Phylogeography and introgressive hybridization: chipmunks (genus Tamias) in the northern Rocky Mountains

Abstract. If phylogeographic studies are to be broadly used for assessing population-level processes relevant to speciation and systematics, the ability to identify and incorporate instances of hybridization into the analytical framework is essential. Here, we examine the evolutionary history of two chipmunk species, Tamias ruficaudus and Tamias amoenus , in the northern Rocky Mountains by integrating multivariate morphometrics of bacular (os penis) variation, phylogenetic estimation, and nested clade analysis with regional biogeography. Our results indicate multiple examples of mitochondrial DNA introgression layered within the evolutionary history of these nonsister species. Three of these events are most consistent with recent and/or ongoing asymmetric introgression of mitochondrial DNA across morphologically defined secondary contact zones. In addition, we find preliminary evidence where a fourth instance of nonconcordant characters may represent complete fixation of introgressed mitochondrial DNA via a more ancient hybridization event, although alternative explanations of convergence or incomplete sorting of ancestral polymorphisms cannot be dismissed with these data. The demonstration of hybridization among chipmunks with strongly differentiated bacular morphology contradicts long-standing assumptions that variation within this character is diagnostic of complete reproductive isolation within Tamias . Our results illustrate the utility of phylogeographic analyses for detecting instances of reticulate evolution and for incorporating this and other information in the inference of the evolutionary history of species.     

Molecular phylogeography and cryptic speciation in the mosses, Mielichhoferia elongata and M. mielichhoferiana (Bryaceae)

Nucleotide sequence variation in the ITS1-5.8S-ITS2 region of nuclear ribosomal DNA (nrDNA) from 70 populations of Mielichhoferia elongata and M. mielichhoferiana, plus two outgroup species, was analysed using maximum parsimony and maximum likelihood methods. High levels of nucleotide substitution and numerous insertion-deletion events were detected within and between the two species. M. elongata is monophyletic with regard to nrDNA variation, but M. mielichhoferiana is paraphyletic. (M. elongata is nested within it.) A clade within M. mielichhoferiana provides evidence of vicariance, with North American and Scandinavian sister groups of populations. Two major clades are resolved in M. elongata by sequence data that are completely congruent with previous isozyme work. One clade includes populations from both North America and Europe whereas the other is strictly North American. These two clades, resolved by multiple independent loci, clearly represent cryptic species within the morphologically uniform M. elongata. Certain geographical areas, most notably southwestern Colorado in Ouray and San Juan Counties, harbour diverse populations of M. elongata with distinct phylogenetic and phylogeographical histories. Morphologically indistinguishable but phylogenetically distant populations were detected a few metres apart at one site. In contrast, all populations collected over hundreds of kilometres in California belong to a single clade. Arctic North American populations belong to a clade that includes disjunct populations in Alaska, northern Ellesmere Island, and the northeastern USA, but not subarctic Swedish populations, which are more closely related to plants from the Rocky Mountains. Morphological uniformity belies complex infraspecific phylogenetic patterns within M. elongata and M. mielichhoferiana.     

Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus)

Phylogeographic patterns of many taxa are explained by Pleistocene glaciation. The temperate rainforests within the Pacific Northwest of North America provide an excellent example of this phenomenon, and competing phylogenetic hypotheses exist regarding the number of Pleistocene refugia influencing genetic variation of endemic organisms. One such endemic is the Pacific giant salamander, Dicamptodon tenebrosus. In this study, we estimate this species' phylogeny and use a coalescent modeling approach to test five hypotheses concerning the number, location and divergence times of purported Pleistocene refugia. Single refugium hypotheses include: a northern refugium in the Columbia River Valley and a southern refugium in the Klamath-Siskiyou Mountains. Dual refugia hypotheses include these same refugia but separated at varying times: last glacial maximum (20,000 years ago), mid-Pleistocene (800,000 years ago) and early Pleistocene (1.7 million years ago). Phylogenetic analyses and inferences from nested clade analysis reveal distinct northern and southern lineages expanding from the Columbia River Valley and the Klamath-Siskiyou Mountains, respectively. Results of coalescent simulations reject both single refugium hypotheses and the hypothesis of dual refugia with a separation date in the late Pleistocene but not hypotheses predicting dual refugia with separation in early or mid-Pleistocene. Estimates of time since divergence between northern and southern lineages also indicate separation since early to mid-Pleistocene. Tests for expanding populations using mismatch distributions and 'g' distributions reveal demographic growth in the northern and southern lineages. The combination of these results provides strong evidence that this species was restricted into, and subsequently expanded from, at least two Pleistocene refugia in the Pacific Northwest.     

Differential regional response of the bushy‐tailed woodrat (Neotoma cinerea) to late Quaternary climate change

Aim To reconstruct the regional biogeographical history of the bushy‐tailed woodrat, Neotoma cinerea (Rodentia: Cricetidae), across its distribution using multiple sources of information, including genetic data, ecological niche models and the palaeorecord. Location Western North America. Methods We analysed complete cytochrome b gene (1143 bp) sequences from 182 specimens of N. cinerea using Bayesian and coalescent methods to infer phylogenetic relationships, time of major divergences, and recent demographic trends. For comparison, we developed clade‐specific ecological niche models for groups of interest and analysed spatial trends of N. cinerea in the palaeorecord as well as temporal frequency trends across strata of individual palaeomiddens. Results We found two largely allopatric clades within N. cinerea, with several regionally distinct subclades showing contrasting recent population dynamics. Niche models showed consistent habitat at the Last Glacial Maximum (LGM) and modern times in the Rocky Mountains and northern United States, while the Great Basin may have been markedly less suitable at the LGM than today. The palaeorecord showed great spatio‐temporal variability in the presence of N. cinerea, but documents broad‐scale patterns of occupancy and regional population trends. Main conclusions The Quaternary dynamics and evolutionary history of N. cinerea appear to have been shaped by both vicariant events associated with geographical barriers and the availability of suitable habitat through time. Divergence of the two major clades dates to the Pliocene–Pleistocene transition, with clades separated by the Green and Colorado rivers and northern Rocky Mountain Pleistocene glaciations. We found largely concordant genetic, niche model and palaeorecord patterns suggesting long‐term population stability in the Rocky Mountains, while extant clades in the Great Basin and far north appear to have expanded or re‐expanded into these regions relatively recently. Furthermore, disjunct haplotype distributions, regional demographic history, and historical distribution of suitable habitat suggest that the Great Basin has been a particularly dynamic region.     

Cryptic Neogene vicariance and Quaternary dispersal of the red-spotted toad (Bufo punctatus): insights on the evolution of North American warm desert biotas

We define the geographical distributions of mitochondrial DNA (mtDNA) lineages embedded within a broadly distributed, arid-dwelling toad, Bufo punctatus. These patterns were evaluated as they relate to hypothesized vicariant events leading to the formation of desert biotas within western North America. We assessed mtDNA sequence variation among 191 samples from 82 sites located throughout much of the species' range. Parsimony-based haplotype networks of major identified lineages were used in nested clade analysis (NCA) to further elucidate and evaluate shallow phylogeographic patterns potentially associated with Quaternary (Pleistocene-Holocene) vicariance and dispersal. Phylogenetic analyses provided strong support for three monophyletic lineages (clades) within B. punctatus. The geographical distributions of the clades showed little overlap and corresponded to the general boundaries of the Peninsular Desert, and two continental desert regions, Eastern (Chihuahuan Desert-Colorado Plateau) and Western (Mojave-Sonoran deserts), geographically separated along the Rocky Mountains and Sierra Madre Occidental. The observed divergence levels and congruence with postulated events in earth history implicate a late Neogene (latest Miocene-early Pliocene) time frame for separation of the major mtDNA lineages. Evaluation of nucleotide and haplotype diversity and interpretations from NCA reveal that populations on the Colorado Plateau resulted from a recent, likely post-Pleistocene, range expansion from the Chihuahuan Desert. Dispersal across historical barriers separating major continental clades appear to be recent, resulting in secondary contacts in at least two areas. Given the observed contact between major clades, we speculated as to why the observed deep phylogeographic structure has not been eroded during the multiple previous interglacials of the Pleistocene.     

Mitochondrial DNA evolution in the Anaxyrus boreas species group

The Anaxyrus boreas species group currently comprises four species in western North America including the broadly distributed A. boreas, and three localized species, Anaxyrus nelsoni, Anaxyrusexsul and Anaxyrus canorus. Phylogenetic analyses of the mtDNA 12S rDNA, cytochrome oxidase I, control region, and restriction sites data, identified three major haplotype clades. The Northwest clade (NW) includes both subspecies of A. boreas and divergent minor clades in the middle Rocky Mountains, coastal, and central regions of the west and Pacific Northwest. The Southwest (SW) clade includes A. exsul, A. nelsoni, and minor clades in southern California. Anaxyrus canorus, previously identified as paraphyletic, has populations in both the NW and SW major clades. The Eastern major clade (E) includes three divergent lineages from southern Utah, the southern Rocky Mountains, and north of the Great Basin at the border of Utah and Nevada. These results identify new genetic variation in the eastern portion of the toad's range and are consistent with previous regional studies from the west coast. Low levels of control region sequence divergence between major clades (2.2-4.7% uncorrected pair-wise distances) are consistent with Pleistocene divergence and suggest that the phylogeographic history of the group was heavily influenced by dynamic Pleistocene glacial and climatic changes, and especially pluvial changes, in western North America. Results reported here may impact conservation plans in that the current taxonomy does not reflect the diversity in the group.     

Phylogeography of the northern hogsucker, Hypentelium nigricans (Teleostei: Cypriniformes): genetic evidence for the existence of the ancient Teays River

Aim To assess the roles of dispersal and vicariance in shaping the present distribution and diversity within Hypentelium nigricans, the northern hogsucker (Teleostei: Cypriniformes). Location Eastern United States. Methods Parsimony analyses, Bayesian analyses, pairwise genetic divergence and mismatch plots are used to examine patterns of genetic variation across H. nigricans. Results Species relationships within the genus Hypentelium were consistent with previous hypotheses. However, relationships between haplotypes within H. nigricans revealed two deeply divergent groups, a clade containing haplotypes from the New and Roanoke rivers (Atlantic Slope) plus Interior Highlands and upper Mississippi River and a clade containing haplotypes from the Eastern Highlands, previously glaciated regions of the Ohio and Wabash rivers, and the Amite and Homochitto rivers of south‐western Mississippi. Main conclusions The phylogenetic history of Hypentelium was shaped by old vicariant events associated with erosion of the Blue Ridge and separation of the Mobile and Mississippi river basins. Within H. nigricans two clades existed prior to the Pleistocene; a widespread clade in the pre‐glacial Teays‐Mississippi River system and a clade in Cumberland and Tennessee rivers. Pleistocene events fragmented the Teays‐Mississippi fauna. Following the retreat of the glaciers H. nigricans dispersed northward into previously glaciated regions. These patterns are replicated in other clades of fishes and are consistent with some of the predictions of Mayden's (Systematic Zoology, 37, 329, 1988) pre‐Pleistocene vicariance hypothesis.     

Historical demography and phylogeography of a specialist bark beetle, Dendroctonus pseudotsugae Hopkins (Curculionidae: Scolytinae)

Contemporary distribution of North American species has been shaped by past glaciation events during the Quaternary period. However, their effects were not as severe in the southern Rocky Mountains and Northern Mexico as elsewhere in North America. In this context, we test hypotheses about the historical demography of Dendroctonus pseudotsugae, based on 136 haplotypes of mitochondrial cytochrome oxidase I. The phylogenetic analysis yielded four haplogroups corresponding to northwestern United States and southwestern Canada (NUS), southwestern United States (Arizona, SUS), northwestern Mexico (Sierra Madre Occidental, SMOC), and northeastern Mexico (Sierra Madre Oriental, SMOR). Predictions of demographic expansion were examined through neutrality tests against population growth and mismatch distribution. Results showed that the NUS and SMOC haplogroups have experienced demographic expansion events, whereas the SUS and SMOR haplogroups have not. Divergence times between pairs of haplogroups were estimated from early to middle Pleistocene. The longer divergence time between NUS and all other haplogroups could be the result of refugia within the Pacific Northwest and northern Rocky Mountains and long-term isolation from southernmost populations in Mexico. The results obtained in this study are in agreement with the evolutionary history of the host Douglas-fir, as the warmer climates of interglacial periods pushed conifers northward of Colorado, New Mexico, and Arizona, whereas environmental changes reduced the population size of Douglas-fir and forced fragmentation of distribution range southward into northern Mexico.     

Extensive chloroplast haplotype variation indicates Pleistocene hybridization and radiation of North American Arabis drummondii, A. x divaricarpa, and A. holboellii (Brassicaceae)

Arabis drummondii, A. holboellii and their hybrid A. x divaricarpa are widespread perennials of open habitats in North America. A phylogenetic analysis based on noncoding chloroplast DNA sequences (trnL intron and trnL/F intergenic spacer) resolved A. drummondii as a monophyletic taxon, but found A. holboellii to bear chloroplast haplotypes from highly diverged evolutionary lineages. This raised the question of a possible polyphyletic origin of A. holboellii. Arabis x divaricarpa was found to be of recent and polytopic origin, a result consistent with its presumed hybrid origin. One hundred and three chloroplast haplotypes were detected within 719 Arabis accessions investigated. The majority of chloroplast-types were estimated to have arisen prior to the Wisconsin glaciation. Phylogeographical analysis using nested clade analysis, suggested for A. holboellii (i). past fragmentation events, partitioning genetic variation in several instances between the Sierra Nevada, the Southern Rocky Mountains and the Colorado Plateau on the one hand and the Central to Northern Rockies of the United States and adjacent Cascades on the other; and for both parental species (ii). recolonization of major areas formerly covered by the Wisconsin glaciation by three haplotypes; and (iii). restricted gene flow indicating isolation by distance in areas south of the last glacial maximum. Arabis x divaricarpa is closely codistributed with its parental species and resampled their haplotypes. The highest genetic diversity was found in the Rocky Mountains from Idaho and Montana south to Utah and Colorado. This area was further hypothesized to have played a major role in the origin of both parental species and probably represented an important glacial refugium. However, evidence for glacial refugia was also found in arctic and boreal regions of Alaska and near the Great Lakes. In comparison to nuclear ribosomal internal transcribed spacer data, chloroplast DNA divergence was very high and evidently predated the origin of A. drummondii and possibly A. holboellii. Divergence of major chloroplast lineages dates back to the middle of the Pleistocene at least. Extensive hybridization is the most likely evolutionary factor working on A. holboellii to explain the revealed discrepancy in nuclear DNA and chloroplast DNA diversification.     

Historic cycles of fragmentation and expansion in Parnassius smintheus (papilionidae) inferred using mitochondrial DNA

Climate oscillations of the Quaternary drove the repeated expansion and contraction of ecosystems. Alpine organisms were probably isolated in sky island refugia during warm interglacials, such as now, and expanded their range by migrating down-slope during glacial periods. We used population genetic and phylogenetic approaches to infer how paleoclimatic events influenced the distribution of genetic variation in the predominantly alpine butterfly Parnassius smintheus. We sequenced a 789 bp region of cytochrome oxidase I for 385 individuals from 20 locations throughout the Rocky Mountains, ranging from southern Colorado to northern Montana. Analyses revealed at lease two centers of diversity in the northern and southern Rocky Mountains and strong population structure. Nested clade analysis suggested that the species experienced repeated cycles of population expansion and fragmentation. The estimated ages of these events, assuming a molecular clock, corresponded with paleoclimatic data on habitat expansion and contraction over the past 400,000 years. We propose that alpine butterflies persisted in an archipelago of isolated sky islands during interglacials and that populations expanded and became more connected during cold glacial periods. An archipelago model implies that the effects of genetic drift and selection varied among populations, depending on their latitude, area, and local environment. Alpine organisms are sensitive indicators of climate change and their history can be used to predict how high-elevation ecosystems might respond to further climate warming.     

Molecular evidence for Pleistocene glacial cycles driving diversification of a North American desert spider, Agelenopsis aperta

The influence of historical climatic vs. geological changes on species diversification patterns was investigated in a widely distributed North American desert spider, Agelenopsis aperta (Araneae: Agelenidae), with particular reference to Pleistocene glacial cycles and earlier patterns of mountain building. Levels of sequence divergence obtained from the mitochondrial gene, cytochrome oxidase I, dated to the Pleistocene, eliminating Rocky Mountain orogeny as a cause of diversification, as orogeny ended 4 million years ago. The results of phylogenetic and network analyses showed the presence of three geographically defined clades, which were consistent with the presence of at least three glacial refugia: (i) east of the Rocky Mountains; (ii) between the Rocky Mountains and Sierra Nevadas; and (iii) west of the Sierra Nevadas. In addition, populations within the Rocky Mountains exhibited significantly lower genetic diversity than populations east of the Rocky Mountains and the haplotypes found within the Rockies were a subset of eastern haplotypes. These patterns suggest that a post-Pleistocene range expansion occurred out of an eastern glacial refugium into the Rocky Mountains. Examination of phylogeographical studies of other North American desert taxa indicated that mountain building explained diversification patterns more effectively for some taxa but Pleistocene climate change was more important for others, including A. aperta.     

Phylogeography of the longhorn cactus beetle Moneilema appressum LeConte (Coleoptera: Cerambycidae): was the differentiation of the Madrean sky islands driven by Pleistocene climate changes?

Although it has been suggested that Pleistocene climate changes drove population differentiation and speciation in many groups of organisms, population genetic evidence in support of this scenario has been ambiguous, and it has often been difficult to distinguish putative vicariance from simple isolation by distance. The sky island communities of the American Southwest present an ideal system in which to compare late Pleistocene range fragmentations documented by palaeoenvironmental studies with population genetic data from organisms within these communities. In order to elucidate the impact of Pleistocene climate fluctuations on these environments, biogeographic patterns in the flightless longhorn cactus beetle, Moneilema appressum were examined using mitochondrial DNA sequence data. Gene tree relationships between haplotypes were inferred using parsimony, maximum-likelihood, and Bayesian analysis. Nested clade analysis, Mantel tests, and coalescent modelling were employed to examine alternative biogeographic scenarios, and to test the hypothesis that Pleistocene climate changes drove population differentiation in this species. The program mdiv was used to estimate migration and divergence times between populations, and to measure the statistical support for isolation over ongoing migration. These analyses showed significant geographic structure in genetic relationships, and implicated topography as a key determinant of isolation. However, although the coalescent analyses suggested that a history of past habitat fragmentation underlies the observed geographic patterns, the nested clade analysis indicated that the pattern was consistent with isolation by distance. Estimated divergence times indicated that range fragmentation in M. appressum is considerably older than the end of the most recent glacial, but coincided with earlier interglacial warming events and with documented range expansions in other, desert-dwelling species of Moneilema.     

A phylogeographic, demographic and historical analysis of the short-tailed pit viper (Gloydius brevicaudus): evidence for early divergence and late expansion during the Pleistocene

The impact of quaternary glaciation in eastern China on local fanua and flora has been a topic of considerable interest. We used mitochondrial DNA (mtDNA) sequence data and coalescent simulations to test two general biogeographic hypothesis related to the effects of Pleistocene climatic fluctuations for a widespread ophidian species (Gloydius brevicaudus) in eastern China and Korean Peninsula. The phylogenetic analysis revealed three major lineages, the southeast Coastal, Yangtze and North Lineages. The latter two are closely related and jointly form a continental lineage. Divergence dating and coalescent simulations indicate a Late Pliocene to Early Pleistocene divergence between lineages from the southeast coast and continental interior, followed by a mid-to-late Pleistocene divergence between lineages from the north and the middle-lower Yangtze Valley across East China, suggesting that all these lineages predated the last glacial maximum. An overlapping range between the two lineages within the continental lineage and a secondary contact associated with ecological transition zones on the margins of the North China Plain were also observed. These results show that vicariance patterns dominated the history of G. brevicaudus. Though the climatic events of the Pleistocene have had a marked effect on the historical distribution and intra-specific divergence of reptiles in China, coalescent and non-coalescent demographic analyses indicate that all lineages of G. brevicaudus seem not to have been adversely affected by glacial cycles during the Late Pleistocene, presumably because of an increase in the amount of climatically mild habitat in East Asia due to a decline in elevation and the development of monsoons since the Mid-End Pleistocene.     

Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshopprers

There is a long-standing debate over whether or not the Pleistocene glaciations promoted speciation. While some models predict that extensive mixing of populations during interglacial expansion would have inhibited divergence, others postulate that divergence among allopatric glacial refuges or founder events during recolonization of previously glaciated areas would have promoted differentiation. Using a combination of traditional and coalescent based population genetic approaches, this study finds that the glaciations did not inhibit divergence among populations of the grasshopper Melanoplus oregonensis. Instead, drift associated with recolonization of previously glaciated areas, as well as divergence among multiple allopatric glacial refugia, have both contributed to differentiation in this montane grasshopper from the 'sky islands' of the northern Rocky Mountains. Significant population structure was detected by phylogenetic and FST analyses, including significant FST values among individual pairs of sky-island populations. In addition to clustering of haplotypes within populations, there is some evidence of regional phylogeographic structure, although none of the 'regional groups' form a monophyletic clade and there is a lack of concordance between the genealogical and geographical positions of some haplotypes. However, coalescent simulations confirm there is significant regional phylogeographic structure that most likely reflects divergence among multiple ancestral refugial populations, and indicate that it is very unlikely that the observed gene tree could have been produced by the fragmentation of a single widespread ancestral population. Thus, rather than inhibiting differentiation, the glaciations appear to have promoted population divergence in M. oregonensis, suggesting that they may have contributed to the radiation of Melanoplus species during the Pleistocene.     

Phylogeography of northern Dolly Varden Salvelinus malma malma based on analysis of mitochondrial DNA

The northern Dolly Varden, Salvelinus malma malma, is a typical representative of arctic fauna distributed in northeastern Asia and northwestern North America. Because its spawning habitats were affected by Pleistocene glacial advances over most of its natural range, S. m. malma is among the most interesting objects of phylogeographic and microevolutionary studies. We reconstructed the genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of glacial and geological vicariance events on the contemporary population genetic structure, phylogeographic subdivision and distribution of the northern Dolly Varden. Analysis of restriction site states in three PCR‐amplified mtDNA regions (ND1/ND2, ND5/ND6, Cytb/D‐loop; 47% of the mitochondrial genome) resolved 75 haplotypes in 436 fish. Similar patterns of subspecific variation apparent from hierarchical diversity and nested clade analyses of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. Our results suggest that (1) demographic history has been influenced by historical range expansions and recent isolation by distance, (2) present populations from Asia and North America were colonized from one main Beringian Refugium, and (3) that this taxon's ancestral population probably experienced a bottleneck in the Beringian Refugium during the late Pleistocene (Wisconsin) glacial period.     

Molecular genetic evidence for the post-Pleistocene divergence of populations of the arctic-alpine ground beetle Amara alpina (Paykull) (Coleoptera: Carabidae)

Aim This study examines the hypothesis that the biogeographic history of a species is reflected in the distribution of molecular genetic diversity and the phylogenies of extant populations. Location Populations of arctic-alpine ground beetle Amara alpina were analysed from Beringia (Alaska and northernmost British Columbia), the Hudson Bay region, the northern Appalachian Mountains, and the central Rocky Mountains of North America. Methods Mitochondrial restriction site variation of specimens from twenty-two populations were assayed by using radioactively labelled mtDNA to probe Southern membranes containing restriction enzyme digested total DNA. Restriction sites were mapped and genetic distances were calculated by pairwise comparison of presence and absence of restriction sites. Genetic distances were used in a molecular analysis of variance and to construct a minimal spanning tree. Parsimony methods were used to investigate the phylogenetic relationships between the haplotypes. These results were compared to an existing model for postglacial dispersal based on fossil and modern occurrences of arctic-alpine beetles. Results Among the twenty-two populations, fifteen haplotypes were detected. Genetic variation within each of the four regions corresponded to that expected from the palaeontologically based model. Beringian populations were the most genetically diverse. In contrast, no restriction site variation was observed in populations from the Hudson Bay region. Intermediate amounts of variation were observed in alpine populations of the Rocky and Appalachian Mountains. Maximum parsimony and cluster analysis provide evidence that at least two ancestral haplotypes existed in the Southern refugium from which the Rocky and the Appalachian Mountains populations were founded. Main conclusions The genetic results are generally consistent with the palaeontologically based model. The diversity of Beringian populations is consistent with this region having been continuously inhabited by Amara alpina throughout the Pleistocene. The Hudson Bay region was not deglaciated until about 6000 years, and its populations have no restriction site variation. The molecular genetic data support the interpretation that the Hudson Bay region was colonized from Beringia based on the occurrence of the same haplotype in both regions.     

Testing hypotheses of speciation timing in Dicamptodon copei and Dicamptodon aterrimus (Caudata: Dicamptodontidae)

Giant salamanders of the genus Dicamptodon are members of the mesic forest ecosystem that occurs in the Pacific Northwest of North America. We estimate the phylogeny of the genus to test several hypotheses concerning speciation and the origin of current species distributions. Specifically, we test competing a priori hypotheses of dispersal and vicariance to explain the disjunct inland distribution of the Idaho giant salamander (D. aterrimus) and to test the hypothesis of Pleistocene speciation of Cope's giant salamander (D. copei) using Bayesian hypothesis testing. We determined that available outgroups were too divergent to root the phylogeny effectively, and we calculated Bayesian posterior probabilities for each of the 15 possible root placements for this four-taxon group. This analysis placed the root on the branch leading to D. aterrimus, indicating that current distribution and speciation of D. aterrimus fit the ancient vicariance hypothesis and are attributable to the orogeny of the Cascade Mountains rather than recent inland dispersal. Furthermore, test results indicate that D. copei is distantly related to other coastal lineages and likely originated much earlier than the Pleistocene. These results suggest that speciation within the genus is attributable to ancient geologic events, while more recent Pleistocene glaciation has shaped genetic variation and distributions within the extant species.     

Pleistocene climatic cycling and diversification of the Andean treefrog, Hypsiboas andinus

Our understanding of the causes of diversification of Neotropical organisms lags behind that of Northern Hemisphere biota, especially for montane and temperate regions of southern South America. We investigated the mitochondrial DNA genealogical patterns in 262 individuals of the frog Hypsiboas andinus from 26 sites across the eastern ranges of the Andes Mountains in Argentina and Bolivia. Our phylogenetic analyses indicate at least three distinct lineages: one representing H. andinus from Northwestern Argentina and southern Bolivia, at least one H. andinus lineage from northern Bolivia, and one clade containing both H. andinus (from the southern portion of the species range) and its putative sister taxon Hypsiboas riojanus. Hypsiboas andinus samples from northern Bolivia are well differentiated and may represent distinct species. The northern Argentine H. andinus lineage and southern H. andinus/H. riojanus lineage likely diverged between 2 and 6 million years ago; their current sympatry may be the result of secondary contact due to range expansion after isolation during Andean uplift or may reflect cryptic species. Within the geographically extensive northern H. andinus clade, we found significant geographical structuring consistent with historical fragmentation and subsequent range expansion. The timing of this fragmentation and range expansion coincide with the Pleistocene, a time of extensive climatic cycling and vegetational shifts. Average divergence among clades is lower than those found for other Neotropical taxa, highlighting the potential importance of recent climatic history in diversification in the southern Andes.     

Range-wide molecular analysis of the western pond turtle (Emys marmorata): cryptic variation, isolation by distance, and their conservation implications

We analysed phylogeography and population genetic variation across the range of the western pond turtle (Emys marmorata) using rapidly evolving mitochondrial and nuclear DNA sequence data. Nuclear DNA sequences from two unlinked introns displayed extremely low levels of variation, but phylogenetic analyses based on mtDNA recovered four well-supported and geographically coherent clades. These included a large Northern clade composed of populations from Washington south to San Luis Obispo County, California, west of the Coast Ranges; a San Joaquin Valley clade from the southern Great Central Valley; a geographically restricted Santa Barbara clade from a limited region in Santa Barbara and Ventura counties; and a Southern clade that occurs south of the Tehachapi Mountains and west of the Transverse Range south to Baja California, Mexico. An analysis of molecular variance (amova) based on regional hydrographic units revealed that populations from the Sacramento Valley north to Washington were virtually invariant, with no evidence of population substructure among northern river drainage basins. In other areas, E. marmorata contains considerable unrecognized variation, particularly in central and southern California and in northern Baja California, Mexico. Our northern clade is congruent with the distribution of the subspecies Emys marmorata marmorata (Washington-central California). However, no clade is congruent with the distribution of the southern subspecies Emys marmorata pallida from central California-Baja. Thus, recognition of the current subspecies split is not warranted, based on the available genetic evidence. Our amova and phylogenetic results, in conjunction with a growing comparative database for other codistributed aquatic taxa, confirm the occurrence of genetic breaks across the Tehachapi Mountains and Transverse Range bounding the southern end of the Great Central Valley, and point to southern California as a rich source of cryptic genetic variation.     

Phylogeographic history of the land snail Candidula unifasciata (Helicellinae,Stylommatophora): fragmentation,corridor migration,and secondary contact

Abstract.— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.