Phylogeography of the tailed frog (Ascaphus truei): implications for the biogeography of the Pacific Northwest

Postglacial range expansion from northern refugia by the wood frog, Rana sylvatica

Although the range dynamics of North American amphibians during the last glacial cycle are increasingly better understood, the recolonization history of the most northern regions and the impact of southern refugia on patterns of intraspecific genetic diversity and phenotypic variation in these regions are not well reconstructed. Here we present the phylogeographic history of a widespread and primarily northern frog, Rana sylvatica. We surveyed 551 individuals from 116 localities across the species' range for a 650-bp region of the NADH dehydrogenase subunit 2 and tRNA(TRP) mitochondrial genes. Our phylogenetic analyses revealed two distinct clades corresponding to eastern and western populations, as well as a Maritime subclade within the eastern lineage. Patterns of genetic diversity support multiple refugia. However, high-latitude refugia in the Appalachian highlands and modern-day Wisconsin appear to have had the biggest impact on northern populations. Clustering analyses based on morphology further support a distinction between eastern and western wood frogs and suggest that postglacial migration has played an important role in generating broad-scale patterns of phenotypic variation in this species.

GEOLOGICAL AND CLIMATIC FORCES DRIVING SPECIATION IN THE CONTINENTALLY DISTRIBUTED TRILLING CHORUS FROGS (PSEUDACRIS)

Tertiary geological events and Quaternary climatic fluctuations have been proposed as important factors of speciation in the North American flora and fauna. Few studies, however, have rigorously tested hypotheses regarding the specific factors driving divergence of taxa. Here, we test explicit speciation hypotheses by correlating geologic events with divergence times among species in the continentally distributed trilling chorus frogs (Pseudacris). In particular, we ask whether marine inundation of the Mississippi Embayment, uplift of the Appalachian Mountains, or modification of the ancient Teays-Mahomet River system contributed to speciation. To examine the plausibility of ancient rivers causing divergence, we tested whether modern river systems inhibit gene flow. Additionally, we compared the effects of Quaternary climatic factors (glaciation and aridification) on levels of genetic variation. Divergence time estimates using penalized likelihood and coalescent approaches indicate that the major lineages of chorus frogs diversified during the Tertiary, and also exclude Quaternary climate change as a factor in speciation of chorus frogs. We show the first evidence that inundation of the Mississippi Embayment contributed to speciation. We reject the hypotheses that Cenozoic uplift of the Appalachians and that diversion of the Teays-Mahomet River contributed to speciation in this clade. We find that by reducing gene flow, rivers have the potential to cause divergence of lineages. Finally, we demonstrate that populations in areas affected by Quaternary glaciation and aridification have reduced levels of genetic variation compared to those from more equable regions, suggesting recent colonization.

Integrating coalescent and ecological niche modeling in comparative phylogeography

Understanding the factors that contribute to the formation of population genetic structure is a central goal of phylogeographic research, but achieving this goal can be complicated by the stochastic variance inherent to genetic processes. Statistical approaches to testing phylogeographic hypotheses accommodate this stochasticity by evaluating competing models of putative historical population structure, often by simulating null distributions of the expected variance. The effectiveness of these tests depends on the biological realism of the models. Information from the fossil record can aid in reconstructing the historical distributions of some taxa. However, for the majority of taxa, which lack sufficient fossils, paleodistributional modeling can provide valuable spatial-geographic data concerning ancestral distributions. Paleodistributional models are generated by projecting ecological niche models, which predict the current distribution of each species, onto a model of past climatic conditions. Here, we generate paleodistributional models describing the suitable habitat during the last glacial maximum for lineages from the mesic forests of the Pacific Northwest of North America, and use these models to generate alternative phylogeographic hypotheses. Coalescent simulations are then used to test these hypotheses to improve our understanding of the historical events that promoted the formation of population genetic structure in this ecosystem. Results from Pacific Northwest mesic forest organisms demonstrate the utility of these combined approaches. Paleodistribution models and population genetic structure are congruent across three amphibian lineages, suggesting that they have responded in a concerted manner to environmental change. Two other species, a willow and a water vole, despite being currently codistributed and having similar population genetic structure, were predicted by the paleodistributional model to have had markedly different distributions during the last glacial maximum. This suggests that congruent phylogeographic patterns can arise from incongruent ancestral distributions. Paleodistributional models introduce a much-needed spatial-geographic perspective to statistical phylogeography. In conjunction with coalescent models of population genetic structure, they have the potential to improve our understanding of the factors that promote population divergence and ultimately produce regional patterns of biodiversity.

The influence of altitude and topography on genetic structure in the long-toed salamander (Ambystoma macrodactulym)

A primary goal of molecular ecology is to understand the influence of abiotic factors on the spatial distribution of genetic variation. Features including altitudinal clines, topography and landscape characteristics affect the proportion of suitable habitat, influence dispersal patterns, and ultimately structure genetic differentiation among populations. We studied the effects of altitude and topography on genetic variation of long-toed salamanders (Ambystoma macrodactylum), a geographically widespread amphibian species throughout northwestern North America. We focused on 10 low altitude sites (< 1200 m) and 11 high-altitude sites in northwestern Montana and determined multilocus genotypes for 549 individuals using seven microsatellite loci. We tested four hypotheses: (1) gene flow is limited between high- and low-altitude sites; and, (2) gene flow is limited among high-altitude sites due to harsh habitat and extreme topographical relief between sites; (3) low-altitude sites exhibit higher among-site gene flow due to frequent flooding events and low altitudinal relief; and (4) there is a negative correlation between altitude and genetic variation. Overall F(ST) values were moderate (0.08611; P < 0.001). Pairwise F(ST) estimates between high and low populations and a population graphing method supported the hypothesis that low-altitude and high-altitude sites, taken together, are genetically differentiated from each other. Also as predicted, gene flow is more prominent among low-altitude sites than high-altitude sites; low-altitude sites had a significantly lower F(ST) (0.03995; P < 0.001) than high altitude sites (F(ST) = 0.10271; P < 0.001). Use of Bayesian analysis of population structure (BAPS) resulted in delineation of 10 genetic groups, two among low-altitude populations and eight among high-altitude populations. In addition, within high altitude populations, basin-level genetic structuring was apparent. A nonequilibrium algorithm for detecting current migration rates supported these population distinctions. Finally, we also found a significant negative correlation between genetic diversity and altitude. These results are consistent with the hypothesis that topography and altitudinal gradients shape the spatial distribution of genetic variation in a species with a broad geographical range and diverse life history. Our study sheds light on which key factors limit dispersal and ultimately species' distributions.

Peptidomic analysis of skin secretions supports separate species status for the tailed frogs, Ascaphus truei and Ascaphus montanus

The tailed frog Ascaphus truei Stejneger, 1899 is the most primitive extant anuran and the sister taxon to the clade of all other living frogs. The species occupies two disjunct ranges in the Northwest region of North America: the Cascade Mountains and coastal area from British Columbia to Northern California, and an inland range in the northern Rocky Mountains and the Blue and Wallowa mountains. A previous study led to the isolation of eight peptides with antimicrobial activity (termed the ascaphins) from skin secretions of A. truei from the coastal range. The present study has used peptidomic analysis to identify the products of orthologous ascaphin genes in electrically-stimulated skin secretions from inland range specimens. Structural characterization of the peptides demonstrated that ascaphins from the inland range contained the following amino acid substitutions compared with orthologs from the coastal range frogs: ascaphin-1 (Ala(12)-->Glu), ascaphin-3 (Asp(4)-->Glu), ascaphin-4 (Ala(19)-->Ser), ascaphin-5 (Lys(12)-->Thr), and ascaphin-7 (Gly(8)-->Ser and Ser(20)-->Asn). Orthologs of ascaphins-2, -6, and -8 were not identified but a paralog of ascaphin-5, identical to ascaphin-5 from coastal range frogs, was found. The data support the claims, derived from analysis of the nucleotide sequences of mitochondrial genes, that the inland populations of the tailed frog should be recognized as a distinct species, the Rocky Mountain tailed frog Ascaphus montanus and that the divergence of the species from A. truei probably occurred in the late Miocene (approximately 10 Mya).

Landscape-scale genetic variation in a forest outbreak species, the mountain pine beetle (Dendroctonus ponderosae)

The mountain pine beetle Dendroctonus ponderosae is a native species currently experiencing large-scale outbreaks in western North American pine forests. We sought to describe the pattern of genetic variation across the range of this species, to determine whether there were detectable genetic differences between D. ponderosae occupying different host trees in common localities, and to determine whether there was molecular evidence for a past demographic expansion. Using a combination of amplified fragment length polymorphism (AFLP) and mitochondrial sequencing analyses, we found evidence of genetic structuring among populations that followed a broad isolation-by-distance pattern. Our results suggest that the geographical pattern of gene flow follows the core distribution of the principal D. ponderosae host species, around rather than across the Great Basin and Mojave Deserts. Patterns of haplotype diversity and divergence were consistent with a range-wide population expansion. This signal was particularly pronounced in the northern part of the species' range, where outbreak activity is currently increasing. Using AFLP markers, we were unable to detect significant differences among groups of insects sampled from different host trees in common locations. Incidentally, we found that a large proportion of the polymorphic AFLP markers were gender-specific, occurring only in males. While we did not include these markers in our analyses, this finding warrants further investigation.

Effects of historical climate change, habitat connectivity, and vicariance on genetic structure and diversity across the range of the red tree vole (Phenacomys longicaudus) in the Pacific Northwestern United States

Phylogeographical analyses conducted in the Pacific Northwestern United States have often revealed concordant patterns of genetic diversity among taxa. These studies demonstrate distinct North/South genetic discontinuities that have been attributed to Pleistocene glaciation. We examined phylogeographical patterns of red tree voles (Phenacomys longicaudus) in western Oregon by analysing mitochondrial control region sequences for 169 individuals from 18 areas across the species' range. Cytochrome b sequences were also analysed from a subset of our samples to confirm the presence of major haplotype groups. Phylogenetic network analyses suggested the presence of two haplotype groups corresponding to northern and southern regions of P. longicaudus' range. Spatial genetic analyses (samova and Genetic Landscape Shapes) of control region sequences demonstrated a primary genetic discontinuity separating northern and southern sampling areas, while a secondary discontinuity separated northern sampling areas into eastern and western groups divided by the Willamette Valley. The North/South discontinuity likely corresponds to a region of secondary contact between lineages rather than an overt barrier. Although the Cordilleran ice sheet (maximum approximately 12,000 years ago) did not move southward to directly affect the region occupied by P. longicaudus, climate change during glaciation fragmented the forest landscape that it inhabits. Signatures of historical fragmentation were reflected by positive associations between latitude and variables such as Tajima's D and patterns associated with location-specific alleles. Genetic distances between southern sampling areas were smaller, suggesting that forest fragmentation was reduced in southern vs. northern regions.

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.

Can common species provide valuable information for conservation?

To demonstrate the importance of genetic data for multispecies conservation approaches, we examined the distribution of genetic variation across the range of the mountain whitefish (Prosopium williamsoni) at microsatellite and allozyme loci. The mountain whitefish is a common species that is particularly well suited for accurately revealing historical patterns of genetic structure and differs markedly from previously studied species in habitat requirements and life history characteristics. As such, comparing the population genetic structure of other native fishes to similar data from mountain whitefish could inform management and conservation strategies. Genetic variation for mountain whitefish was hierarchically distributed for both allozymes and microsatellites. We found evidence for a total of five major genetically differentiated assemblages and we observed subdivision among populations within assemblages that generally corresponded to major river basins. We observed little genetic differentiation within major river basins. Geographic patterns of genetic differentiation for mountain whitefish were concordant with other native species in several circumstances, providing information for the designation of conservation units that reflect concordant genetic differentiation of multiple species. Differences in genetic patterns between mountain whitefish and other native fishes reflect either differences in evolutionary histories of the species considered or differences in aspects of their ecology and life history. In addition, mountain whitefish populations appear to exchange genes over a much larger geographic scale than co-occurring salmonids and are likely to be affected differently by disturbances such as habitat fragmentation.

Effects of Pleistocene glaciations on population structure of North American chestnut-backed chickadees

The postglacial recolonization of northern North America was heavily influenced by the Pleistocene glaciation. In the Pacific Northwest, there are two disjunct regions of mesic temperate forest, one coastal and the other interior. The chestnut-backed chickadee is one of the species associated with this distinctive ecosystem. Using seven microsatellite markers we found evidence of population structure among nine populations of chestnut-backed chickadees. High levels of allelic variation were found in each of the populations. Northern British Columbia and central Alaska populations contained a large number of private alleles compared to other populations, including those from unglaciated regions. The disjunct population in the interior was genetically distinct from the coastal population. Genetic and historical records indicate that the interior population originated from postglacial inland dispersal. Population structuring was found within the continuous coastal population, among which the peripheral populations, specifically those on the Queen Charlotte Islands and the central Alaska mainland, were genetically distinct. The pattern of population structure among contemporary chickadee populations is consistent with a pioneer model of recolonization. The persistence of genetic structure in western North American chestnut-backed chickadees may be aided by their sedentary behaviour, linear distribution, and dependence on cedar-hemlock forests.

Phylogeography of Pseudacris regilla (Anura: Hylidae) in western North America, with a proposal for a new taxonomic rearrangement

The Baja California populations of Pseudacris regilla, a widespread species in Western North America ranging from British Columbia to southern Baja California, are characterized by extensive geographic fragmentation. We performed phylogeographic and historical demographic analyses on 609 bp of the cytochrome b mitochondrial gene of 110 individuals representing 28 populations to determine the relative influences of current and historical processes in shaping the present distribution of genetic diversity on the Baja California Peninsula. Haplotypes from this area were nested in a clade with three well-differentiated groups. Two of these groups are from Baja California Sur and another is from California and Baja California. The estimated date for the split of these groups, between 0.9-1 Ma, fits with previously proposed hypotheses of vicariance due to different transpeninsular seaways, although successive population fragmentation and expansion due to climatic oscillations during Pleistocene glaciations cannot be discarded. Historical demographic analyses detected signs of past population expansions, especially in the southernmost group. With respect to populations north of this region, two older clades were identified, one with haplotypes mainly distributed in central California, and the other corresponding to the northern half of the species range, in what apparently is a recurrent pattern in the Pacific coast of North America. Based on the concordance between mt-DNA and available allozyme data indicating that these species have a long independent evolutionary history, we propose to consider the three major clades as distinct species: P. regilla, P. pacifica, and P. hypochondriaca.

Multi-character perspectives on the evolution of intraspecific differentiation in a neotropical hylid frog

Background

Multi-character empirical studies are important contributions to our understanding of the process of speciation. The relatively conserved morphology of, and importance of the mate recognition system in anurans, combined with phylogenetic tools, provide an opportunity to address predictions about the relative role of each in the process of speciation. We examine the relationship among patterns of variation in morphology, call characters, and 16S gene sequences across seven populations of a neotropical hylid frog, Hyla leucophyllata, to infer their relative importance in predicting the early stages of population differentiation.

Results

Multivariate analyses demonstrate that both morphological and call characteristics were significantly variable among populations, characterized by significantly lower intra-population dispersion in call space than morphological space, and significantly greater among-population variation in call structure. We found lack of concordance between a 16S DNA phylogeny of Hyla leucophyllata and the significant population-level differentiation evident in both external morphology and male advertisement call. Comparisons of the reconstructed gene trees to simulated lineages support the notion that variation in call cannot be simply explained by population history.

Conclusion

Discordance among traits may reflect sampling biases (e.g. single genetic marker effects), or imply a decoupling of evolution of different suites of characters. Diagnostic differences among populations in call structure possibly reflect local selection pressures presented by different heterospecific calling assemblages and may serve as a precursor of species-wide differentiation. Differentiation among populations in morphology may be due to ecophenotypic variation or to diversifying selection on body size directly, or on frequency attributes of calls (mediated by female choice) that show a strong relationship to body size.

Population genetic structure of tailed frogs (Ascaphus truei) in clearcut and old-growth stream habitats in south coastal British Columbia

Ascaphus truei Stejneger, 1899 relies on cool, fast-flowing, forested mountain streams, which receive little protection from logging activities. During recovery of post-logging habitats, local extirpation of Ascaphus is a concern because their recolonization may be slow. In British Columbia, Oregon, and California, coastal Ascaphus populations are designated as "at risk". To infer fragmentation impacts from patterns of genetic structure, we used RAPD molecular markers and compared population genetic structures of Ascaphus larvae in an old growth with an adjacent clearcut stream located in coastal British Columbia. In the clearcut, larvae were less genetically diverse than in the old growth and exhibited no relationship between physical distance and genetic relatedness, whereas in the old growth, genetic similarity decreased with physical distance. Patterns of gene flow between the clearcut and old-growth streams were significantly different. The clearcut population went through a bottleneck/founding event, but also exhibited greater dispersal. The frogs were perhaps searching for new habitat (which would lower isolation by distance) and suffering mortality (which would decrease diversity). Most problems in conservation will require genetic and ecological data, and future research should aim to incorporate methodologies from both fields.

Bradykinin-related peptides and tryptophyllins in the skin secretions of the most primitive extant frog, Ascaphus truei

The tailed frog Ascaphus truei occupies a unique position in phylogeny as the most primitive extant anuran and is regarded as the sister taxon to the clade of all other living frogs. A previous study led to the isolation of eight antimicrobial peptides, termed ascaphins, from norepinephrine-stimulated skin secretions. Peptidomic analysis (HPLC separation followed by MALDI mass spectrometry and Edman degradation) of these secretions has led to the identification and structural characterization of 13 additional peptides present in relatively high concentration. In addition to bradykinin (BK; RPPGFSPFR), a C-terminally extended bradykinin (peptide RD-11; RPPGFSPFRVD), a bradykinin-like peptide (peptide AR-10; APVPGLSPFR), and a C-terminally extended form of this peptide (peptide AV-12; APVPGLSPFRVV) were obtained in pure form. These peptides produced concentration-dependent relaxation of precontracted mouse tracheal rings with a rank order of potency of BK>RD-11>AR-10>AV-12 but only RD-11 caused the same maximal relaxation as bradykinin. Four small peptides were also isolated from the skin secretions that contain the Pro-Trp motif that is a characteristic of the tryptophyllin family of peptides previously identified in skins of frogs of the family Hylidae. The data show that the synthesis of dermal peptides that may play a role in defense against predators arose early in the evolution of anurans.

Isolation by distance and post-glacial range expansion in the rough-skinned newt, Taricha granulosa

Allozymes and mitochondrial DNA sequences were used to examine the phylogeographical history of the rough-skinned newt, Taricha granulosa, in western North America. Nineteen populations were analysed for allozyme variation at 45 loci, and 23 populations were analysed for cytochrome b sequence variation. Both data sets agree that populations in the southern part of the range are characterized by isolation by distance, whereas northern populations fit the expectations of a recent range expansion. However, the northern limit of isolation by distance (and the southern limit of range expansion) is located in Oregon State by the mtDNA data, and in Washington State by the allozyme data. Nevertheless, both data sets are consistent with the known Pleistocene history of western North America, with phylogenetically basal populations in central and northern California, and a recent range expansion in the north following the retreat of the Cordilleran ice sheet 10,000 years ago. Additionally, a population in Idaho, previously considered introduced from central California based on morphometric analyses, possesses a distinct mtDNA haplotype, suggesting it could be native. The relevance of these results for Pacific Northwest biogeography is discussed.

Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus

Several theoretical studies have demonstrated the importance of accounting for coalescent stochasticity in phylogeographical studies, however, there are few empirical examples that do so in the context of explicit hypothesis testing. Here, we provide an example from the Idaho giant salamander (Dicamptodon aterrimus) using 118 mtDNA sequences, nearly 2 kb in length. This species is endemic to mesic forests in northern and central Idaho, and several a priori hypotheses have been erected based both on palaeoclimatic grounds and from phylogeographical studies of codistributed amphibians. Phylogenetic analysis of the D. aterrimus data suggests an expansion from a single refugium south of the Salmon River, whereas the inference from nested clade analysis is one of expansion from a single refugium in the Clearwater drainage. Explicit testing of these hypotheses, using geographically structured coalescent simulations to erect null distributions, indicates we can reject expansion from the Clearwater drainage (pCLW = 0.089), but not expansion from the South Fork of the Salmon drainage (pSAL = 0.329). Furthermore, data from codistributed amphibians suggest that there may have been two refugia, and an amova shows that most of the molecular variance partitioned between the Clearwater and the Salmon drainages (54.40%; P < 0.001) and within drainages (43.61%; P < 0.001). As a result, we also tested three a priori hypotheses which predicted that both the Clearwater and Salmon drainages functioned as refugia during the late Pleistocene; we could reject (PCORD = 0.019) divergence dates during the Cordilleran glacial maxima [c. 20 000 years before present (ybp)], during the Sangamon interglacial (c. 35 000 ybp; pSANG = 0.032), as well as pre-Pleistocene divergence (c. 1.7 Ma; ppP < 0.001). Mismatch distributions and Tajima's D within the individual drainages provide further support to recent population expansion. This work demonstrates coalescent stochasticity is an important phenomenon to consider in testing phylogeographical hypotheses, and suggests that analytical methods which fail to sufficiently quantify this uncertainty can lead to false confidence in the conclusions drawn from these methods.

Geological barriers and restricted gene flow in the holarctic skipper Hesperia comma (Hesperiidae)

Patterns of genetic variation within a species may be a consequence of historical factors, such as past fragmentation, as well as current barriers to gene flow. Using sequence data from the mitochondrial cytochrome oxidase subunit II region (COII) and the nuclear gene wingless, we conducted a phylogeographical study of the holarctic skipper Hesperia comma to elucidate patterns of genetic diversity and to infer historical and contemporary processes maintaining genetic variation. One hundred and fifty-one individuals were sampled from throughout North America and Eurasia, focusing on California and adjacent regions in the western United States where morphological diversity is highest compared to the rest of the range. Analyses of sequence data obtained from both genes revealed a well-supported division between the Old and New World. Within western North America, wingless shows little geographical structure, while a hierarchical analysis of genetic diversity of COII sequences indicates three major clades: a western clade in Oregon and Northern California, an eastern clade including the Great Basin, Rocky Mountains and British Columbia, and a third clade in southern California. The Sierra Nevada and the Transverse Ranges appear to be the major barriers to gene flow for H. comma in the western United States. Relatively reduced haplotype diversity in Eurasia compared to North America suggests that populations on the two continents have been affected by different historical processes.

Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group

Mesic forests in the North American Pacific Northwest occur in two disjunct areas: along the coastal and Cascade ranges of Oregon, Washington, and British Columbia as well as the Northern Rocky Mountains of Idaho, Montana, and British Columbia. Over 150 species or species complexes have disjunct populations in each area, and a priori hypotheses based on phytogeography and geology potentially explain the disjunction via either dispersal or vicariance. Here, we test these hypotheses in the disjunct salamander complex Plethodon vandykei and P. idahoensisby collecting genetic data (669 bp of Cyt b) from 262 individuals. Maximum likelihood analysis indicated reciprocal monophyly of these species, supporting the ancient vicariance hypothesis, whereas parametric bootstrap and Bayesian hypothesis testing allow rejection of the dispersal hypothesis. The coalescent estimate of the time since population divergence (estimated using MDIV) is 3.75 x 106 years, and the 95%credibility interval of this value overlaps with the geological estimate of vicariance, but not the hypothesized dispersal. These results are congruent with the pattern seen in other mesic forest amphibian lineages and suggest disjunction in amphibians may be a concerted response to a geological/climatological event. WithinP. idahoensis, we tested the corollary hypothesis of an inland Pleistocene refugium in the Clearwater drainage with nested clade analysis and coalescent estimates of population growth rate (g). Both analyses support post-Pleistocene expansion from the Clearwater refugium. We corroborated this result by calculating Tajima's Dand mismatch distribution within each drainage, showing strong evidence for recent population expansion within most drainages. This work demonstrates the utility of statistical phylogeography and contributes two novel analytical tools: tests of stationarity with respect to topology in the Bayesian estimation, and the use of coalescent simulations to test the significance of the population growth-rate parameter.

The structure of biodiversity - insights from molecular phylogeography

DNA techniques, analytical methods and palaeoclimatic studies are greatly advancing our knowledge of the global distribution of genetic diversity, and how it evolved. Such phylogeographic studies are reviewed from Arctic, Temperate and Tropical regions, seeking commonalities of cause in the resulting genetic patterns. The genetic diversity is differently patterned within and among regions and biomes, and is related to their histories of climatic changes. This has major implications for conservation science.

The ascaphins: a family of antimicrobial peptides from the skin secretions of the most primitive extant frog, Ascaphus truei

The tailed frog Ascaphus truei occupies a unique position in phylogeny as the most primitive extant anuran and is regarded as the sister taxon to the clade of all other living frogs. Eight structurally related peptides, termed ascaphins 1-8, were isolated from norepinephrine-stimulated skin secretions of A. truei and were shown to possess differential growth inhibitory activity against Escherichia coli and Staphylococcus aureus. Ascaphins 2-7 may be represented by the consensus amino acid sequence GX2DX2KGAAKX3KTVAX2IANX.COOH whereas ascaphin-1 (GFRDVLKGAAKAFVKTVAGHIAN.NH2) and ascaphin-8 (GFKDLLKGAAKALVKTVLF.NH2) contain a C-terminally alpha-amidated residue. The ascaphins show no appreciable structural similarity with other families of antimicrobial peptides from frog skin but display limited sequence identity with the cationic, amphipathic alpha-helical peptides pandinin 1 and opistoporin 1, isolated from the venoms of African scorpions. Ascaphin-8 shows the highest potency against a range of pathogenic microorganisms but has the greatest haemolytic activity. The data indicate that the host defence strategy of using antimicrobial peptides in skin secretions arose early in the evolution of anurans.

Phylogeographical patterns in the American Pacific Northwest: lessons from the arionid slug Prophysaon coeruleum

Some of the earliest studies of phylogenetic concordance involve native plants from the Pacific Northwest where many taxa showed clear genetic breaks between southern and northern populations. To test whether similar breaks also occur in invertebrate species with low dispersal capacities, genetic data from two mitochondrial genes are assembled for individuals of the arionid slug Prophysaon coeruleum throughout the species' range. Bayesian inference revealed three major clades and a total of eight subclades. It is argued that the demographic and genealogical past of P. coeruleum has resulted in a deep and shallow phylogeographical structure. The deep structure is at least 2.6-5.9 million years old and therefore clearly predates the Pleistocene period. Superimposed on this structure is a shallow structure that is most likely less than 2 million years old and probably the result of Pleistocene perturbations. Molecular analyses revealed that the three known colour traits in P. coeruleum do not represent monophyletic groups and that they do not match the patterns of genetic structure found. It is argued that the colour traits are perhaps a response to different levels of UV-radiation. The study adds to the increasing evidence that the phylogeographical structure of some taxa is more complex than previously thought. Moreover, it shows that genealogical concordance should not be deduced from phylogeographical patterns alone but should be based on an understanding of timing and causes of historical processes that lead to those patterns.

Genetic consequences of climatic oscillations in the Quaternary

An appreciation of the scale and frequency of climatic oscillations in the past few million years is modifying our views on how evolution proceeds. Such major events caused extinction and repeated changes in the ranges of those taxa that survived. Their spatial effects depend on latitude and topography, with extensive extinction and recolonization in higher latitudes and altitudinal shifts and complex refugia nearer the tropics. The associated population dynamics varied with life history and geography, and the present genetic constitution of the populations and species carry attenuated signals of these past dynamics. Phylogeographic studies with DNA have burgeoned recently and studies are reviewed from the arctic, temperate and tropical regions, seeking commonalities of cause in the resulting genetic patterns. Arctic species show distinct shallow genetic clades with common geographical boundaries. Thus Beringia is distinct phylogeographically, but its role as a refugial source is complex. Arctic taxa do not show the common genetic pattern of southern richness and northern purity in north-temperate species. Temperate refugial regions in Europe and North America show relatively deep DNA divergence for many taxa, indicating their presence over several Ice Ages, and suggesting a mode of speciation by repeated allopatry. DNA evidence indicates temperate species in Europe had different patterns of postglacial colonization across the same area and different ones in previous oscillations, whereas the northwest region of North America was colonized from the north, east and south. Tropical montane regions contain deeply diverged lineages, often in a relatively small geographical area, suggesting their survival there from the Pliocene. Our poor understanding of refugial biodiversity would benefit from further combined fossil and genetic studies.

Biogeographic patterns and current distribution of molecular-genetic variation among populations of speckled dace, Rhinichthys osculus (Girard)

We examined genetic diversity within- and among-populations of speckled dace (Rhinichthys osculus) in five major drainage systems in the state of Oregon in western North America. Analysis of sequence variation in a 670-bp segment of the mitochondrial cytochrome b gene revealed deep divergence among basins and high genetic diversity within basins. Application of a molecular clock indicated that the divergence time among basins reflects vicariant events during the late Miocene to early Pliocene. The high levels of genetic diversity observed within basins is likely due to large historic population sizes, in particular, within the Klamath Basin. Two highly divergent mtDNA lineages were found to co-occur in populations in the Klamath Basin. This result may be indicative of a complex history of isolation and reconnection in this basin and/or multiple colonization events. Based on the observed level of mtDNA divergence these lineages may represent two reproductively isolated sympatric taxa. We recommend that major basins be regarded as distinct ESUs based on high levels of subdivision, deep divergences, and reciprocal monophyly among basins.

Genetic structure in a montane ranid frog: restricted gene flow and nuclear-mitochondrial discordance

There is substantial debate over the criteria that should be used to group populations of a species into distinct units for conservation (e.g. evolutionarily significant units, management units, distinct population segments). However, in practice molecular genetic differentiation is often the only or main criterion used to identify such units. Most genetic studies attempting to define conservation units in animals use a single molecular marker, most often mitochondrial, and use samples from a limited number of populations throughout the species' range. Although there are many benefits to using mtDNA, certain features can cause it to show patterns of differentiation among populations that do not reflect the history of differentiation at the nuclear genome where loci controlling traits of adaptive significance presumably occur. Here we illustrate an example of such mitochondrial-nuclear discordance in a ranid frog, and show how using mtDNA or nuclear loci alone could have led to very different conservation recommendations. We also found very high genetic differentiation among populations on a local scale, and discuss the conservation implications of our results.

Protamines in the internally fertilizing neobatrachian frogEleutherodactylus coqui

The internally fertilizing primitive frog Ascaphus truei (family Ascaphidae) from the Pacific Northwest is the only frog with an intromittent organ. The more advanced neobatrachian frog Eleutherodactylus coqui (family Leptodactylidae) from Puerto Rico has secondarily acquired internal fertilization but mates by cloacal apposition. Nonetheless, both frogs have introsperm with an elongated head containing highly condensed chromatin. Characterization of sperm nuclear basic proteins (SNBPs) in E. coqui by acid-urea polyacrylamide gel electrophoresis indicates that, as in A. truei, testes from a single animal contain several protamines. Amino acid analysis indicates a composition for the most rapidly moving protamine of each species as follows: in E. coqui, ARG (35.6 mol %) + LYS (3.8 mol %) + HIS (7.6 mol %) = 47 mol % total basic residues and in A. truei, ARG (42.1 mol %) + LYS (11.1 mol %) = 53.2 mol % total basic residues. Transmission electron microscopy shows that E. coqui introsperm, like those in A. truei, are elongate with highly condensed chromatin. However, E. coqui introsperm lacks an axial perforatorium that extends into an endonuclear canal. These morphological features are plesiomorphic (primitive) and shared by A. truei with urodeles and basal amniotes (Jamieson et al. (1993) Herpetologica 49:52-65). In E. coqui introsperm, the nucleoprotein complex has a cross-sectional axis of 420 + 20 angstroms and shows a knobby chromatin structural organization in TEM. The presence of arginine-enriched protamines in both a basal anuran like the ascaphid A. truei and a more advanced neobatrachian like the leptodactylid E. coqui supports the hypothesis that internal fertilization acts as a constraint on the range of SNBP diversity in animals.

Molecular systematics and phylogeography of the Plethodon elongatus species group: combining phylogenetic and population genetic methods to investigate species history

Plethodon elongatus and P. stormi (Caudata: Plethodontidae) are Pacific Northwest endemic species which occur in northwestern California and southwestern Oregon. Studies on these salamanders have resulted in differing taxonomic conclusions, but the underlying historical hypotheses, at both inter- and intraspecific levels, have never been examined in a molecular framework. Here, representatives of 81 populations from throughout the range of both taxa are sequenced. Portions of three mitochondrial protein-coding genes (cytochrome b, NADH dehydrogenase subunit 4, and ATPase 6) were sequenced. Four haplotype groups with nonoverlapping geographical ranges were recovered in separate and combined analyses of the data. One clade corresponds to the distribution of P. stormi, while the remaining three comprise P. elongatus. Phylogenetic relationships among haplotype groups differ in separate analyses of the genes but converge on a well-supported topology, with P. elongatus and P. stormi as monophyletic sister taxa, in combined Maximum Parsimony and Maximum Likelihood analyses. Population genetic analyses of mismatch distributions and Tajima's D-statistic are consistent with range expansion for the largest clade within P. elongatus, covering the northern two-thirds of the species range. In contrast, the P. stormi haplotype clade and the P. elongatus clade from the southern third of the species range may have been relatively stable. Morphological boundaries between P. elongatus and P. stormi are largely congruent with mitochondrial DNA breaks and continued treatment as sister taxa is supported. Although mitochondrial DNA haplotype groups may reflect historical separation within P. elongatus, genetic barriers are incongruent with intraspecific patterns of morphological variation.

Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwest North America

The yellow-pine chipmunk, Tamias amoenus, is common in xerophytic forests throughout much of northwest North America. We analyzed cytochrome b sequence variation from 155 individuals representing 57 localities across the distribution of T. amoenus including 10 additional species of Tamias. Maximum likelihood and parsimony tree estimation methods were used in conjunction with nested clade analysis to infer both deep and population-level processes. Our results indicate that two currently recognized subspecies of T. amoenus (T. a. canicaudus and T. a. cratericus) are not nested within other samples of T. amoenus. Maximum uncorrected levels of intraspecific sequence divergence within remaining samples of T. amoenus are >7%. Substantial geographic variation is characterized by 12 well-supported clades that correspond to distinct mountain ranges, but do not necessarily follow existing subspecific taxonomy. Significant association between geography and genealogy was detected within many of these clades and can be attributed to different population-level processes including past fragmentation, recent range expansion, and isolation by distance.

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

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.

Contrasting patterns of genetic variation in the two sympatric geckos Gekko tawaensis and G. japonicus (Reptilia: Squamata) from western Japan, as revealed by allozyme analyses

Allozyme variation in two congeneric sympatric geckos, Gekko tawaensis and G. japonicus, from western Japan was examined. These species show similar densities and spatial arrangements of populations in this region, and their genetic structures are thus expected to have been formed under the influences of comparable geohistorical, environmental, and demographic factors. Results of the analyses, however, revealed strikingly different genetic patterns in the two species. Populations of G. tawaensis invariably showed a remarkably lowered heterozygosity (0-0.017) compared to G. japonicus (0.089-0.124). On the other hand, the genetic heterogeneity among populations is much greater in G. tawaensis (F(ST)=0.726) than in G. japonicus (F(ST)=0.101). The Mantel test failed to detect any significant correlations between log (estimated migration rate) and log (geographic distance) in either species, or between matrices of interpopulation pairwise F(ST) for the two species. These results suggest that, in each species, formation of the current genetic structure in western Japan has been chiefly influenced by stochastic factors, rather than the geohistorical architecture of this region. The high F(ST) and low heterozygosity in G. tawaensis suggest the effects of severe local fragmentation. On the other hand, the relatively low F(ST) and high heterozygosity in G. japonicus imply extensive gene flow among populations. Absence of significant correlations between the estimated migration rate and geographic distance in G. japonicus may suggest that such gene flow is promoted by human-mediated transport of this primarily house-dwelling lizard.

Molecular phylogeography of common garter snakes (Thamnophis sirtalis) in western North America: implications for regional historical forces

Complete ND2 and partial ND4 and cytochrome b mitochondrial DNA (mtDNA) sequences were analysed to evaluate the phylogeographic patterns of common garter snakes (Thamnophis sirtalis) in western North America. This species is widely distributed throughout North America, and exhibits extensive phenotypic variation in the westernmost part of its range. The overall phylogeographic pattern based on mtDNA sequences is concordant with results from studies of other species in this region, implicating historical vicariant processes during the Pleistocene and indicating bottleneck effects of recent dispersal into postglacial habitat. Indeed, the topology is statistically consistent with the hypothesis of both southern (Great Basin and California) and northern (Haida Gwaii) refugia. Specifically, we identified genetic breaks among three major clades: Northwest Coastal populations, Intermountain populations, and all California populations. The California clade contained the only other well-supported branching patterns detected; relationships among populations within the two northern clades were indistinguishable. These molecular splits contrast sharply with all prior geographical analyses of phenotypic variation in T. sirtalis in this region. Our results suggest that the extensive phenotypic variation in western T. sirtalis has been shaped more by local evolutionary forces than by shared common ancestry. Consequently, we consider all morphologically based subspecies designations of T. sirtalis in this region invalid because they do not reflect reciprocal monophyly of the mtDNA sequences.

The Atlas mountains as a biogeographical divide in North-West Africa: evidence from mtDNA evolution in the Agamid lizard Agama impalearis

Since the early Miocene there have been several physical events within NW Africa that are likely to have had a major impact on its faunal diversity. Phylogeographical studies will shed new light on the biogeography of the region. We analysed mitochondrial DNA diversity in the agamid lizard Agama impalearis (also called A. bibronii) based on sequences from mitochondrial genes with very different evolutionary rates (16S rRNA and ND2). Well-supported topologies of rooted maximum parsimony trees (with a Laudakia outgroup) and unrooted haplotype networks indicated two major clades with similar branch lengths. These clades have non-overlapping distributions representing respective areas to the North and West and South and East of the Atlas mountain chain and each could be given full species recognition. Nested clade analyses indicate that historical and possible present-day allopatry account for the primary phylogeographic pattern. Further evidence is provided by the estimated timing of cladogenesis, based on calibration of evolutionary rates in the ND2 gene of another continental Agamid. Sequence divergence between clades corresponds to 8.5-9.4mya, coinciding with the main period of orogenic uplift of the Atlas. Additional evidence of cladogenesis by allopatric fragmentation is also detected within the North/West Atlas clade, although contiguous range expansion is the most predominant explanation of more recent phylogeographic effects in this species. Miocene vicariance mediated by the Atlas may provide a general explanation of intra- and interspecific biogeographical patterns in NW African species.

Out of Africa again and again

The publication of a haplotype tree of human mitochondrial DNA variation in 1987 provoked a controversy about the details of recent human evolution that continues to this day. Now many haplotype trees are available, and new analytical techniques exist for testing hypotheses about recent evolutionary history using haplotype trees. Here I present formal statistical analysis of human haplotype trees for mitochondrial DNA, Y-chromosomal DNA, two X-linked regions and six autosomal regions. A coherent picture of recent human evolution emerges with two major themes. First is the dominant role that Africa has played in shaping the modern human gene pool through at least two--not one--major expansions after the original range extension of Homo erectus out of Africa. Second is the ubiquity of genetic interchange between human populations, both in terms of recurrent gene flow constrained by geographical distance and of major population expansion events resulting in interbreeding, not replacement.

Phylogeography of the red-tailed chipmunk (Tamias ruficaudus), a northern Rocky Mountain endemic

The northern Rocky Mountains have experienced a complex history of geological events and environmental fluctuation, including Pleistocene glaciation. To provide an initial assessment of the genetic impact of this history on the regional biota we estimated phylogenetic relationships within Tamias ruficaudus, a regional endemic, from cytochrome b sequence variation using parsimony, maximum likelihood, and nested clade analysis. Analyses of sequence variation in 187 individuals from 43 localities across the distribution of T. ruficaudus indicate a history of vicariance events and range fluctuation consistent with successive periods of extensive Pleistocene glaciation in the northern Rocky Mountains. Intraspecific divergence levels (c. 4.7% uncorrected) and phylogenetic structure are consistent with a genealogical vicariance initiated prior to the Late Pleistocene, whereas nested clade analyses indicate more recent population history structured by both fragmentation and range expansion. A comparison of sequence variation with bacular morphology indicates that the two genetically and morphologically differentiated entities exhibit a zone of differential character introgression. Sequence data support a multiple refugia hypothesis and provide a phylogeographical case study for the ongoing synthesis of regional biogeography for northern Rocky Mountain endemics.

Phylogeography of the dusky shrew, Sorex monticolus (Insectivora, Soricidae): insight into deep and shallow history in northwestern North America

Phylogenetic relationships among the dusky shrew (Sorexmonticolus) and eight related species (S. bairdi, S. bendirii, S. neomexicanus, S.ornatus, S. pacificus, S. palustris, S. sonomae and S.vagrans) were assessed using sequences from the mitochondrial cytochrome b gene (801 bp). Analyses using parsimony and maximum likelihood revealed significant molecular variation not reflected in previous morphological studies of these species. Conversely, three morphologically defined species (S.bairdi, S.neomexicanus and S.pacificus) were poorly differentiated. Sorexornatus and S.vagrans represented basal taxa for a more inclusive group that included: (i) a widespread Continental clade containing S.monticolus (Arizona to Alaska, including S. neomexicanus); (ii) a Coastal clade containing S.monticolus (Oregon to south-east Alaska, including S. bairdi and S. pacificus); (iii) the semiaquatic species (S. bendirii and S. palustris); and (iv) S.sonomae. Additional subdivision was observed within the Continental clade corresponding to populations from the northern and southern Rocky Mountains. Average uncorrected sequence divergence between the Coastal and Continental clades was 5.3% (range 4.5-6.2%), which exceeds many interspecific comparisons within this species complex and within the genus Sorex. Lack of resolution of internal nodes within topologies suggests a deep history of rapid diversification within this group. Late Pleistocene/Holocene glacial perturbations are reflected in the shallow phylogeographic structure within these clades in western North America. Our results suggest also that S. monticolus is not monophyletic under current taxonomic nomenclature. This perspective on phylogeographic history was developed within a growing comparative framework for other organisms in western North America.