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.     

Pleistocene glaciation is implicated in the phylogeographical structure of Potamopyrgus antipodarum, a New Zealand snail

Pleistocene glaciation has been identified as an important factor shaping present-day patterns of phylogeographical structure in a diverse array of taxa. The purpose of this study was to use mitochondrial sequence data to address whether Pleistocene glaciation is also a major determinant of phylogeographical patterns in Potamopyrgus antipodarum, a freshwater snail native to New Zealand. We found that haplotypes were separated by no more than 3.7% sequence divergence, and major genetic divisions tended to occur on a north-south axis. These data fit the predictions of the hypothesis that isolation of P. antipodarum in glacial refugia at the northern and southern tip of the South Island of New Zealand during the Pleistocene glaciation underlies the present-day phylogeographical structure. Because sexual P. antipodarum occasionally produce asexual offspring, we also used these data to show that the appearance of asexuality is not phylogeographically constrained. This means that the maintenance of sex in P. antipodarum cannot be wholly due to limited contact between sexual and asexual lineages and must instead be linked to a selective advantage of sexual reproduction.     

Chloroplast DNA phylogeography of a distylous shrub (Palicourea padifolia, Rubiaceae) reveals past fragmentation and demographic expansion in Mexican cloud forests

Several phylogeographic studies in northern Mesoamerica have examined the influence of Pleistocene glaciations on the genetic structure of temperate tree species with their southern limit by the contact zone between species otherwise characteristic of North or South America, but few have featured plant species that presumably colonized northern Mesoamerica from South America. A phylogeographical study of Palicourea padifolia, a fleshy-fruited, bird dispersed distylous shrub, was conducted to investigate genetic variation at two chloroplast regions (trnS-trnG and rpl32-trnL) across cloud forest areas to determine if such patterns are consistent with the presence of Pleistocene refugia and/or with the historical fragmentation of the Mexican cloud forests. We conducted population and spatial genetic analyses as well as phylogenetic and isolation with migration analyses on 122 individuals from 22 populations comprising the distribution of P. padifolia in Mexico to gain insight of the evolutionary history of these populations. Twenty-six haplotypes were identified after sequencing 1389 bp of chloroplast DNA. These haplotypes showed phylogeographic structure (N(ST) = 0.508, G(ST) = 0.337, N(ST) > G(ST), P < 0.05), including a phylogeographic break at the Isthmus of Tehuantepec, with private haplotypes at either side of the isthmus, and a divergence time of the split in the absence of gene flow dating back c. 309,000-103,000 years ago. The patterns of geographic structure found in this study are consistent with past fragmentation and demographic range expansion, supporting the role of the Isthmus of Tehuantepec as a biogeographical barrier in the dispersal of P. padifolia. Our data suggest that P. padifolia populations were isolated throughout glacial cycles by the Isthmus of Tehuantepec, accumulating genetic differences due to the lack of migration across the isthmus in either direction, but the results of our study are not consistent with the existence of the previously proposed Pleistocene refugia for rain forest plant species in the region.     

DIVERSIFICATION AND PERSISTENCE AT THE ARID–MONSOONAL INTERFACE: AUSTRALIA‐WIDE BIOGEOGRAPHY OF THE BYNOE'S GECKO (HETERONOTIA BINOEI; GEKKONIDAE)

Late Neogene aridification in the Southern Hemisphere caused contractions of mesic biota to refugia, similar to the patterns established by glaciation in the Northern Hemisphere, but these episodes also opened up new adaptive zones that spurred range expansion and diversification in arid‐adapted lineages. To understand these dynamics, we present a multilocus (nine nuclear introns, one mitochondrial gene) phylogeographic analysis of the Bynoe's gecko (Heteronotia binoei), a widely distributed complex spanning the tropical monsoon, coastal woodland, and arid zone biomes in Australia. Bayesian phylogenetic analyses, estimates of divergence times, and demographic inferences revealed episodes of diversification in the Pliocene, especially in the tropical monsoon biome, and range expansions in the Pleistocene. Ancestral habitat reconstructions strongly support recent and independent invasions into the arid zone. Our study demonstrates the varied responses to aridification in Australia, including localized persistence of lineages in the tropical monsoonal biome, and repeated invasion of and expansion through newly available arid‐zone habitats. These patterns are consistent with those found in other arid environments in the Southern Hemisphere, including the South African succulent karoo and the Chilean lowlands, and highlight the diverse modes of diversification and persistence of Earth's biota during the glacial cycles of the Pliocene and Pleistocene.     

The demographic history of the New Zealand short-tailed bat Mystacina tuberculata inferred from modified control region sequences

Short-tailed bats Mystacina tuberculata were widespread throughout the forest that dominated prehuman New Zealand, but extensive deforestation has restricted them to scattered populations in forest fragments. In a previous study, the species' intraspecific phylogeny was investigated using multiple mitochondrial gene sequences. Six phylogroups were identified with estimated divergences of 0.93-0.68 Ma. In the current study, the phylogeographical structure and demographic history of the phylogroups were investigated using control region sequences modified by removing homoplasic sites. Phylogeographical structure in the North Island was generally consistent with an isolation-by-distance dispersal model. Coalescent-based analyses (i.e. mismatch distributions, skyline plots, lineage dispersal analysis and nested clade analysis) indicated that the three phylogroups found in central and southern North Island expanded before the last glacial maximum, presumably during interstadials when Nothofagus forest was most extensive. Genetic structure within a central North Island hybrid zone was consistent with range expansion from separate refugia following reforestation after catastrophic volcanic eruptions. Phylogeographical structure in the South Island was consistent with southern populations originating during rapid southward range expansion from refugia in northern South Island following postglacial reforestation of the South Island 10-9 kya.     

Identification of glacial refugia in south-eastern North America by phylogeographical analyses of a forest understorey plant, Trillium cuneatum

Aim We examine several hypotheses emerging from biogeographical and fossil records regarding glacial refugia of a southern thermophilic plant species. Specifically, we investigated the glacial history and post‐glacial colonization of a forest understorey species, Trillium cuneatum. We focused on the following questions: (1) Did T. cuneatum survive the Last Glacial Maximum (LGM) in multiple refugia, and (if so) where were they located, and is the modern genetic structure congruent with the fossil record‐based reconstruction of refugia for mesic deciduous forests? (2) What are the post‐glacial colonization patterns in the present geographical range? Location South‐eastern North America. Methods We sampled 45 populations of T. cuneatum throughout its current range. We conducted phylogeographical analyses based on maternally inherited chloroplast DNA (cpDNA haplotypes) and used TCS software to reconstruct intraspecific phylogeny. Results We detected six cpDNA haplotypes, geographically highly structured into non‐overlapping areas. With one exception, none of the populations had mixed haplotype composition. TCS analysis resulted in two intraspecific cpDNA lineages, with one clade subdivided further by shallower diversification. Main conclusions Our investigation revealed that T. cuneatum survived the LGM in multiple refugia, belonging to two (western, eastern) genealogical lineages geographically structured across south‐eastern North America. The western clade is confined to the south‐western corner of T. cuneatum’s modern range along the Lower Mississippi Valley, where fossil records document a major refugium of mesic deciduous forest. For the eastern clade, modern patterns of cpDNA haplotype distribution suggest cryptic vicariance, in the form of forest contractions and subsequent expansions associated with Pleistocene glacial cycles, rather than simple southern survival and subsequent northward colonization. The north–south partitioning of cpDNA haplotypes was unexpected, suggesting that populations of this rather southern thermophilic species may have survived in more northern locations than initially expected based on LGM climate reconstruction, and that the Appalachian Mountains functioned as a barrier to the dispersal of propagules originating in more southern refugia. Furthermore, our results reveal south‐west to north‐east directionality in historical migration through the Valley and Ridge region of north‐west Georgia.     

Genetic divergences pre-date Pleistocene glacial cycles in the New Zealand speckled skink, Oligosoma infrapunctatum

Aim To examine the hypothesis raised by Graham S. Hardy that Pleistocene glacial cycles suffice to explain divergence among lineages within the endemic New Zealand speckled skink, Oligosoma infrapunctatum Boulenger. Location Populations were sampled from across the entire range of the species, on the North and South Islands of New Zealand. Methods We sequenced the mitochondrial genes ND2 (550 bp), ND4 + tRNAs (773 bp) and cytochrome b (610 bp) of 45 individuals from 21 locations. Maximum likelihood, maximum parsimony and Bayesian methods were used for phylogenetic reconstruction. The Shimodaira–Hasegawa test was used to examine hypotheses about the taxonomic status of morphologically distinctive populations. Results Our analysis revealed four strongly supported clades within O. infrapunctatum. Clades were largely allopatric, except on the west coast of the South Island, where representatives from all four clades were found. Divergences among lineages within the species were extremely deep, reaching over 5%. Two contrasting phylogeographical patterns are evident within O. infrapunctatum. Main conclusions The deep genetic divisions we found suggest that O. infrapunctatum is a complex of cryptic species which diverged in the Pliocene, contrary to the existing Pleistocene‐based hypothesis. Although Pleistocene glacial cycles do not underlie major divergences within this species, they may be responsible for the shallower phylogeographical patterns that are found within O. infrapunctatum, which include a radiation of haplotypes in the Nelson and Westland regions.     

Response of a southern temperate marsupial, the Tasmanian pademelon (Thylogale billardierii), to historical and contemporary forest fragmentation

Despite only limited Pleistocene glacial activity in the southern hemisphere, temperate forest species experienced complex distributional changes resulting from the combined effects of glaciation, sea level change and increased aridity. The effects of these historical processes on population genetic structure are now overlain by the effects of contemporary habitat modification. In this study, 10 microsatellites and 629 bp of the mitochondrial control region were used to assess the effects of historical forest fragmentation and recent anthropogenic habitat change on the broad-scale population genetic structuring of a southern temperate marsupial, the Tasmanian pademelon. A total of 200 individuals were sampled from seven sites across Tasmania and two islands in Bass Strait. High mitochondrial and nuclear genetic diversity indicated the maintenance of large historical population sizes. There was weak phylogeographical structuring of haplotypes, although all King Island haplotypes and three Tasmanian haplotypes formed a divergent clade implying the mid-Pleistocene isolation of a far northwestern population. Both the mitochondrial and nuclear data indicated a division of Tasmanian populations into eastern and western regions. This was consistent with a historical barrier resulting from increased aridity in the lowland 'midlands' region during glacial periods, and with a contemporary barrier resulting from recent habitat modification in that region. In Tasmania, gene flow appears to have been relatively unrestricted during glacial maxima in the west, while in the east there was evidence for historical expansion from at least one large glacial refuge and recolonization of Flinders Island.     

Surviving glacial ages within the Biotic Gap: phylogeography of the New Zealand cicada Maoricicada campbelli

Aim New Zealand is an ideal location in which to investigate the roles of landscape and climate change on speciation and biogeography. An earlier study of the widespread endemic cicada Maoricicada campbelli (Myers) found two phylogeographically distinguishable major clades – northern South Island plus North Island (northern‐SI + NI) and Otago. These two clades appeared to have diverged on either side of an area of the South Island known as the Biotic Gap. We sampled more intensively to test competing theories for this divergence. We aimed to discover if M. campbelli had survived within the Biotic Gap during recent glacial maxima, and if predicted areas of secondary contact between the two major clades existed. Location New Zealand. Methods We analysed mitochondrial DNA sequences (1520 bp; 212 individuals; 91 populations) using phylogenetic (maximum likelihood, Bayesian), population genetic (analysis of molecular variance) and molecular dating methods (Bayesian relaxed clock with improved priors). Results We found strong geographical structuring of genetic variation. Our dating analyses suggest that M. campbelli originated 1.83–2.58 Ma, and split into the two major clades 1.45–2.09 Ma. The main subclades in the northern‐SI + NI clade arose almost simultaneously at 0.69–1.03 Ma. Most subclades are supported by long internal branches and began to diversify 0.40–0.78 Ma. We found four narrow areas of secondary contact between the two major clades. We also found a difference between calling songs of the Otago vs. northern‐SI + NI clades. Main conclusions Phylogeographical patterns within M. campbelli indicate an early Pleistocene split into two major clades, followed by late Pleistocene range expansion and in situ population differentiation of subclades. The northern‐SI + NI clade diversified so rapidly that the main subclade relationships cannot be resolved, and we now have little evidence for a disjunction across the Biotic Gap. Structure within the main subclades indicates rapid divergence after a common bottlenecking event, perhaps attributable to an extremely cold glacial maximum at c. 0.43 Ma. Clade structure and dating analyses indicate that M. campbelli survived in many refugia during recent glacial maxima, including within the Biotic Gap. The narrow overlap between the two major clades is attributed to recent contact during the current interglacial and slow gene diffusion. The two major clades appear to be in the early stages of speciation based on genetic and behavioural differences.     

Testing hypotheses of Pleistocene population history using coalescent simulations: phylogeography of the pygmy nuthatch (Sitta pygmaea)

In this paper, we use mitochondrial NADH dehydrogenase subunit 2 sequences to test Pleistocene refugial hypotheses for the pygmy nuthatch (Sitta pygmaea). Pygmy nuthatches are a common resident of long-needle pine forests in western North America and demonstrate a particular affinity with ponderosa pine (Pinus ponderosa). Palaeoecological and genetic data indicate that ponderosa pine was isolated in two Pleistocene refugia corresponding to areas in the southern Sierra Nevada in the west and southern Arizona and New Mexico in the east. We use coalescent simulations to test the hypothesis that pygmy nuthatches tracked the Pleistocene history of their preferred habitat and persisted in two refugia during the periods of glacial maxima. Coalescent simulation of population history does not support the hypothesis of two Pleistocene refugia for the pygmy nuthatch. Instead, our data are consistent with a single refuge model. Nucleotide diversity is greatest in the western populations of southern and coastal California. We suggest that the pygmy nuthatch expanded from a far western glacial refuge into its current distribution since the most recent glacial maximum.     

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

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

Fire and ice: volcanic and glacial impacts on the phylogeography of the New Zealand forest fern Asplenium hookerianum

In the Southern Hemisphere there has been little phylogeographical investigation of forest refugia sites during the last glacial. Hooker's spleenwort, Asplenium hookerianum, is a fern that is found throughout New Zealand. It is strongly associated with forest and is a proxy for the survival of woody vegetation during the last glacial maximum. DNA sequence data from the chloroplast trnL-trnF locus were obtained from 242 samples, including c. 10 individuals from each of 21 focal populations. Most populations contained multiple, and in many cases unique, haplotypes, including those neighbouring formerly glaciated areas, while the predominant inference from nested clade analysis was restricted gene flow with isolation by distance. These results suggest that A. hookerianum survived the last glacial maximum in widespread populations of sufficient size to retain the observed phylogeography, and therefore that the sheltering woody vegetation must have been similarly abundant. This is consistent with palynological interpretations for the survival in New Zealand of thermophilous forest species at considerably smaller distances from the ice sheets than recorded for the Northern Hemisphere. Eastern and central North Island populations of A. hookerianum were characterized by a different subset of haplotypes to populations from the remainder of the country. A similar east-west phylogeographical pattern has been detected in a diverse array of taxa, and has previously been attributed to recurrent vulcanism in the central North Island.     

Evolutionary history of the scorpionfly Dicerapanorpa magna (Mecoptera,Panorpidae)

Climate changes can have fundamental impacts on the distributional patterns of montane species, and range shifts frequently lead to allopatric divergence followed by the establishment of secondary contact zones. Many European and North American organisms have retreated to southern refugia during glacial periods and colonized northward during postglacial periods, but little is known about the evolutionary response of cold‐adapted insects to Pleistocene climate changes in eastern Asia. The scorpionfly Dicerapanorpa magna (Chou), with cold temperate habitat preference and weak dispersal ability, provides a good model system to explore how climate changes have influenced the distribution and divergence of cold‐adapted insects in eastern Asia. This study reconstructed the demographic dynamics and evolutionary history of D. magna with phylogeographic approaches, and predicted the species’ suitable areas under the Last Glacial Maximum (LGM) and current scenarios with the ecological niche modelling analysis. The mitochondrial cytochrome c oxidase subunit I resolved three phylogenetic lineages in D. magna dating back to Pleistocene, corresponding well with the geographically isolated Qinling, Bashan and Minshan Mountains. The ecological niche modelling recovered the suitable habitats for D. magna were the Qinling and Bashan Mountains under LGM and current conditions. The three lineages of D. magna might be in a process of incipient speciation, and likely derived their current distribution from separate glacial origins, followed by vicariance and divergence.     

Refugia within refugia – patterns in endemism and genetic divergence are linked to Late Quaternary climate stability in the Iberian Peninsula

In Europe, southern peninsulas served as major refugia during Pleistocene cold periods. However, growing evidence has revealed complex patterns of glacial survival within these southern regions, with multiple glacial refugia within each larger refugial area. We investigated the extent to which patterns of endemism and phylogeographic are concordant across animal species in the Iberian Peninsula, one of the most important unglaciated areas in Europe during the Pleistocene, can be explained in terms of climatic stability. We found that historical climatic stability (notably climate velocity measures integrating macroclimatic shifts with local spatial topoclimate gradients) was often among the most important predictors of endemic species richness for different taxonomic groups using models that also incorporated measures of modern climate. Furthermore, for some taxonomic groups, climatic stability was also correlated with patterns of spatial concordance in interpopulation genetic divergence across multiple taxa, and private haplotypes were more frequently found in relatively stable areas. Overall, our results suggest that both endemism patterns and cross‐taxa concordant phylogeographic patterns across the Iberian Peninsula to some extent are linked to spatial variation in Late Quaternary climate stability, in agreement with the proposed ‘refugia‐within‐refugia’ scenario. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 13–28.     

Amphibian phylogeography in the Antipodes: Refugia and postglacial colonization explain mitochondrial haplotype distribution in the Patagonian frog Eupsophus calcaratus (Cycloramphidae)

Climatic oscillations, heterogeneity in elevation, topographical position, and isolation time in southwestern Patagonia have been important in promoting diversification of the biota. Geological studies have shown that this region had wide ice-free areas during periods of the last glacial maximum and provided forested refugia for the biota during Pleistocene glaciations. In this study, we sampled the endemic frog Eupsophus calcaratus from 20 localities, covering most of its distribution and including glaciated and non-glaciated regions. We collected DNA sequences for three mitochondrial regions (D-loop, cyt b, 16S), and describe patterns of variation consistent with a history of both the displacement to glacial refugia and recent recolonization to extensively glaciated regions. The inferred demographic history and divergence times of the lineages of E. calcaratus suggest that the Pleistocene had profound effects on the genetic patterns within this taxon in which some populations were able to survive in refugia within colder regions followed by demographic increases but without evidence of significant range expansion. The mtDNA gene tree recovers six major haploclades of E. calcaratus, which we consider diagnostic of species lineages. These results contribute to our understanding of how geological events, predominately glacial oscillations, have influenced current population structure of a broad-ranging, ectothermic vertebrate in the Valdivian Forest region of southern South America.     

Phylogeography and ecological niche modelling of the New Zealand stick insect Clitarchus hookeri (White) support survival in multiple coastal refugia

Aim Increasing our understanding of the effects of the Last Glacial Maximum (LGM) and determining the location of refugia requires studies on widely distributed species with dense sampling of populations. We have reconstructed the biogeographic history of Clitarchus hookeri (White), a widespread species of New Zealand stick insect that exhibits geographic parthenogenesis, using phylogeographic analysis and ecological niche modelling. Location New Zealand. Methods We used DNA sequence data from the mitochondrial cytochrome c oxidase subunit I gene to reconstruct phylogenetic relationships among haplotypes from C. hookeri and two undescribed Clitarchus species. We also used distribution data from our own field surveys and museum records to reconstruct the geographic distribution of C. hookeri during the present and the LGM, using ecological niche modelling. Results The ecological niche models showed that the geographic distribution of C. hookeri has expanded dramatically since the LGM. Our model predicted large areas of suitable LGM habitat in upper North Island, and small patches along the east coast of South Island. The phylogeographic analysis shows that populations in the northern half of North Island contain much higher levels of genetic variation than those from southern North Island and South Island, and is congruent with the ecological niche model. The distribution of bisexual populations is also non-random, with males completely absent from South Island and very rare in southern North Island. Main conclusions During the LGM C. hookeri was most likely restricted to several refugia in upper North Island and one or more smaller refugia along the east coast of South Island. The unisexual populations predominate in post-glacial landscapes and are clearly favoured in the recolonization of such areas. Our study exemplifies the utility of integrating ecological niche modelling and phylogeographic analysis.     

Range expansions in the flightless longhorn cactus beetles, Moneilema gigas and Moneilema armatum, in response to Pleistocene climate changes

Pollen cores and plant and animal fossils suggest that global climate changes at the end of the last glacial period caused range expansions in organisms indigenous to the North American desert regions, but this suggestion has rarely been investigated from a population genetic perspective. In order to investigate the impact of Pleistocene climate changes and glacial/interglacial cycling on the distribution and population structure of animals in North American desert communities, biogeographical patterns in the flightless, warm-desert cactus beetles, Moneilema gigas and Moneilema armatum, were examined using mitochondrial DNA (mtDNA) sequence data from the cytochrome oxidase I (COI) gene. Gene tree relationships between haplotypes were inferred using parsimony, maximum-likelihood, and Bayesian analysis. Nested clade analysis and coalescent modelling using the programs mdiv and fluctuate were used to identify demographically independent populations, and to test the hypothesis that Pleistocene climate changes caused recent range expansions in these species. A sign test was used to evaluate the probability of observing concerted population growth across multiple, independent populations. The phylogeographical and nested clade analyses reveal a history of northward expansion in both of these species, as well as a history of past range fragmentation, followed by expansion from refugia. The coalescent analyses provide highly significant evidence for independent range expansions from multiple refugia, but also identify biogeographical patterns that predate the most recent glacial period. The results indicate that widespread desert environments are more ancient than has been suggested in the past.     

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.     

HOT SPOTS OF GENETIC DIVERSITY DESCENDED FROM MULTIPLE PLEISTOCENE REFUGIA IN AN ALPINE UNGULATE

Species that inhabit naturally fragmented environments are expected to be spatially structured and exhibit reduced genetic diversity at the periphery of their range. Patterns of differentiation may also reflect historical processes such as recolonization from glacial refugia. We examined the relative importance of these factors in shaping the spatial patterns of genetic differentiation across the range of an alpine specialist, the North American mountain goat (Oreamnos americanus). Contrary to fossil evidence that suggests a single southern refugium, we detected evidence for additional refugia in northern British Columbia and the Alaskan coast using both mitochondrial and microsatellite DNA. A core area of elevated genetic diversity characterized both regions, and molecular dating suggested a recent Pleistocene split was followed by demographic expansion. Across their range, mountain goats were highly genetically structured and displayed the expected pattern of declining diversity toward the periphery. Gene flow was high within contiguous mountain ranges, but cross‐assignments paradoxically suggest that long‐distance contemporary dispersal movements are not uncommon. These results improve our understanding of how historical vicariance and contemporary fragmentation influence population differentiation, and have implications for conserving the adaptive potential of alpine populations and habitat.     

Concerted versus independent evolution and the search for multiple refugia: comparative phylogeography of four forest beetles

Phylogeographic structure and its underlying causes are not necessarily shared among community members, with important implications for using individual organisms as indicators for ecosystem evolution, such as the identification of forest refugia. We used mitochondrial DNA (cox1), Bayesian coalescent ancestral state reconstruction (implemented in BEAST), and ecological niche models (ENMs) to construct geospatial histories for four codistributed New Zealand forest beetles (Leiodidae, Nitidulidae, Staphylinidae, and Zopheridae) to examine the extent to which they have tracked environmental changes together through time. Hindcast ENMs identified potential forest refugia during the Last Glacial Maximum, whereas ancestral state reconstruction identified key geographic connections for each species, facilitating direct comparison of dispersal patterns supported by the data and the time frame in which they occurred. Well-supported geographic state transitions for each species were mostly between neighboring regions, favoring a historical scenario of stepping stone colonization of newly suitable habitat rather than long distance dispersal. No geographic state transitions were shared by all four species, but three shared multiple projected South Island refugia and recent dispersal from the southernmost refugium. In contrast, strongly supported dispersal patterns in the refugia-rich northern South Island suggest more individualistic responses to environmental change in these ecologically similar forest species.