management and conservation of bat species.     

Phylogeography of Varicorhinus barbatulus (Cyprinidae) in Taiwan based on nucleotide variation of mtDNA and allozymes

The phylogeographical patterns and population genetic structures of Varicorhinus barbatulus in Taiwan were investigated based on genetic diversity of 34 allozyme loci and nucleotide sequences of 3' end of the cytochrome b gene, tRNA genes, D-loop control region, and the 5' end of the 12S rRNA of mtDNA. Allozyme and mtDNA analyses revealing evident geographical structuring suggest limited gene flow between populations (F(ST)=0.511 and 0.791, respectively). Low genetic variability within populations (P=5.56%; He=0.018) based on allozymes and significantly negative Tajima's D statistics based on mtDNA suggest that most populations in Taiwan may have originated from a small number of founders followed by demographic expansion. The gene genealogy of mtDNA identified six lineages corresponding to major drainages that were separated by the geological barriers due to vicariant events. A minimum spanning network based on nucleotide substitutions reflects divergence from populations of the Miao-li Plateau to northern and southern regions of the island. In contrast to a previous hypothesis that suggests an early invasion to eastern part of Taiwan prior to the lifting of central mountain range some one million years ago, the mtDNA genealogy and molecular dating reveal very recent colonization of the eastern population. Nested clade analyses revealing significant associations between genetic structure and geographical division identify past fragmentation and range expansion as major phylogeographical events that shaped the geographical distribution of this species in Taiwan.     

Population genetic structure in Atlantic and Pacific Ocean common murres (Uria aalge): natural replicate tests of post‐Pleistocene evolution

Understanding the factors that influence population differentiation in temperate taxa can be difficult because the signatures of both historic and contemporary demographics are often reflected in population genetic patterns. Fortunately, analyses based on coalescent theory can help untangle the relative influence of these historic and contemporary factors. Common murres (Uria aalge) are vagile seabirds that breed in the boreal and low arctic waters of the Northern Hemisphere. Previous analyses revealed that Atlantic and Pacific populations are genetically distinct; however, less is known about population genetic structure within ocean basins. We employed the mitochondrial control region, four microsatellite loci and four intron loci to investigate population genetic structure throughout the range of common murres. As in previous studies, we found that Atlantic and Pacific populations diverged during the Pleistocene and do not currently exchange migrants. Therefore, Atlantic and Pacific murre populations can be used as natural replicates to test mechanisms of population differentiation. While we found little population genetic structure within the Pacific, we detected significant east–west structuring among Atlantic colonies. The degree that population genetic structure reflected contemporary population demographics also differed between ocean basins. Specifically, while the low levels of population differentiation in the Pacific are at least partially due to high levels of contemporary gene flow, the east–west structuring of populations within the Atlantic appears to be the result of historic fragmentation of populations rather than restricted contemporary gene flow. The contrasting results in the Atlantic and Pacific Oceans highlight the necessity of carefully considering multilocus nonequilibrium population genetic approaches when reconstructing the demographic history of temperate Northern Hemisphere taxa.     

Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co-distributed species

Coalescent samplers are computational time machines for inferring the historical demographic genetic processes that have given rise to observable patterns of spatial genetic variation among contemporary populations. We have used traditional characterizations of population structure and coalescent‐based inferences about demographic processes to reconstruct the population histories of two co‐distributed marine species, the frilled dog whelk, Nucella lamellosa, and the bat star, Patiria miniata. Analyses of population structure were consistent with previous work in both species except that additional samples of N. lamellosa showed a larger regional genetic break on Vancouver Island (VI) rather than between the southern Alexander Archipelago as in P. miniata. Our understanding of the causes, rather than just the patterns, of spatial genetic variation was dramatically improved by coalescent analyses that emphasized variation in population divergence times. Overall, gene flow was greater in bat stars (planktonic development) than snails (benthic development) but spatially homogeneous within species. In both species, these large phylogeographic breaks corresponded to relatively ancient divergence times between populations rather than regionally restricted gene flow. Although only N. lamellosa shows a large break on VI, population separation times on VI are congruent between species, suggesting a similar response to late Pleistocene ice sheet expansion. The absence of a phylogeographic break in P. miniata on VI can be attributed to greater gene flow and larger effective population size in this species. Such insights put the relative significance of gene flow into a more comprehensive historical biogeographic context and have important implications for conservation and landscape genetic studies that emphasize the role of contemporary gene flow and connectivity in shaping patterns of population differentiation.     

Population Explosion in the Yellow-Spined Bamboo Locust Ceracris kiangsu and Inferences for the Impact of Human Activity

Geographic distance and geographical barriers likely play a considerable role in structuring genetic variation in species, although some migratory species may have less phylogeographic structure on a smaller spatial scale. Here, genetic diversity and the phylogenetic structure among geographical populations of the yellow-spined bamboo locust, Ceracris kiangsu, were examined with 16S rDNA and amplified fragment length polymorphisms (AFLPs). In this study, no conspicuous phylogeographical structure was discovered from either Maximum parsimony (MP) and Neighbor-joining (NJ) phylogenetic analyses. The effect of geographical isolation was not conspicuous on a large spatial scale.At smaller spatial scales local diversity of some populations within mountainous areas were detected using Nei''s genetic distance and AMOVA. There is a high level of genetic diversity and a low genetic differentiation among populations in the C. kiangsu of South and Southeast China. Our analyses indicate that C. kiangsu is a monophyletic group. Our results also support the hypothesis that the C. kiangsu population is in a primary differentiation stage. Given the mismatch distribution, it is likely that a population expansion in C. kiangsu occurred about 0.242 Ma during the Quaternary interglaciation. Based on historical reports, we conjecture that human activities had significant impacts on the C. kiangsu gene flow.     

Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history

Since the 1920s, population geneticists have had measures that describe how genetic variation is distributed spatially within a species' geographical range. Modern genetic survey techniques frequently yield information on the evolutionary relationships among the alleles or haplotypes as well as information on allele frequencies and their spatial distributions. This evolutionary information is often expressed in the form of an estimated haplotype or allele tree. Traditional statistics of population structure, such as F statistics, do not make use of evolutionary genealogical information, so it is necessary to develop new statistical estimators and tests that explicitly incorporate information from the haplotype tree. One such technique is to use the haplotype tree to define a nested series of branches (clades), thereby allowing an evolutionary nested analysis of the spatial distribution of genetic variation. Such a nested analysis can be performed regarding the geographical sampling locations either as categorical or continuous variables (i.e. some measure of spatial distance). It is shown that such nested phylogeographical analyses have more power to detect geographical associations than traditional, nonhistorical analyses and, as a consequence, allow a broader range of gene-flow parameters to be estimated in a precise fashion. More importantly, such nested analyses can discriminate between phylogeographical associations due to recurrent but restricted gene flow vs. historical events operating at the population level (e.g. past fragmentation, colonization, or range expansion events). Restricted gene flow and historical events can be intertwined, and the cladistic analyses can reconstruct their temporal juxtapositions, thereby yielding great insight into both the evolutionary history and population structure of the species. Examples are given that illustrate these properties, concentrating on the detection of range expansion events.     

Population demography and genetic structure of the fat greenling (Hexagrammos otakii) inferred from mtDNA control region sequence analyses

Pleistocene ice ages in addition to geographical and geological modifications have affected the natural range and habitat of marine organisms in Northwestern Pacific. The effects of glacial events have left a genomic signature, resulting in concordant phylogeographical structures among many species. To investigate the effects of Quaternary climatic changes on the evolution in H. otakii, fragments of 471 bp at the 5′ end of mitochondrial DNA control region were sequenced for 275 individuals from 10 localities in the Northern China and Japan. Both mismatch distribution analyses and neutrality tests suggested recent population expansion (64,000–227,000 years ago). Although estimated value of pairwise population differentiation (F_ST) was low, half (23 of 45) of the comparisons showed statistically significant. Coalescent-based estimates show that gene flow was asymmetric or directional, most of all comparisons (57 of 65) among populations showed low evaluation value of N_m (N_m < 10). Analysis of molecular variance (AMOVA) showed genetic structuring among groups when the data was partitioned into six groups in this study. The defined pattern of genetic variation suggested a crucial role of habitat requirement, marine current, marine gyres and history process. Absence of genetic structure over hundreds of kilometers between AO and assemblage of QD, RZ and GY might imply the common coalescent other than current gene flow. Specific exchange mechanism and fine scale genetic structure need further research using faster evolution molecular markers (microsatellite markers) and further sampling.     

Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation

ABSTRACT: BACKGROUND: As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species. RESULTS: Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; pi = 0.00314) were almost as high as at PAL (h = 0.836; pi = 0.00417). Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989), suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222; NST = 0.301) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST; P < 0.01). The analysis of PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel's test of nrDNA haplotypes (r = 0.234, P < 0.001). We found that chlorotype C1 was fixed in seven populations of Lancang River Region, implying that the Lancang River might have provided a corridor for the long-distance dispersal of the species. CONCLUSIONS: We found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developing in situ conservation of natural populations.     

Diversity and demography in Beringia: multilocus tests of paleodistribution models reveal the complex history of arctic ground squirrels

To assess effects of historical climate change on northern species, we quantified the population history of the arctic ground squirrel (Spermophilus parryii), an arctic-adapted rodent that evolved in Beringia and was strongly influenced by climatic oscillations of the Quaternary. Competing hypotheses for the species' population history were derived from patterns of mitochondrial (mtDNA) structure and a bioclimatic envelope model (BEM). Hypotheses invoked (1) sequential isolation of regional populations beginning with the Arctic, (2) deep isolation only across central Alaska, and (3) widespread panmixia, and were tested using coalescent methods applied to eight nuclear (nDNA) loci. The data rejected strict interpretations of all three hypotheses, but perspectives underlying each encompassed aspects of the species' history. Concordance between mtDNA and nDNA geographic structure revealed three semi-independently evolving phylogroups, whereas signatures of gene flow at nDNA loci were consistent with a historical contact between certain populations as inferred by the BEM. Demographic growth was inferred for all regions despite expectations of postglacial habitat contraction for parts of Beringia. Our results highlight the complementary perspectives on species' histories that multiple lines of evidence provide, and underscore the utility of multilocus data for resolving complex population histories relevant to understanding effects of climate change.