Phylogeographic evidence for two mesic refugia in a biodiversity hotspot

Phylogeographic studies of flora in species-rich south-western Australia point to complex evolutionary histories, reflecting patterns of persistence and resilience to climatic changes during the Pleistocene. We asked whether coastal areas of the mid-west and south, as well as granite outcrops and inland ranges, have acted as major refugia within this region during Pleistocene climatic fluctuations by analysing phylogeographic patterns in the shrub Calothamnus quadrifidus R.Br. (Myrtaceae). We determined variation in chloroplast DNA data for 41 populations across the geographic range. Relationships and major clades were resolved using parsimony and Bayesian analyses. We tested for demographic and spatial expansion of the major clades and estimated clade divergence dates using an uncorrelated, lognormal relaxed clock based on two conservative chloroplast mutation rates. Two distinct phylogeographic clades were identified showing divergence during the Pleistocene, consistent with other phylogeographic studies of south-west Australian flora, emphasising the impact of climatic oscillations in driving divergence in this landscape. The southern clade was more diverse, having higher haplotype diversity and greater genetic structure, while the northern clade showed evidence of fluctuation in population size. Regions of high haplotype diversity with adjacent areas of low diversity observed in each clade indicated the locations of two coastal refugia: one on the south coast and another along the mid-west coast. This is the first evidence for major Pleistocene refugia using chloroplast genetic data in a common, widespread species from this region.     

Postglacial expansion of the southern red-backed vole (Clethrionomys gapperi) in North America

Dynamic climatic oscillations of the Pleistocene dramatically changed the distributions of high latitude species. Molecular investigations of a variety of organisms show that processes of postglacial colonization of boreal regions were more complex than initially thought. Phylogeographical and coalescent analyses were conducted on partial sequences of the cytochrome b gene (600 bp) from 64 individuals of Clethrionomys gapperi from North Carolina, Pennsylvania, Minnesota, Idaho, Washington, British Columbia, Northwest Territories, and Alaska to test hypotheses relating to Pleistocene refugia and postglacial colonization routes. Three divergent clades (east, west, central) were identified with highest net divergence (dA = 5.2%) between the eastern and western clades. Populations from the recently deglaciated higher latitudes of Canada and Alaska are closely related to lower latitude populations of the central clade (dA = 1.2%) suggesting recent expansion from this midwestern region. No representatives from the east or west clade were found at latitudes higher than 50 degrees N, indicating that postglacial colonization occurred through a midcontinental route. The high latitude population from the Northwest Territories exhibited demographic patterns and genetic diversity consistent with a stable noncolonizing population. This population is found near the Mackenzie range, where the two continental ice sheets were believed to have coalesced. Molecular variation observed in this population may be the result of leading edge population diversifying in the continental corridor or may reflect the signal of a high latitude refugial population.     

A mitogenic view on the evolutionary history of the Holarctic freshwater gadoid, burbot (Lota lota)

Climatic oscillations during the Pleistocene epoch had a dramatic impact on the distribution of biota in the northern hemisphere. In order to trace glacial refugia and postglacial colonization routes on a global scale, we studied mitochondrial DNA sequence variation in a freshwater fish (burbot, Lota lota; Teleostei, Gadidae) with a circumpolar distribution. The subdivision of burbot in the subspecies Lota lota lota (Eurasia and Alaska) and Lota lota maculosa (North America, south of the Great Slave Lake) was reflected in two distinct mitochondrial lineages (average genetic distance is 2.08%). The lota form was characterized by 30 closely related haplotypes and a large part of its range (from Central Europe to Beringia) was characterized by two widespread ancestral haplotypes, implying that transcontinental exchange/migration was possible for cold-adapted freshwater taxa in recent evolutionary time. However, the derived mitochondrial variants observed in peripheral populations point to a recent separation from the core group and postglacial recolonization from distinct refugia. Beringia served as refuge from where L. l. lota dispersed southward into North America after the last glacial maximum. Genetic variation in the maculosa form consisted of three mitochondrial clades, which were linked to at least three southern refugia in North America. Two mitochondrial clades east of the Continental Divide (Mississippian and Missourian clades) had a distinct geographical distribution in the southern refuge zones but intergraded in the previously glaciated area. The third clade (Pacific) was exclusively found west of the Continental Divide.     

Identifying glacial refugia in a geographic parthenogen using palaeoclimate modelling and phylogeography: the New Zealand stick insect Argosarchus horridus (White)

We have used phylogeographic analysis of mitochondrial DNA (COI and COII genes) and ecological niche modelling (ENM) to reconstruct the population history of Argosarchus horridus (White), a widespread species of New Zealand stick insect. These data were used to address outstanding questions on the role of glacial refugia in determining the distribution and genetic structure of New Zealand species. Phylogeographic analysis shows a general pattern of high diversity in upper North Island and reduced diversity in lower North Island and South Island. The ENM indicates that during the last glacial maximum, A. horridus was largely restricted to refugia around coastal areas of North Island. The ENM also suggests refugia on the northeast coast of South Island and southeast coast of North Island and this prediction is verified by phylogeographic analysis, which shows a clade restricted to this region. Argosarchus horridus is also most likely a geographic parthenogen where males are much rarer at higher latitudes. The higher levels of genetic variation in northern, bisexual populations suggest southern and largely unisexual populations originated from southwardly expanding parthenogenetic lineages. Bayesian skyline analysis also provides support for a recent population size increase consistent with a large increase in geographic distribution in the late Pleistocene. These results exemplify the utility of integrating ENM and phylogeographic analysis in testing hypotheses on the origin of geographic parthenogenesis and effects of Pleistocene environmental change on biodiversity.     

Geographic pattern of genetic variation in Pinus resinosa: area of greatest diversity is not the origin of postglacial populations

Genetic diversity is low in natural populations of red pine, Pinus resinosa, a species that has a vast range across north-eastern North America. In this study, we examined 10 chloroplast microsatellite or simple sequence repeats (cpSSR) loci in 136 individuals from 10 widespread populations. Substantial variation for the cpSSR loci was observed in the study populations. The contrast with red pine's lack of variation for other types of loci is likely to be due to the higher mutation rates typical of SSR loci. The amount of variation is lower than that generally found for cpSSR loci in other pine species. In addition, the variation exhibits a striking geographical pattern. Most of the genetic diversity is among populations, with little within populations, indicating substantial isolation of and genetic drift within many populations in the southern half of the species distribution. The greatest diversity now occurs in the north-eastern part of New England, which is especially intriguing because this entire area was glaciated. Thus the centre of diversity cannot be the origin of postglacial populations, rather it is likely caused by admixture, most probably because of influences from two separate refugia. Furthermore, the pattern indicates that the spread of red pine since the last glaciation is rather more complex than usually described, and it likely includes more than one refugia, complex migration routes, and postglacial-retreat isolation and genetic drift among shrinking populations in regions of the present southern range.     

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.     

Dynamics in the evolution of sexual traits: losses and gains,radiation and convergence in yellow wagtails (Motacilla flava)

We analyse patterns of genetic diversity and song complexity in the Palaearctic yellow wagtail (Motacilla flava), a highly polytypic species complex. Mitochondrial and nuclear DNA show that the complex is polyphyletic, despite parallel plumage variation in western and eastern clades. In the western clade there is genetic structure among southern subspecies, haplotype diversity decreases with latitude, and northern subspecies show evidence of bottlenecking and rapid expansions, as expected from isolation in glacial refugia followed by postglacial colonization. However, northern subspecies, which have more divergent male plumages, lack genetic structure and sing simpler songs. Loss of song complexity and evolution of plumage in founder populations are consistent with the Kaneshiro model, which posits that variation among species is a consequence of founder-induced shifts in female preference leading to loss of ancestral male sexual traits. Our results suggest possible postglacial founder-effect mechanisms for the morhological diversification of the yellow wagtail complex.     

HOLARCTIC PHYLOGEOGRAPHY OF AN ASEXUAL SPECIES COMPLEX I. MITOCHONDRIAL DNA VARIATION IN ARCTIC DAPHNIA

Pleistocene glacial cycles undoubtedly altered the evolutionary trajectories of many taxa, yet few studies have examined the impact of such events on genetic differentiation and phylogeography at large geographic scales. Here we present the results of a circumarctic survey of mitochondrial DNA diversity in members of the Daphnia pulex complex. The analysis involved the survey of restriction site polymorphisms in a 2100-bp fragment of the NADH-4 (ND4) and NADH-5 (ND5) genes for 276 populations representing the two major groups (tenebrosa and pulicaria) in this complex across their Holarctic range. A comparison of the distribution patterns for seven clades in this complex revealed very clear phylogeographic structuring. Most notably, pulicaria group lineages were restricted primarily to the Nearctic, with some colonization of formerly glaciated portions of northern Europe. This group was not detected from vast expanses of northern Eurasia, including the Beringian glacial refuge. In contrast, tenebrosa group haplotypes showed considerable intercontinental divergence between Eurasian and North American lineages, but were absent from Greenland and Iceland, as well as the Canadian arctic archipelago. Dispersal in Eurasia was primarily in a westerly direction from Beringia, whereas dispersal in the Nearctic followed proglacial drainage patterns. Long-distance dispersal of certain lineages was observed in both groups, and variation in haplotype richness and nucleotide diversity allowed us to make inferences about the positioning of putative glacial refugia. Overall, the phylogeographic pattern of diversification in this arctic complex is characterized by the apparently unique postglacial histories for each clade, indicating that even closely allied taxa can respond independently to the allopatric effects of glacial cycles. This is in sharp contrast to other phylogeographic studies of species assemblages from more southern (unglaciated) latitudes, which are often characterized by concordant patterns.     

Phylogeography reveals latitudinal population structure in the common herb Plantago coronopus

The increase in gene diversity from high to low latitudes is a widely recognized biogeographical pattern, often shaped by differential effects of Late Quaternary climatic changes. Here, we evaluate the effects of Pleistocene climatic changes from northern Europe to North Africa and their implications on the population differentiation of the widespread, short‐lived herb Plantago coronopus. We used amplified fragment length polymorphism to investigate the population structure and phylogeography of P. coronopus in 273 individuals from 29 populations covering its complete latitudinal range. Although Bayesian clustering, principal coordinates analysis and a consensus UPGMA tree were not fully congruent, two well‐supported clades, associated with distinct latitudinal zones (northern Europe and the Mediterranean region), were revealed as a general pattern. Moreover, populations from the western Atlantic edge and, to a lesser extent, the central Mediterranean region exhibited signs of admixture, suggesting secondary contacts. The admixed populations in the western Atlantic and central Mediterranean are geographically intermediate between the northern and southern lineages. The northernmost lineage exhibited low genetic diversity, a clear sign of a recent colonization. In contrast, populations from the southernmost part of the range showed the highest level of genetic diversity, indicating possible refugia for the species during the Quaternary ice ages. Overall, our study allows spatial structure of the genetic variation of a widespread herb across its latitudinal range to be disentangled and provides insights into how past climatic history influences present genetic patterns. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 618–634.     

Refugia in the Cordilleran ice sheet of western North America: chloroplast DNA diversity in the Arctic–alpine plant Oxyria digyna

Aim  Late Pleistocene ice sheets are thought to have covered most of western Canada, including all of British Columbia (BC). We examine patterns of genetic variation in an Arctic–alpine plant to evaluate the possibility of full glacial refugia within the area covered by the Cordilleran ice sheet (CIS) and to uncover post-glacial migration routes.
Location  Western North America.
Methods  We sampled 1030 individuals of the Arctic–alpine plant Oxyria digyna from 117 populations distributed over much of its range in western and northern North America. DNA haplotypes were identified using restriction site analysis of two chloroplast DNA intergene spacer regions, psb A- trn H and trn T-L. We examined the geographical distribution of haplotype diversity in relation to latitude, and also compared various indices of diversity in putatively glaciated and unglaciated regions. Patterns of migration were inferred using nested clade analysis.
Results  We detected a total of 20 haplotypes. High haplotype diversity was found in Beringia, in unglaciated western USA, and in northern BC at 57–59° N, well within the accepted limits of the CIS. Ancestral haplotypes were also centred in northern BC.
Main conclusions  High genetic diversity of Oxyria digyna is expected in unglaciated regions, but unexpected in northern BC if British Columbia was entirely covered by ice during the late Pleistocene. Our observations suggest the presence of unglaciated areas providing late Pleistocene refugia in northern BC. Such refugia would have important implications for the origins and migrations of many plant and animal species in north-western North America.     

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.     

Late Quaternary climate change and spatial genetic structure in the shrub Banksia hookeriana

Spatial genetic variation within species is influenced by both contemporary and historical factors. We attempted to assess the impact of increased aridity and lower temperatures associated with the last glacial maximum on possible refugia and the structuring of genetic variation in Banksia hookeriana, a shrub species restricted to deep sands on the Eneabba sandplain and adjacent Gingin Scarp/Dandaragan Plateau, centred 300 km north of Perth, Western Australia. We used optically stimulated luminescence (OSL) dating to estimate the last time these sands were mobile, as well as amplified fragment length polymorphisms (AFLP) to infer spatial patterns and the phylogeographical history of genetic variation among 15 populations of B. hookeriana. While genetic variation at the species level was high, with 96.6% of 238 AFLP markers polymorphic, average within population gene diversity was low (H(pop) = 0.16). Of the total genetic variation, an analysis of molecular variance (amova) partitioned 70% within populations, 24% among populations within substrate and 6% between substrates. There was an isolation-by-distance effect among populations within the same substrate, but not across substrates, and ordination highlighted genetic differentiation between the sandplain and scarp/plateau populations. A neighbour-joining tree identified the sandplain populations as a distinct clade, with the exception of the most northern sandplain population, which clustered with two northern and eastern plateau populations. The most southern plateau populations formed a clade sister to the sandplain clade. OSL dating of sand at six extant populations suggested that dunes were last mobile 15,000-35,000 years ago, with no clear difference in the ages of sandplain and plateau dunes. These data are consistent with a historical scenario of (re)colonization from isolated refugia of smaller populations either within the patchily vegetated sandplain and/or refugia at the northern, eastern and southern sandplain/scarp margins following postglacial climate amelioration and dune stabilization. Historic interpretations were confounded by the possible effects of long-distance dispersal, natural selection by substrate, and weak and/or ancient introgression with the sister species, Banksia prionotes.     

Phylogeography and post-glacial colonization patterns of the rainbow darter, Etheostoma caeruleum (Teleostei: Percidae)

Aim To examine the effects of historical climate change and drainage isolation on the distribution of mitochondrial DNA cytochrome b genetic variation within the rainbow darter, Etheostoma caeruleum (Percidae: Etheostomatinae). Location Eastern North American streams including tributaries to the Mississippi River, Great Lakes, Potomac River and Hudson Bay drainages. Methods Parsimony analyses, Bayesian analyses and haplotype networks of mitochondrial DNA sequences. Results Four major clades were recovered from sampled populations of E. caeruleum. Three of four clades are distributed in the western portion of the species’ range (primarily west of the Mississippi River). Samples from this region do not form a monophyletic group, and sequences often vary greatly between samples from adjacent stream systems (up to 7.2% divergence). A basal clade includes samples from the White River system in the Ozark Highlands. The northern Ozarks–upper Midwest clade includes samples from Missouri River tributaries and the upper Midwest (Hudson Bay, upper Mississippi River, and western Lake Michigan drainage). The eastern clade is composed of individuals from the Ohio River, Great Lakes and Potomac River. The Mississippi River corridor clade includes samples from middle and lower Mississippi River tributaries. Main conclusions The four major clades of E. caeruleum are deep allopatric lineages with well‐defined boundaries and have additional phylogeographical structure within each clade. The Ozark Highlands have the greatest levels of diversity relative to distributional area, with marked cytochrome b subdivisions between adjacent stream systems. Samples from previously glaciated areas do not have a subset of the cytochrome b diversity found in unglaciated areas, but four separate source areas are identified based on phylogenetic analyses. Dispersal into previously glaciated areas followed several known glacial outlets and, based on sequence divergence between populations, may have occurred during different glacial or interglacial stages. The disjunct distribution and cytochrome b pattern of E. caeruleum in the Mississippi River corridor clade is consistent with late Pleistocene and Recent changes in the course and characteristics of the middle and lower Mississippi River. Phylogeographical boundaries between clades of E. caeruleum correspond to independent sources of biogeographical information and provide insight into historical stream drainage relationships, post‐glacial colonization and drainage isolation patterns.     

Genetic diversity and structure of western white pine (Pinus monticola) in North America: a baseline study for conservation, restoration, and addressing impacts of climate change

Western white pine (Pinus monticola) is an economically and ecologically important species in western North America that has declined in prominence over the past several decades, mainly due to the introduction of Cronartium ribicola (cause of white pine blister rust) and reduced opportunities for regeneration. Amplified fragment length polymorphism (AFLP) markers were used to assess the genetic diversity and structure among populations at 15 sites (e.g., provenances) across the native range of western white pine. The level of genetic diversity was different among 15 populations tested using 66 polymorphic AFLP loci. Nei’s gene diversity (H _E) at the population level ranged from 0.187 to 0.316. Genetic differentiation (G _ST) indicated that 20.1% of detected genetic variation was explained by differences among populations. In general, populations below 45^oN latitude exhibited a higher level of genetic diversity than higher latitude populations. Genetic distance analysis revealed two major clades between northern and southern populations, but other well-supported relationships are also apparent within each of the two clades. The complex relationships among populations are likely derived from multiple factors including migration, adaptation, and multiple glacial refugia, especially in higher latitudes. Genetic diversity and structure revealed by this study will aid recognition and selection of western white pine populations for species management and conservation programs, especially in consideration of current and future climate changes.     

Highest genetic diversity at the northern range limit of the rare orchid Isotria medeoloides

Populations in previously glaciated regions are often genetically depauperate in comparison with populations at lower latitudes, due either to bottlenecks experienced in post-glacial colonization or to contemporary genetic drift in small, peripheral populations. Populations of the rare self-fertilizing North American orchid Isotria medeoloides are largest in the previously glaciated region near the northern range limit, allowing us to examine the role of historical versus contemporary processes in determining population genetic diversity and structure. If contemporary processes predominate, genetic diversity should increase with increasing census size. In contrast, if sequential bottlenecks associated with colonization are paramount, diversity should decrease with latitude and be relatively insensitive to census size. We genotyped 299 individuals from 20 populations at four variable microsatellite loci to contrast genetic diversity and structure for populations in previously glaciated regions versus previously unglaciated regions. Populations were highly inbred (F=0.95) and highly differentiated (R(ST)=0.485). Across all sampled populations, genetic diversity decreased and genetic differentiation increased with declining population size. Small southern populations were especially differentiated and genetically depauperate. In the glaciated part of the range, genetic diversity increased as populations approached the northern range limit, demonstrating the centrality of contemporary processes for this post-glacial colonist.     

Phylogeographical patterns and genetic diversity in three species of Eurasian boreal forest beetles

Many species that occur in formerly glaciated areas of Fennoscandia have reached their current ranges from glacial refugial areas in Eurasia. Little is known of the refugia and postglacial colonization routes of insect species that are confined to boreal forests. Here, we investigate the phylogeography of three species of saproxylic beetles distributed across Eurasia: two rare boreal forest specialists, Pytho kolwensis and Pytho abieticola , and a common, less specialized species, Pytho depressus . In all species, there were two well-defined haplotype clades based on 645 bp of cytochrome oxidase subunit I gene sequence. In each species one clade was found only in China. The other clade occurred from China to north-western Europe in both P. kolwensis and P. depressus , but was apparently absent from China in P. abieticola. In spite of common phylogeographical patterns, the distribution of genetic variation differed markedly between the three species. In P. kolwensis , a highly-threatened species in old-growth forests in Fennoscandia, there was an extremely low level of genetic variation throughout Eurasia. One common haplotype, represented by 86% of the samples, dominated in all sampling localities. Levels of genetic variation were higher in both P. abieticola and P. depressus , with 31% and 58%, respectively, of the samples representing a unique haplotype. In each species, relationships between haplotypes were not well resolved, and haplotypes from one sampling locality were generally not clustered in either Neighbour-joining trees or statistical parsimony networks. These patterns in the distribution of genetic variation can be attributed to differences in the species' population sizes, ecologies, glacial refugial areas, and postglacial colonization dynamics.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 267–279.     

A multilocus study of pine grosbeak phylogeography supports the pattern of greater intercontinental divergence in Holarctic boreal forest birds than in birds inhabiting other high-latitude habitats

Aim Boreal forest bird species appear to be divided into lineages endemic to each northern continent, in contrast to Holarctic species living in open habitats. For example, the three-toed woodpecker (Picoides tridactylus) and the winter wren (Troglodytes troglodytes) have divergent Nearctic and Palaearctic mitochondrial DNA clades. Furthermore, in these species, the next closest relative of the Nearctic/Palaearctic sister lineages is the Nearctic clade, suggesting that the Palaearctic may have been colonized from the Nearctic. The aim of this study is to test this pattern of intercontinental divergence and colonization in another Holarctic boreal forest resident – the pine grosbeak (Pinicola enucleator). Location The Holarctic. Methods We sequenced the mitochondrial ND2 gene and Z-specific intron 9 of the ACO1 gene for 74 pine grosbeaks collected across the Holarctic. The sequences were used to reconstruct the phylogeographical history of this species using maximum likelihood analysis. Results We discovered two distinct mitochondrial and Z-specific lineages in the Nearctic and one in the Palaearctic. The two Nearctic mtDNA lineages, one in the northern boreal forest and one in south-western mountain forest, were more closely related to each other than either was to the Palaearctic clade. Two Nearctic Z-chromosome clades were sympatric in the boreal and south-western mountain forests. Unlike the topology of the mtDNA tree, the relationship among the Z-chromosome clades was the same as in the three-toed woodpecker and winter wren [Nearctic (Nearctic, Palaearctic)]. The Palaearctic Z-chromosome clade had much lower genetic diversity and a single-peak mismatch distribution with a mean < 25% of that for either Nearctic region, both of which had ragged mismatch distributions. Main conclusions Our data suggest that, similar to the other boreal forest species, the pine grosbeak has divergent lineages in each northern continent and could have colonized the Palaearctic from the Nearctic. Compared with many Holarctic birds inhabiting open habitats, boreal forest species appear to be more differentiated, possibly because the boreal forests of the Nearctic and Palaearctic have been isolated since the Pliocene (3.5 Ma).     

Phylogeography and spatial genetic structure of the Southern torrent salamander: implications for conservation and management

The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.     

Pleistocene glaciation leaves deep signature on the freshwater crab Aegla alacalufi in Chilean Patagonia

Quaternary glacial cycles have played an important role in shaping the biodiversity in temperate regions. This is well documented in Northern Hemisphere, but much less understood for Southern Hemisphere. We used mitochondrial DNA and nuclear elongation factor 1α intron sequences to examine the Pleistocene glacial impacts on the phylogeographical pattern of the freshwater crab Aegla alacalufi in Chilean Patagonia. Phylogenetic analyses, which separated the glaciated populations on eastern continent into a north group (seven populations) and a south group (one population), revealed a shallow phylogenetic structure in the north group but a deep one in the non-glaciated populations on western islands, indicating the significant influence of glaciation on these populations. Phylogenies also identified the Yaldad population on Chiloé Island as a potentially unrecognized new species. The non-glaciated populations showed higher among population genetic divergence than the glaciated ones, but lower population genetic diversity was not detected in the latter. The two glaciated groups, which diverged from the non-glaciated populations at ~96 800–29 500 years ago and ~104 200–73 800 years ago, respectively, seem to have different glacial refugia. Unexpectedly, the non-glaciated islands did not serve as refugia for them. Demographic expansion was detected in the glaciated north group, with a constant population increase after the last glacial maximum. Nested clade analyses suggest a possible colonization from western islands to eastern continent. After arriving on the continent and surviving the last glacial period there, populations likely have expanded from high to low altitude, following the flood of melting ice. Aegla alacalufi genetic diversity has been primarily affected by Pleistocene glaciation and minimally by drainage isolation.     

The influence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western Europe

The glacial refugia hypothesis indicates that during the height of the Pleistocene glaciations the temperate species that are today widespread in western Europe must have survived in small and climatically favourable areas located in the southern peninsulas of Iberia, Italy and Balkans. One such species is the tawny owl, a relatively sedentary, nonmigratory bird presently distributed throughout Europe. It is a tree-nesting species closely associated with deciduous and mixed coniferous woodlands. In this study I used control region mtDNA sequences from 187 individuals distributed among 14 populations to determine whether current genetic patterns in tawny owl populations were consistent with postglacial expansion from peninsular refugia. European, North African and Asian tawny owls were found to represent three distinct lineages, where North Africa is the sister clade to all European owls. Within Europe, I found three well-supported clades that correspond to each of the three allopatric refugia. Expansion patterns indicate that owls from the Balkan refugium repopulated most of northern Europe, while expansion out of Iberia and Italy had only regional effects leading to admixture in France. Estimates of population divergence times between refugia populations are roughly similar, but one order of magnitude smaller between Greece and northern Europe. Based on a wide range of mutation rates and generation times, divergence between refugia appears to date to the Pleistocene.