Evidence for multiple Pleistocene refugia in the postglacial expansion of the eastern tiger salamander,Ambystoma tigrinum tigrinum

Abstract Pleistocene glaciations were important determinants of historical migration and, hence, current levels of genetic diversity within and among populations. In many cases, these historical migrations led to the existence of disjunct populations of plants and animals. However, the origin and timing of arrival of these disjunct populations is often debated. In the current study, we identify potential refugia and estimate the timing of vicariance events of the eastern tiger salamander, Ambystoma tigrinum tigrinum , using mitochondrial sequence data. The results suggest a vicariant event 0.75–2 million years ago, separating the tiger salamanders to the east and west of the Apalachicola River Basin. East of the Appalachians, there appear to be multiple independent refugia with little migration among the remaining populations. In particular, populations along the Atlantic Coastal Plain were likely isolated in a coastal plain refugium in the Carolinas. Migrants from this refugium were the likely source of colonists for populations occupying previously glaciated areas along the northeastern Atlantic Coast. A second potential refugium occurs in the Blue Ridge Mountains of western Virginia. This refugium contains a disjunct population of the eastern tiger salamander, as well as a community of nearly 70 other disjunct plant and animal species. The tiger salamanders here have been isolated from other populations for 200,000–500,000 years. These results suggest that disjunct mountain populations of Coastal Plain species may have existed in situ throughout the Pleistocene in Appalachian refugia. Therefore, these disjunct populations are not of recent origin, but rather exist as relicts of a warmer, more widespread fauna and flora that is now restricted to the Coastal Plain.     

Historical demography and genetic structure of sister species: deermice (Peromyscus) in the North American temperate rain forest

To investigate the evolutionary and biogeographical history of Peromyscus keeni and P. maniculatus within the coastal forest ecosystem of the Pacific Northwest of North America, we sampled 128 individuals from 43 localities from southeastern Alaska through Oregon. We analysed mitochondrial DNA variation using DNA sequence data from the mitochondrial cytochrome-b (cyt-b) gene and control region, and we found two distinct clades consistent with the morphological designation of the two species. The sequence divergence between the two clades was 0.0484 substitutions per site for cyt-b and 0.0396 for the control region, suggesting that divergence of the two clades occurred during the middle to late Pleistocene. We also examined the historical demography of the two clades using stepwise and exponential expansion models, both of which indicated recent rapid population growth. Furthermore, using the program migrate we found evidence of migration from populations north of the Fraser River (British Columbia) to the south in both clades. This study demonstrates the utility of these model-based demographic methods in illuminating the evolutionary and biogegographic history of natural systems.     

Phylogeography and Pleistocene refugia of the adder (Vipera berus) as inferred from mitochondrial DNA sequence data

In order to contribute to the debate about southern glacial refugia used by temperate species and more northern refugia used by boreal or cold-temperate species, we examined the phylogeography of a widespread snake species (Vipera berus) inhabiting Europe up to the Arctic Circle. The analysis of the mitochondrial DNA (mtDNA) sequence variation in 1043 bp of the cytochrome b gene and in 918 bp of the noncoding control region was performed with phylogenetic approaches. Our results suggest that both the duplicated control region and cytochrome b evolve at a similar rate in this species. Phylogenetic analysis showed that V. berus is divided into three major mitochondrial lineages, probably resulting from an Italian, a Balkan and a Northern (from France to Russia) refugial area in Eastern Europe, near the Carpathian Mountains. In addition, the Northern clade presents an important substructure, suggesting two sequential colonization events in Europe. First, the continent was colonized from the three main refugial areas mentioned above during the Lower-Mid Pleistocene. Second, recolonization of most of Europe most likely originated from several refugia located outside of the Mediterranean peninsulas (Carpathian region, east of the Carpathians, France and possibly Hungary) during the Mid-Late Pleistocene, while populations within the Italian and Balkan Peninsulas fluctuated only slightly in distribution range, with larger lowland populations during glacial times and with refugial mountain populations during interglacials, as in the present time. The phylogeographical structure revealed in our study suggests complex recolonization dynamics of the European continent by V. berus, characterized by latitudinal as well as altitudinal range shifts, driven by both climatic changes and competition with related species.     

Pleistocene divergence of Dinaric Drusus endemics (Trichoptera, Limnephilidae) in multiple microrefugia within the Balkan Peninsula

The Balkan Peninsula is one of three major European refugial areas. It has high biodiversity and endemism, but data on the age and origin of its fauna, especially endemics, are limited. Mitochondrial sequence data (COI and 16S genes) were used to study the population structure and phylogeography of the caddisfly Drusus croaticus and the phylogeny and divergence of seven other Drusus species, mostly range-restricted endemics of the Dinaric region of the Balkan Peninsula. The divergence of D. croaticus populations in Croatia and allopatric Drusus species in Bosnia dated to the Pleistocene, showing the importance of this time period for the origin and diversification of Balkan endemic taxa. The divergence of more distantly related species dated to the Late Miocene/Early Pliocene. Population genetic and phylogeographic analysis of 115 individuals from 11 populations of D. croaticus revealed a high level of genetic differentiation and absence of gene flow between populations separated by more than 10 km. The existence of allopatrically fragmented lineages in D. croaticus and the endemic Bosnian species is most likely the result of long-term isolation in multiple microrefugia, probably due to the specific habitat requirements and life-history traits of Drusinae coupled with the topographic complexity and historical changes in geomorphology of the region. Overall, these findings shed light on the processes generating the high genetic complexity of this refugial region that parallels the 'refugia within refugia' pattern widely reported from the Iberian refugium.     

Global population structure of the tope (Galeorhinus galeus) inferred by mitochondrial control region sequence data

In order to properly manage and conserve exploited shark species, detailed analyses of their population structure is needed. Global populations of Galeorhinus galeus are in decline due to the exploitation of the fishery over the past 80 years. Currently, the genetic structure of eastern Pacific populations of G. galeus is not known and recent observations in the northeastern Pacific suggest an increase in numbers. To evaluate gene flow among populations of G. galeus , 116 samples were collected and analysed from six geographically dispersed locations: Australia, North America, South Africa, South America (Argentina and Peru), and the UK. Analysis of 968 to 1006 bp of the 1068-bp mitochondrial control region revealed 38 unique haplotypes that were largely restricted to their collecting locality. Significant genetic structure was detected among populations (Φ_ST = 0.84; P  < 0.000001) and migration estimates were low ( Nm  = 0.05–0.97). Due to an apparent lack of migration, populations of G. galeus appear to be isolated from each other with little to no gene flow occurring among them. As a consequence of this isolation, increasing numbers of G. galeus in the northeastern Pacific can be best explained by local recruitment and not by input from geographically distant populations.     

Northern and Southern expansions of Atlantic brown trout (Salmo trutta) populations during the Pleistocene

The phylogeography of Atlantic brown trout ( Salmo trutta ) was analysed using mitochondrial DNA control region complete sequences of 774 individuals from 57 locations. Additionally, the available haplotype information from 100 published populations was incorporated in the analysis. Combined information from nested clade analysis, haplotype trees, mismatch distributions, and coalescent simulations was used to characterize population groups in the Atlantic basin. A major clade involved haplotypes assigned to the Atlantic (AT) lineage, but another major clade should be considered as a distinct endemic lineage restricted to the Iberian Peninsula. The phylogeography of the Atlantic populations showed the mixed distribution of several Atlantic clades in glaciated areas of Northern Europe, whereas diverged haplotypes dominated the coastal Iberian rivers. Populations inhabiting the Atlantic rivers of southern France apparently contributed to postglacial colonization of northern basins, but also comprised the source of southern expansions during the Pleistocene.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 904–917.     

Around or across the Carpathians: colonization model of the Danube basin inferred from genetic diversification of stone loach (Barbatula barbatula) populations

Despite increasing information about postglacial recolonization of European freshwater systems, very little is known about pre-Pleistocene history. We used data on the recent distribution and phylogenetic relationships of stone loach mitochondrial lineages to reconstruct the initial colonization pattern of the Danube river system, one of the most important refuges for European freshwater ichthyofauna. Fine-scale phylogeography of the Danubian populations revealed five highly divergent lineages of pre-Pleistocene age and suggested the multiple origin of the Danubian stone loach. The mean sequence divergence among lineages extended from 7.0% to 13.4%, which is the highest intraspecific divergence observed so far within this river system. Based on the phylogeographical patterns, we propose the following hypothesis to relate the evolution and dispersal of the studied species with the evolution of the Danube river system and the Carpathian Mountains: (i) during the warmer period in the Miocene, the areas surrounding the uplifting Alps and Carpathians served as mountainous refuges for cold-water adapted fish and promoted the diversification of its populations, and (ii) from these refuges, colonization of the emerging Danube river system may have taken place following the retreat of the Central Paratethys. Co-existence of highly divergent mtDNA lineages in a single river system shows that range shifts in response to climatic changes during the Quaternary did not cause extensive genetic homogenization in the stone loach populations. However, the wide distribution of some mtDNA lineages indicates that the Pleistocene glaciations promoted the dispersal and mixing of populations through the lowlands.     

A phylogeographic analysis of populations of the wood turtle (Glyptemys insculpta) throughout its range

We investigated the phylogeography of wood turtles, Glyptemys insculpta, in North America using 750 bp of the mitochondrial control region from 117 individuals sampled at 29 localities across the species' range. A total of 21 haplotypes were identified and little genetic variation was found. The highest pairwise difference was 2%. From nested clade analysis (NCA), one main postglacial dispersal route was inferred along the east coast, with subsequent westward dispersal. NCA further revealed some patterns of restricted gene flow/dispersal. We propose that wood turtles experienced a combined effect of bottleneck during the Pleistocene as well as of selective sweep, which produced the low level of variation observed. Following the Pleistocene, wood turtles would have undergone a rapid northward expansion from a common southern refugium as glaciers retreated. These findings shed light on where to direct conservation priorities, on conservation strategies needed, and on the potential effects of interpopulation transfers for this vulnerable species.     

Morphometric convergence and molecular divergence: the taxonomic status and evolutionary history of Gymnura crebripunctata and Gymnura marmorata in the eastern Pacific Ocean

To clarify the taxonomic status of Gymnura crebripunctata and Gymnura marmorata , the extent of morphological and nucleotide variation between these nominal species was examined using multivariate morphological and mitochondrial DNA comparisons of the same characters with congeneric species. Discriminant analysis of 21 morphometric variables from four species ( G. crebripunctata , G. marmorata , Gymnura micrura and Gymnura poecilura ) successfully distinguished species groupings. Classification success of eastern Pacific species improved further when specimens were grouped by species and sex. Discriminant analysis of size-corrected data generated species assignments that were consistently accurate in separating the two species (100% jackknifed assignment success). Nasal curtain length was identified as the character which contributed the most to discrimination of the two species. Sexual dimorphism was evident in several characters that have previously been relied upon to distinguish G. crebripunctata from G. marmorata . A previously unreported feature, the absence of a tail spine in G. crebripunctata , provides an improved method of field identification between these species. Phylogenetic and genetic distance analyses based on 698 base pairs of the mitochondrial cytochrome b gene indicate that G. crebripunctata and G. marmorata form highly divergent lineages, supporting their validity as distinct species. The closely related batoid Aetoplatea zonura clustered within the Gymnura clade, indicating that it may not represent a valid genus. Strong population structuring (overall Φ _ST = 0·81 ,P < 0·01) was evident between G. marmorata from the Pacific coast of the Baja California peninsula and the Gulf of California, supporting the designation of distinct management units in these regions.     

Late Pleistocene lineage divergence among populations of Neolitsea sericea (Lauraceae) across a deep sea‐barrier in the Ryukyu Islands

Aim Our goals were: (1) to assess the population genetic structure and demographic divergence history of a bird‐dispersed tree, Neolitsea sericea, endemic to East Asian land‐bridge islands; and (2) to interpret the results in the light of controversies over the dating and configurations of land bridges through the Japanese Ryukyu Island Arc. Location Japan–Ryukyu–Taiwan Island Arc and Chinese/Korean offshore islands. Methods We applied 10 nuclear microsatellites (nSSRs) and one chloroplast (cp) DNA sequence marker (psbA–trnH intergenic spacer) to 31 populations (397 and 326 individuals, respectively) from throughout the species’ range to infer current patterns of genetic diversity and structure, and pollen‐to‐seed migration ratios (r). A coalescent‐based isolation‐with‐migration (IM) model was applied to the combined nSSR/cpDNA data set to estimate lineage divergence times and population demographic parameters. Results The geographic structure of nSSRs and the distribution of most cpDNA haplotypes revealed two distinct lineages located in areas north and south of the ‘Tokara Gap’, a narrow (c. 37 km wide) but deep (> 1000 m) sea‐strait between the northern and central Ryukyus. Based on the IM analyses, we (1) dated the divergence of these northern and southern lineages to c. 0.07 Ma (90% highest posterior density interval: 0.02–0.38 Ma); (2) estimated a slightly smaller effective population size for the northern compared to the southern lineage; and (3) recovered only trivial signals of post‐divergence gene flow between them. Main conclusions The estimated divergence time for northern and southern lineages is consistent with geological evidence for the existence of land connections in the Tokara region during cold stages of the latest Pleistocene; it is thus incompatible with an ‘ancient sea‐barrier hypothesis’ for the Ryukyu Arc, where we would have expected much older divergences related to the initial formation of the Tokara and Kerama tectonic straits during the Pliocene. Multiple factors are likely to have had a role in the divergence of N. sericea, including not only land‐bridge submergence, but also island configuration, and/or constraints on adaptation along a latitudinal temperature gradient.     

Divergence and biogeography of the recently evolved Macaronesian red Festuca (Gramineae) species inferred from coalescence-based analyses

Studying the biogeography and the phylogeography of the endemic Macaronesian red Festuca species (Loliinae, Poaceae) is of prime interest in understanding the speciation and colonization patterns of recently evolved groups in oceanic archipelagos. Coalescence‐based analyses of plastid trnLF sequences were employed to estimate evolutionary parameters and to test different species‐history scenarios that model the pattern of species divergence. Bayesian IM estimates of species divergence times suggested that ancestral lineages of diploid Macaronesian and Iberian red fescues could have diverged between 1.2 and 1.57 Ma. When empirical data were compared to coalescence‐based simulated distributions of discordance and p‐distance statistics, two species‐history models were chosen in which the first branching lineage derived in Canarian Festuca agustinii. Its sister lineage could have involved a recent polytomy leading to the Madeiran Festuca jubata, the Azorean Festuca francoi + Festuca petraea and the continental Festuca rivularis lineages (Canarian model) or the sequential branching of lineages leading to F. jubata and finally to the sister clades of F. rivularis and F. francoi + F. petraea (Sequential model). Nested clade phylogeographic analysis (NCPA) and a first adapted host–parasite co‐evolutionary ParaFit method were used to detect the phylogeographic signal. NCPA inferred long‐distance colonizations for the entire diploid red Festuca complex, but allopatric‐fragmentation and isolation‐by‐distance (IBD) patterns were inferred within archipelagos. In addition, the ParaFit method suggested a generalized pattern of a stepping‐stone model at all hierarchical levels. Maximum‐likelihood‐based dispersal‐extinction‐cladogenesis (DEC) models were superimposed on the Sequential model species tree. The three‐independent‐colonization (3IC) model was the best supported biogeographic scenario, concurring with previous analysis based on multilocus AFLP data.     

Phylogeography of the white-breasted nuthatch (Sitta carolinensis): diversification in North American pine and oak woodlands

Pine and oak woodlands are common North American floral communities with distinct regional species composition. The white-breasted nuthatch (Aves: Sitta carolinensis) is a common resident bird of North American pine and oak woodlands, and is distributed continentally across the highly disjunct distribution of these woodlands. We propose three historical hypotheses to explain the evolution of the white-breasted nuthatch in its principal habitat. (i) The species evolved in situ in the regional pine-oak communities and the isolation of populations in these regions is captured in cryptic genetic variation. (ii) Migration of individuals between regions is frequent enough to maintain the widespread distributions and prevent regional divergence. (iii) The species have recently expanded to occupy their current distributions and an insufficient amount of time has passed for divergence to occur. Phylogenetic analysis of mitochondrial DNA (ND2 gene) variation (N = 216) in the white-breasted nuthatch reveals four reciprocally monophyletic clades concordant with the distribution of the regional North American pine and oak woodlands, and supports hypothesis 1 of in situ evolution of populations in the regional pine and oak communities. Within-clade population structure and demographic history are also discussed.     

Mitogenomic phylogenetic analyses of Leptogorgia virgulata and Leptogorgia hebes (Anthozoa: Octocorallia) from the Gulf of Mexico provides insight on Gorgoniidae divergence between Pacific and Atlantic lineages

The use of genetics in recent years has brought to light the need to reevaluate the classification of many gorgonian octocorals. This study focuses on two Leptogorgia species—Leptogorgia virgulata and Leptogorgia hebes—from the northwestern Gulf of Mexico (GOM). We target complete mitochondrial genomes and mtMutS sequences, and integrate this data with previous genetic research of gorgonian corals to resolve phylogenetic relationships and estimate divergence times. This study contributes the first complete mitochondrial genomes for L. ptogorgia virgulata and L. hebes. Our resulting phylogenies stress the need to redefine the taxonomy of the genus Leptogorgia in its entirety. The fossil‐calibrated divergence times for Eastern Pacific and Western Atlantic Leptogorgia species based on complete mitochondrial genomes shows that the use of multiple genes results in estimates of more recent speciation events than previous research based on single genes. These more recent divergence times are in agreement with geologic data pertaining to the formation of the Isthmus of Panama.     

Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards

Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z‐linked sex chromosome loci. Between the two taxa, Z‐linked loci (Φ_ST = 0.088) were 5.2 times more differentiated than autosomal DNA (Φ_ST = 0.017) but comparable to mtDNA (Φ_ST = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z‐linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (Φ_ST) and absolute (d_XY) estimates of divergence. In contrast, the ratio of Z‐linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (Φ_ST = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.     

Chloroplast DNA supports a hypothesis of glacial refugia over postglacial recolonization in disjunct populations of black pine (Pinus nigra) in western Europe

European black pine (Pinus nigra Arn.) is a widely distributed Mediterranean conifer. To test the hypothesis that fragmented populations in western Europe survived in situ during the last glacial rather than having been re-colonized in the postglacial period, genetic variation was assessed using a suite of 10 chloroplast DNA microsatellites. Among 311 individuals analysed, 235 haplotypes were detected revealing high levels of chloroplast haplotype diversity in most populations. Bayesian analysis using a model of linked loci, with no prior assumption of population structure, assigned individuals to 10 clusters that corresponded well with the six predefined sampling regions, while an analysis carried out at the population level and assuming unlinked loci, recovered the original six sampling regions. This regional structure was supported by a biogeographical analysis that detected five barriers, with the two most significant separating Alps from Corsica and southern Italy, and southern Spain from the Pyrenees. No signals of demographic expansion were detected, and comparisons of R(ST) with pR(ST) suggested that a stepwise mutational model was important in regional differentiation, but not in population-within-region differentiation. These tests support long-term persistence of the species within the six regions. The temporal depth estimate, assuming a high mutation rate in coalescent modelling, placed the deepest split between the Alps and the other regions at about 150 000 years ago, and the most recent split of Pyrenees from southern France at about 30 000 years ago. Taken together, the data suggest that chloroplast DNA is structured in black pine and disjunct populations in western Europe are likely to have been present during the Last Glacial Maximum.     

Effects of Pleistocene climatic fluctuations on the phylogeographic and demographic histories of Pacific herring (Clupea pallasii)

We gathered mitochondrial DNA sequences (557 bp from the control region in 935 specimens and 668 bp of the cytochrome b gene in 139 specimens) of Pacific herring collected from 20 nearshore localities spanning the species' extensive range along the North Pacific coastlines of Asia and North America. Haplotype diversity and nucleotide diversity were high, and three major phylogeographic lineages (sequence divergences ca. 1.5%) were detected. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidence, we infer that the genetic make-up of extant populations of C. pallasii was shaped by Pleistocene environmental impacts on the historical demography of this species. A deep genealogical split that cleanly distinguishes populations in the western vs. eastern North Pacific probably originated as a vicariant separation associated with a glacial cycle that drove the species southward and isolated two ancestral populations in Asia and North America. Another deep genealogical split may have involved either a vicariant isolation of a third herring lineage (perhaps originally in the Gulf of California) or it may have resulted simply from the long coalescent times that are possible in large populations. Coalescent analyses showed that all the three evolutionary lineages of C. pallasii experienced major expansions in their most recent histories after having remained more stable in the preceding periods. Independent of the molecular calibration chosen, populations of C. pallasii appear to have remained stable or grown throughout the periods that covered at least two major glaciations, and probably more.     

Time to the most recent common ancestor and divergence times of populations of common chaffinches (Fringilla coelebs) in Europe and North Africa: insights into Pleistocene refugia and current levels of migration

We analyzed sequences from a 275-bp hypervariable region in the 5' end of the mitochondrial DNA control region in 190 common chaffinches (Fringilla coelebs) from 19 populations in Europe and North Africa, including new samples from Greece and Morocco. Coalescent techniques were applied to estimate the time to the most recent common ancestor (TMRCA) and divergence times of these populations. The first objective of this study was to infer the locations of refugia where chaffinches survived the last glacial episode, and this was achieved by estimating the TMRCA of populations in regions surrounding the Mediterranean that were unglaciated in the late Pleistocene. Although extant populations in Iberia, Corsica, Greece, and North Africa harbor haplotypes that are basal in a phylogenetic tree, this information alone cannot be used to infer that these localities served as refugia, because it is impossible to infer the ages of populations and their divergence times without also considering the population genetic processes of mutation, migration, and drift. Provided we assume the TMRCAs of populations are a reasonable estimate of a population's age, coalescent-based methods place resident populations in Iberia, Corsica, Greece, and North Africa during the time of the last glacial maximum, suggesting these regions served as refugia for the common chaffinch. The second objective was to determine when populations began diverging from each other and to use this as a baseline to estimate current levels of gene flow. Divergence time estimates suggest that European populations began diverging about 60,000 years before present. The relatively recent divergence of populations in North Africa, Italy, and Iberia may explain why classic migration estimates based on equilibrium assumptions are high for these populations. We compare these estimates with nonequilibrium-based estimates and show that the nonequilibrium estimates are consistently lower than the equilibrium estimates.     

Genetic consequences of Pleistocene glaciations for the tundra vole (Microtus oeconomus) in Beringia

Repeated glacial events during the Pleistocene fragmented and displaced populations throughout the northern continents. Different models of the effects of these climate-driven events predict distinct phylogeographic and population genetic outcomes for high-latitude faunas. The role of glaciations in (i) promoting intraspecific genetic differentiation and (ii) influencing genetic diversity was tested within a phylogeographic framework using the rodent Microtus oeconomus. The spatial focus for the study was Beringia, which spans eastern Siberia and northwestern North America, and was a continental crossroads and potential high arctic refugium during glaciations. Variation in mitochondrial DNA (cytochrome b and control region; 214 individuals) and nuclear DNA (ALDH1 intron; 63 individuals) was investigated across the Beringian region. Close genetic relationships among populations on either side of the Bering Strait are consistent with a history of periodic land connections between North America and Asia. A genetic discontinuity observed in western Beringia between members of a Central Asian clade and a Beringian clade is geographically congruent with glacial advances and with phylogeographic discontinuities identified in other organisms. Divergent island populations in southern Alaska were probably initially isolated by glacial vicariance, but subsequent differentiation has resulted from insularity. Tests of the genetic effects of postglacial colonization were largely consistent with expansion accompanied by founder effect bottlenecking, which yields reduced diversity in populations from recently deglaciated areas. Evidence that populations in the Beringian clade share a history of expansion from a low-diversity ancestral population suggests that Beringia was colonized by a small founder population from central Asia, which subsequently expanded in isolation.     

Late Pleistocene divergence and postglacial expansion in the Brazilian Atlantic Forest: multilocus phylogeography of Rhopias gularis (Aves: Passeriformes)

In the last decade, phylogeographic studies have revealed a complex evolutionary history of the Brazilian Atlantic Forest (AF) biota. Here, we investigated the evolutionary history of Rhopias gularis, an endemic bird of the AF, based on sequences of two mitochondrial genes and three nuclear introns from 64 specimens from 15 localities. We addressed three main questions: (1) Does the genetic diversity of R. gularis exhibit a distribution pattern congruent with the refuge hypothesis postulated for the AF? (2) Is the population genetic structure of R. gularis congruent with those observed in other AF species? (3) What were the possible historical events responsible for the population structure of this species? Our mtDNA data revealed two phylogroups: (1) phylogroup central‐south, with samples from the central and southern parts of the range; (2) and phylogroup north, which included individuals from southern Bahia. Nevertheless, nuclear loci did not reveal any evidence of population structure. Bottleneck tests indicated that the central‐south lineage experienced demographic expansion, starting around 20 kya, which coincides with the end of the last glacial maximum. However, there was no evidence of population growth in phylogroup north. Isolation with migration analysis indicated that these phylogroups split c.a. 304 kya, with limited gene flow among them. Palaeodistribution models indicated that R. gularis had a reduced distribution in the south and central AF during the last glacial maximum. Our results support a diversification scenario that is in accordance with proposed Pleistocene refugia. The phylogeographic results from our study exhibited spatial and temporal concordances and discordances with previous studies of organisms from the AF. Differences in habitat requirements of these species could be behind this complex scenario. Future studies correlating variables of the niche of these species with the observed phylogeographic patterns may help understand why there are congruent and incongruent results.