Nested Clade Phylogeographic Analysis Research Articles

Chloroplast DNA polymorphism reveals geographic structure and introgression in theQuercus crassifolia ×Quercus crassipeshybrid complex in Mexico

Quercus crassifolia H. & B. and Quercus crassipes H. & B. are two common temperate forest species in Mexico that form hybrids when they occur in mixed (sympatric) areas. In this study, we used chloroplast microsatellite haplotypes to infer phylogeographic patterns onto the genetic structure of populations of both parental species, thus defining probable colonization routes throughout Mexico. Haplotype diversity in seven hybrid zones and four allopatric sites with nonmixed (allopatric) populations of both putative parental species was analyzed. To determine the expansion and colonization routes for the two species, we carried out a nested clade phylogeographic analysis that would allow us to infer the haplotype correspondence to a phylogeographical approach. In spite of sharing many common populations, we determined that there is a different genetic historical colonization for Q. crassipes and for Q. crassifolia. Hybrid populations had the highest levels of genetic variation (Gv), Shannon diversity index (H), and haplotype number (nh) in comparison with nonmixed/allopatric populations of their putative parentals. Furthermore, populations of hybrid zones showed the highest values of genetic differentiation FST, RST. Moreover, both species share four distinctive cpDNA haplotypes, which were most likely acquired by introgression through hybrids located in several populations throughout the Eje Neovolcánico area. This last region was confirmed to be a “hot spot” for oak diversity, a place in which different maternal lineages merged.

Babies and bathwater: a comment on the premature obituary for nested clade phylogeographical analysis

Babies and bathwater: a comment on the premature obituary for nested clade phylogeographical analysis

The coup de grâce for the nested clade phylogeographic analysis?

Nested clade phylogeographic analysis (NCPA) has become a popular method for reconstructing the history of populations across species ranges. Ever since its invention in 1995, criticisms have been formulated, but the method, which has been regularly updated, continues to attract investigators. Molecular Ecology has published a large fraction of the literature on the topic--both pro and con. A recent study by Panchal and Beaumont (2007) finally allows a precise evaluation of the method by developing software that automates the somewhat complicated NCPA procedure. Using simulations of random-mating populations, Panchal and Beaumont find a high frequency of false-positives with their automated NCPA procedure (over 75%). These findings, which echo and amplify earlier warnings, appear serious enough to suggest to researchers to await further evaluation of the method. Although no other all-encompassing method such as the NCAP currently exists to evaluate phylogeographic data sets, researchers have many alternative methods to test ever more refined hypotheses.

Recent volcanism and mitochondrial DNA structuring in the lizard Gallotia atlantica from the island of Lanzarote

The phylogeography of the lacertid lizard Gallotia atlantica from the small volcanic island of Lanzarote (Canary Islands) was analysed based on 1075 bp of mitochondrial DNA (mtDNA) sequence (partial cytochrome b and ND2) for 157 individuals from 27 sites (including three sites from neighbouring islets). Levels of sequence divergence were generally low, with the most distant haplotypes separated by only 14 mutational steps. MtDNA divergence appears to coincide with formation of the middle Pleistocene lowland that united formerly separate ancient islands to form the current island of Lanzarote, allowing rejection of a two-island model of phylogeographical structure. There was evidence of large-scale population expansion after island unification, consistent with the colonization of new areas. A nested clade phylogeographical analysis (NCPA) revealed significant phylogeographical structuring. Two-step and higher-level clades each had disjunct distributions, being found to the east and west of a common area with a north-south orientation that extends between coasts in the centre-east of the island (El Jable). Other clades were almost entirely restricted to the El Jable region alone. Bayesian Markov chain Monte Carlo analyses were used to separate ongoing gene flow from historical associations. These supported the NCPA by indicating recent (75,000-150,000 years ago) east-west vicariance across the El Jable region. Lava flows covered El Jable and other parts of the central lowland at this time and likely led to population extinctions and temporary dispersal barriers, although present-day evidence suggests some populations would have survived in small refugia. Expansion of the latter appears to explain the presence of a clade located between the eastern and western components of the disjunct clades. Direct relationships between mtDNA lineages and morphology were not found, although one of two morphological forms on the island has a disjunct distribution that is broadly concordant with east-west components of the phylogeographical pattern. This work demonstrates how recent volcanic activity can cause population fragmentation and thus shape genetic diversity on microgeographical scales.

Comparative phylogeography of bagrid catfishes in Taiwan

A phylogeographic analysis of two bagrid catfishes in Taiwan was conducted using sequence data from a portion of the mitochondrial DNA (mtDNA) control region. For Pseudobagrus brevianalis, which is most probably endemic to Taiwan, a total of eight haplotypes were detected in 189 specimens from nine river systems covering its entire distribution range, from northern to central western areas of the island. Obvious genetic differentiation was observed among its populations (average F ST = 0.753); in particular, the northernmost Tamsui River population was fixed for a single endemic haplotype. Nested clade phylogeographic analysis (NCPA) indicated that the dispersal center of mtDNA was the area around the Touchien River and Holong River, north to the Miaoli Plateau, in northwestern Taiwan, suggesting both northward and southward dispersal in this species. There was no evidence for the validity of P. taiwanensis, the nominal species described from Taiwan, morphologically similar to P. brevianalis. We confirmed that P. adiposalis was distributed discontinuously in three river systems; analysis of 42 specimens from the rivers indicated a total of four haplotypes and population differentiation (average F ST = 0.876). Fixation into a largely differentiated haplotype in the northernmost Tamsui River population was also found in this species, but different processes for this phylogeographic pattern were implied for the two species. Comparison with P. ussuriensis, a widespread continental species morphologically similar to P. adiposalis, suggested the possibility that P. adiposalis is a group of local populations of P. ussuriensis in Taiwan. Two migration routes vs. random fixation scenarios for the population structure of P. adiposalis are discussed with information on other fishes and the geological history of the island.

Fossorial but widespread: the phylogeography of the common spadefoot toad (Pelobates fuscus), and the role of the Po Valley as a major source of genetic variability

Pelobates fuscus is a fossorial amphibian that inhabits much of the European plain areas. To unveil traces of expansion and contraction events of the species' range, we sequenced 702 bp of the mitochondrial cytochrome b gene. To infer the population history we applied phylogeographical methods, such as nested clade phylogeographical analysis (NCPA), and used summary statistics to analyse population structure under a neutral model of evolution. Populations were assigned to different drainage systems and we tested hypotheses of explicit refugial models using information from analysis of molecular variance, nucleotide diversity, effective population size estimation, NCPA, mismatch distribution and Bayesian dating. Coalescent simulations were used as post hoc tests for plausibility of derived or a priori assumed biogeographical hypotheses. Our combination of all approaches enabled the reconstruction of the colonization history and phylogeography of P. fuscus and confirmed a previous assumption of the existence of two major genetic lineages within P. fuscus. Using the Afro-European vicariance of Pelobates cultripes and Pelobates varaldii and applying Bayesian dating we estimated the divergence of these phylogeographical lineages to the Pliocene. We suggest the existence of three different glacial refugia: (i) the area between the Caspian and Black Seas as the origin for the expansion of the 'eastern lineage'; (ii) the Danube system as a centre of diversity for part of the 'western lineage'; (iii) the Po Valley, the largest centre of genetic variability. This fits the hypothesis that climatic fluctuation was a key event for differentiation processes in P. fuscus.

Phylogeography of a ground beetle species in La Gomera (Canary Islands): the effects of landscape topology and population history

Paraeutrichopus pecoudi (Coleoptera, Carabidae) is a species endemic to the mountain laurel forests of La Gomera in the Canary archipelago. La Gomera is an island of volcanic origin (9.4 mya), where a well-preserved laurel forest is partly fragmented by valleys and ridges. Historically restricted gene flow with isolation by distance are deduced at different clade levels for P. pecoudi populations, an expected scenario arising from landscape discontinuity, which has caused local isolation of these flightless insects. Methodological considerations were investigated for nested clade phylogeographic analysis (NCPA), comparing the results obtained using either (a) pairwise distances between collecting sites measured as surface (route) distances or (b) standard geographical distances calculated from latitude-longitude coordinates. Some differences were found in the NCPA statistics and associated inferences at the higher clade levels in relation to the assumed distance criteria. Coalescent simulations and posterior automated NCPAs assuming different geographical distances were performed to test the robustness of the method when considering the distances used. These analyses showed no significant differences in NCPA conclusions, and the scenario of restricted gene flow was recovered using both distance calculators at the same rate, although the parameter statistics were slightly different. We suggest that in landscapes with extreme topography, geographical distances separating populations are certainly underestimated by standard techniques. More complex and explicit descriptions of the potential dispersal of terrestrial organisms should be explored for implementation in statistical phylogeography in such cases.

THE AUTOMATION AND EVALUATION OF NESTED CLADE PHYLOGEOGRAPHIC ANALYSIS

Nested clade phylogeographic analysis (NCPA) is a popular method for reconstructing the demographic history of spatially distributed populations from genetic data. Although some parts of the analysis are automated, there is no unique and widely followed algorithm for doing this in its entirety, beginning with the data, and ending with the inferences drawn from the data. This article describes a method that automates NCPA, thereby providing a framework for replicating analyses in an objective way. To do so, a number of decisions need to be made so that the automated implementation is representative of previous analyses. We review how the NCPA procedure has evolved since its inception and conclude that there is scope for some variability in the manual application of NCPA. We apply the automated software to three published datasets previously analyzed manually and replicate many details of the manual analyses, suggesting that the current algorithm is representative of how a typical user will perform NCPA. We simulate a large number of replicate datasets for geographically distributed, but entirely random-mating, populations. These are then analyzed using the automated NCPA algorithm. Results indicate that NCPA tends to give a high frequency of false positives. In our simulations we observe that 14% of the clades give a conclusive inference that a demographic event has occurred, and that 75% of the datasets have at least one clade that gives such an inference. This is mainly due to the generation of multiple statistics per clade, of which only one is required to be significant to apply the inference key. We survey the inferences that have been made in recent publications and show that the most commonly inferred processes (restricted gene flow with isolation by distance and contiguous range expansion) are those that are commonly inferred in our simulations. However, published datasets typically yield a richer set of inferences with NCPA than obtained in our random-mating simulations, and further testing of NCPA with models of structured populations is necessary to examine its accuracy.

Phylogeography and Introgressive Hybridization of the Ground Beetle Carabus yamato in Japan Based on Mitochondrial Gene Sequences

To study the phylogeography of the ground beetle Carabus yamato in Japan, we compared 1,020-bp sequences of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene from 373 specimens from 37 localities with those of three parapatric species (C. albrechti, C. kimurai, and C. japonicus) that might share mitochondrial lineages with C. yamato through introgressive hybridization. We found 81 haplotypes from C. yamato. Of these, 17 haplotypes were considered to be of an introgressed lineage from C. albrechti, based on the phylogeny and geographic distribution. In addition, one haplotype of C. kimurai was likely an introgressant from C. yamato. Putative introgression events among the four species were restricted to these two directional cases. We analyzed the phylogeography of C. yamato using nested clade phylogeographical analysis and population genetic parameters. The mitochondrial lineages of C. yamato were estimated to have diverged no more than approximately 1.12 million years ago, implying that the estimated historical events occurred after the Early Pleistocene. Carabus yamato was inferred to have experienced a contraction of its distribution range, followed by recent range expansion. Populations in the western and eastern regions, segregated by Ise Bay and the Nobi and Okazaki Plains, diverged in the mitochondrial clades. The northern and most western populations possessed one clade only (except an introgressed lineage), whereas eastern and some southwestern populations possessed several diverged clades, which were considered to be ancestral; these populations may have been associated with refugia during glacial periods.

Phylogeographic patterns of trans‐Amazonian vicariants and Amazonian biogeography: the Neotropical rattlesnake (Crotalus durissus complex) as an example

AbstractAim To investigate the phylogeography and execute a historical‐demographic analysis of the Neotropical rattlesnake, Crotalus durissus, thereby testing the hypothesis of a Pleistocene central Amazon corridor of dry forest or savanna that partitioned the Amazonian rain forest into western and eastern portions.Location South America.Methods Using sequences of three mitochondrial genes, we estimated the phylogeography, gene and nucleotide diversity across the South American range of C. durissus. Tree topology tests were used to test alternative biogeographical hypotheses, and tests of population genetic structure and statistical parsimony networks and nested clade phylogeographic analysis (NCPA) were used to infer connectivity and historical population processes on both sides of the Amazon basin.Results Tree topology tests rejected the hypothesis of a coastal dispersal in favour of a central corridor scenario. Gene diversity was similar on both sides of the Amazon basin. Nucleotide diversity indicated that the populations from north of the Amazon basin represented ancestral populations. Analysis of molecular variance (amova) showed that intra‐population molecular variation was greater than between regions. Historical‐demographic statistics showed significant population expansion south of the Amazon, and little differentiation in the north, indicating moderate past gene flow between north and south of the Amazon. The parsimony network connected clades from the Roraima and Guyana populations with Mato Grosso, suggesting an Amazonian central corridor, and NCPA supported allopatric fragmentation between north and south of the Amazon.Main conclusions The distribution of C. durissus on both sides of the Amazon basin is evidence of changes in the distribution of rain forest vegetation during the Pleistocene. Our results suggest a formerly continuous distribution of this rattlesnake along a central Amazonian corridor during the middle Pleistocene. Allopatric fragmentation inferred from NCPA is consistent with vicariance resulting from a subsequent closure of this habitat corridor. This study emphasizes the potential of trans‐Amazonian open formation species to inform the debate on the past distribution of rain forests in the Amazon Basin.

Genetic diversity and historical population structure of Schizopygopsis pylzovi (Teleostei: Cyprinidae) in the Qinghai–Tibetan Plateau

Summary1. Complete sequences of 1140 base pair of the cytochrome b gene from 133 specimens were obtained from nine localities including the inflow drainage system, isolated lakes and outflow drainage system in Qinghai–Tibetan Plateau to assess genetic diversity and to infer population histories of the freshwater fish Schizopygopsis pylzovi.2. Nucleotide diversities (π) were moderate (0.0024–0.0045) in populations from the outflow drainage system and Tuosuo Lake, but low (0.0018–0.0021) in populations from Qiadam Basin. It is probable that the low intra‐population variability is related with the paleoenvironmental fluctuation in Qiadam Basin, suggesting that the populations from Qiadam Basin have experienced severe bottleneck events in history.3. Phylogenetic tree topologies indicate that the individuals from different populations did not form reciprocal monophyly, but the populations from the adjacent drainages cluster geographically. Most population pairwise FST tests were significant, with non‐significant pairwise tests between Tuosu Lake and Tuosuo Lake in the north‐west of the Qinghai–Tibetan Plateau. Analysis of molecular variance (amova) indicates that the significant genetic variation was explained at the levels of catchments within and among, not among specific boundaries or inflow and outflow drainage systems.4. The nested clade phylogeographical analysis indicates that historical processes are very important in the observed geographical structuring of S. pylzovi, and the contemporary population structure and differentiation of S. pylzovi may be consistent with the historical tectonic events occurred in the course of uplifts of the Qinghai–Tibetan Plateau. Fluctuations of the ecogeographical environment and major hydrographic formation might have promoted contiguous range expansion of freshwater fish populations, whereas the geological barriers among drainages have resulted in the fragmentation of population and restricted the gene flow among populations.5. The significantly large negative Fs‐value (−24.91, P < 0.01) of Fu's Fs‐test and the unimodal mismatch distribution indicate that the species S. pylzovi underwent a sudden population expansion after the historical tectonic event of the Gonghe Movement.6. The results of this study indicate that each population from the Qinghai–Tibetan Plateau should be managed and conserved separately and that efforts should be directed towards preserving the genetic integrity of each group.

Intraspecific genetic analysis of the summer tanagerPiranga rubra: implications for species limits and conservation

The summer tanagerPiranga rubrais a Neotropical migrant that has experienced noted declines in the southwestern United States caused by extensive habitat loss of native riparian woodlands. This species is composed of two morphologically and behaviorally distinct taxa that traditionally have been recognized as subspecies, each occupying unique habitats in the southern part of North America. Genetic analyses of intraspecific variation are important in studies of threatened or endangered species because they can indicate whether smaller management units exist below the species level and they also provide estimates of within population variability. Using a mitochondrial DNA marker, the intraspecific genetic variation of this species is explored to determine whether the morphologically and behaviorally distinct subspecies are also genetically unique. By using traditional phylogenetic methods and building haplotype networks, results from this study indicate that the subspecies represent two phylogenetic species and should be managed as separate units. In addition, the level of gene flow among geographically isolated populations of the western subspecies is explored using Nested Clade Phylogeographic Analysis and population genetic tests. These analyses show that populations are genetically diverse and that haplotypes are shared across populations. Newly colonized populations are as diverse as older populations. This suggests that as habitat degrades in traditional breeding areas of the summer tanager, if suitable habitat elsewhere becomes available for new populations, these new colonies should be genetically diverse.

PHYLOGEOGRAPHY AND GENETIC STRUCTURE IN THE CNEMIDOPHORUS LONGICAUDA COMPLEX (SQUAMATA, TEIIDAE)

Cnemidophorus longicauda is a poorly-studied species of whiptail lizard distributed in the Monte Desert region of Argentina. Some variation in dorsal color pattern has been observed between northern and southern populations along the latitudinal range of the species. Recently, a new species of Cnemidophorus (C. tergolaevigatus) previously considered as C. longicauda has been described, although no comparative morphological study has been conducted. In this study we use the mitochondrial ND4 gene region to examine the phylogeography and genetic structure of this species complex. Phylogenetic reconstruction, Nested Clade Phylogeographic Analysis, and AMOVA reveal deep genetic divergence between northern and southern populations that are geographically separated by the Famatina-Sanogasta Mountains. Because most of the localities of C. tergolaevigatus are from the general region of the ''northern group'' recovered in this study, there is general concordance between geographic patterns of mtDNA and morphological (color pattern) variation, and thus support for the recognition of this species. We discuss this genetic break and the phylogenetic/phylogeographic history of the Cnemidophorus in the context of other lizard species with similar distributions, and the implications for understanding the evolutionary history of the temperate South American biota.

The automation of Nested Clade Phylogeographic Analysis

ANeCA is a fully automated implementation of Nested Clade Phylogeographic Analysis. This was originally developed by Templeton and colleagues, and has been used to infer, from the pattern of gene sequence polymorphisms in a geographically structured population, the historical demographic processes that have shaped its evolution. Until now it has been necessary to perform large parts of the procedure manually. We provide a program that will take data in Nexus sequential format, and directly output a set of inferences. The software also includes TCS v1.18 and GeoDis v2.2 as part of automation. The software is available free of charge from http://www.rubic.rdg.ac.uk/~mahesh/software.html. The program is written in Java and requires the Java 1.4 Runtime Environment (or later) to run. The source code is included in the package, and includes the source from TCS and GeoDis. ANeCA, TCS and GeoDis are released under the GNU General Public License.

Congeneric phylogeography: hypothesizing species limits and evolutionary processes in Patagonian lizards of the Liolaemus boulengeri group (Squamata: Liolaemini)

In poorly known groups for which data are insufficient to develop biologically plausible model-based approaches to phylogeographical analyses, a ‘first hypotheses’ protocol is suggested as offering the best way to generate hypotheses for subsequent model-based tests. Preliminary hypotheses are formulated about species boundaries and population processes in three species complexes of the Liolaemus boulengeri group in the context of mtDNA ‘congeneric phylogeography’. The temperate South American Liolaemus provides a model with ancient and recent allopatric divergence across ecologically and geologically complex landscapes, incipient speciation, secondary contact, and discordance between molecular and morphological patterns of variation. Moderately dense sampling of widely distributed ‘inertial’ species in the Patagonian Steppe has revealed hidden genetic and probably species diversity, and also hinted at demographic and historical processes that may have shaped the histories of these taxa. Five of the seven focal species of the present study were paraphyletic for mtDNA genealogies, suggesting that they represent complexes of species, and nested clade phylogeographical analysis (NCPA) analyses suggest that different historical and demographic processes have shaped the observed patterns. Introgression and incomplete lineage sorting are hypothesized as being the cause of some of the observed paraphyly. Provisional delimitations of species are proposed and NCPA is used to generate hypotheses of population history, all of which are subject to further testing. Multi-faceted studies, involving phylogenetic assessments of independent molecular markers and morphological variation across codistributed taxa with estimates of niche breadths in a landscape context, will likely yield the most promising returns for cross-validation of hypotheses of population and speciation histories. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89, 241–275.

Intraspecific Phylogeography and Adaptive Divergence in the White-Headed Woodpecker

AbstractThis study uses mitochondrial DNA (mtDNA) to examine the phylogeography of the White-headed Woodpecker (Picoides albolarvatus), one of the least-studied woodpeckers in North America. A mismatch distribution and calculation of Tajima's D indicate that the overall phylogeographic history of the species is characterized by a recent range expansion that probably occurred after the start of the Pleistocene. In addition, a nested clade phylogeographic analysis indicates that additional processes such as allopatric fragmentation and restricted gene flow have influenced the evolutionary history of this species. Traditionally, the White-headed Woodpecker has been split into two subspecies whose distributions meet in the northern part of the Transverse Ranges in California. The two subspecies differ morphologically, with the southern subspecies having a larger bill in proportion to its body size than the northern subspecies. Geographical variation in mtDNA is concordant with a division at the Transverse Ranges that corresponds to the morphological variation seen between the two subspecies. An analysis of molecular variance indicates that 27% of the genetic variation results from differences between the northern and southern subspecies. Furthermore, birds in the northern part of the range differ from those in the southern part of the range by at least one base substitution. These results agree with the hypothesis that the larger bill of the southern subspecies is the result of recent local adaptation to feeding on the large cones of Coulter pines (Pinus coulteri).

Heterogeneous colonization pattern of European Cyprinids, as highlighted by the dace complex (Teleostei: Cyprinidae)

The dace ( Leuciscus leuciscus), with a very large geographic distribution all over Europe, represents an interesting species model for studies of the global mechanisms underlying aquatic system biodiversity. To assess the congruence with the past colonization process hypothesis of the freshwater fauna in Western Europe, we investigated the evolutionary history of this species, by integrating morphological variation (eight meristic characters), mitochondrial (cytochrome b, 16S rDNA and control region, over a total of 2169 bp) and nuclear (12 allozymes loci) phylogenetic relationships, and investigating population dynamics via expansion, migration, bottleneck, and divergence time analyses. We carried out nested clade phylogeographic analysis for a total of 663 specimens from 31 populations taken from all over the distribution area. Unlike previous studies, we found that L. leuciscus is currently constituted by five lineages belonging to two clades (yielding 6.3% of pairwise divergence). The relationships between these lineages were accounted for by complex biogeographical patterns due to Pliocene and Pleistocene paleoclimatic events, validating the identification of new glacial refuges for freshwater fish in Western Europe. Finally, we demonstrated hybridization between L. leuciscus and Leuciscus idus.

Phylogeography of the flat‐tailed horned lizard (Phrynosoma mcallii) and systematics of the P. mcallii–platyrhinos mtDNA complex

Two species of horned lizards are sympatric along the periphery of the Salton Trough. Phrynosoma mcallii, endemic to the trough, is of conservation concern because its limited habitat has been fragmented by human activities. A more common and widespread species, Phrynosoma platyrhinos, occurs around the periphery of the trough and much further to the North. The two species are syntopic at a few localities, where morphological intermediates have also been found. Here, we used nested clade phylogeographical analysis (NCPA) and analysis of molecular variance (amova), to examine 781 bp of mitochondrial DNA (nad4 and two tRNAs) from 82 individuals of P. mcallii. We tested whether populations of this species were recently connected, or if they were historically isolated prior to human modification of the region. Our NCPA results indicated significant population structure associated with the Colorado River, suggesting limited gene flow and potential isolation across this barrier. Populations west of the Colorado River, currently isolated from one another by human development, show less genetic differentiation. We also collected homologous sequence data from 34 individuals of P. platyrhinos and seven specimens morphologically intermediate between P. mcallii and P. platyrhinos, as a preliminary investigation of hybridization between these two species. From phylogenetic results of these data, we identified a species (Phrynosoma goodei) previously recognized as a subspecies of P. platyrhinos. Six of the morphologically intermediate specimens shared mtDNA haplotypes with P. goodei, while one was nested among P. mcallii haplotypes.

Nested Phylogeographical Clade Analysis of Trochodendron aralioides (Trochodendraceae) in Taiwan

Nested clade phylogeographical analysis (NCPA), developed by A. R. Templeton and his colleague, was used to infer the evolutionary events that shaped the spatial genetic structure of Trochodendron aralioides in Taiwan. Genetic variation of two intergenic spacers of chloroplast DNA (petG-trnP and trnA-psbJ) among 24 populations, in which two from Japan, two from the Ryukyus and 20 from Taiwan, was examined. The NCPA suggests that the populations in Taiwan were first isolated from those of Japan proper. Since then, the spatial genetic structure in Taiwan was attributable to restricted gene flow.

PHYLOGEOGRAPHY AND CONSERVATION GENETICS OF SOUTHERN FLYING SQUIRRELS (GLAUCOMYS VOLANS) FROM NOVA SCOTIA

Mitochondrial cytochrome-b (Cytb) and control region (CR) sequence data were used to investigate the phylogeography of the disjunct population of southern flying squirrels (Glaucomys volans) from Nova Scotia. Consistent with previous studies, there is little differentiation in Cytb sequences (0–1.3% sequence divergence) across the entire range of G. volans in North America. Nested clade phylogeographic analysis of CR sequences (which exhibited 0.5–5.7% sequence divergence) provided a finer scale of differentiation and allowed for inferences to be made regarding the phylogeographic history of the population from Nova Scotia. We propose that G. volans rapidly expanded its range from a southern refugium after the Wisconsin glaciation (∼ 12,000 years ago) and was then isolated in southwestern Nova Scotia during subsequent climactic fluctuations. More specifically, the population from Nova Scotia was isolated from extant populations in Ontario by the loss of intermediate populations. Although the population of G. volans in Nova Scotia would not be considered an evolutionarily significant unit under some definitions, examination of CR sequence data suggests that this population may nevertheless be diverging from other populations.