How do Snow Partridge (Lerwa lerwa) and Tibetan Snowcock (Tetraogallus tibetanus) coexist in sympatry under high‐elevation conditions on the Qinghai–Tibetan Plateau?

The Qinghai–Tibetan Plateau (QTP) has the highest elevations of all biodiversity hotspots. Difficulties involved in fieldwork at high elevations cause challenges in researching mechanisms facilitating species coexistence. Herein, we investigated Snow Partridge (Lerwa lerwa) and Tibetan Snowcock (Tetraogallus tibetanus), the only two endemic Galliformes on the QTP, to understand species coexistence patterns and determine how they live in sympatry for the first time. We assembled occurrence data, estimated habitat suitability differences and the underlying factors between two species at different scales using ecological niche models. Niche overlap tests were used to investigate whether niche differences between these species allow for their coexistence. We found that elevation was the most important factor determining habitat suitability for both species. At the meso‐scale, two species have similar ecological niches with their suitable habitats lying predominantly along ridge crests. However, ridge crests were more influential for habitat suitability by L. lerwa than for that of T. tibetanus because the latter species ranges further afield than ridge crests. Thus, differences in habitat suitability between these species lead to habitat partitioning, which allows stable coexistence. At the macro‐scale, temperature and precipitation were major factors influencing habitat suitability differences between these species. Tetraogallus tibetanus extended into the hinterland of the QTP and occurred at higher elevations, where colder and drier alpine conditions are commonplace. Conversely, L. lerwa occurred along the southeastern margin of the QTP with a lower snow line, an area prone to rainy and humid habitats. Niche overlap analysis showed that habitat suitability differences between these species are not driven by niche differentiation. We concluded that the coexistence of these two pheasants under high‐elevation conditions could be an adaption to different alpine conditions.     

Glacial survival east and west of the 'Mekong-Salween Divide' in the Himalaya-Hengduan Mountains region as revealed by AFLPs and cpDNA sequence variation in Sinopodophyllum hexandrum (Berberidaceae)

Molecular phylogeographic studies have recently begun to elucidate how plant species from the Qinghai-Tibetan Plateau (QTP) and adjacent regions responded to the Quaternary climatic oscillations. In this regard, however, far less attention has been paid to the southern and south-eastern declivities of the QTP, i.e. the Himalaya-Hengduan Mountains (HHM) region. Here, we report a survey of amplified fragment length polymorphisms (AFLPs) and chloroplast DNA (cpDNA) sequence variation in the HHM endemic Sinopodophyllum hexandrum, a highly selfing alpine perennial herb with mainly gravity-dispersed berries (105 individuals, 19 localities). We specifically aimed to test a vicariant evolutionary hypothesis across the 'Mekong-Salween Divide', a known biogeographic and phytogeographic boundary of north-to-south trending river valleys separating the East Himalayas and Hengduan Mts. Both cpDNA and AFLPs identified two divergent phylogroups largely congruent with these mountain ranges. There was no genetic depauperation in the more strongly glaciated East Himalayas (AFLPs: H(E)=0.031; cpDNA: h(S)=0.133) compared to the mainly ice-free Hengduan Mts. (AFLPs: H(E)=0.037; cpDNA: h(S)=0.082), while population differentiation was consistently higher in the former region (AFLPs: Φ(ST)=0.522 vs. 0.312; cpDNA: Φ(ST)=0.785 vs. 0.417). Our results suggest that East Himalayan and Hengduan populations of S. hexandrum were once fragmented, persisted in situ during glacials in both areas, and have not merged again, except for a major instance of inter-lineage chloroplast capture identified at the MSD boundary. Our coalescent time estimate for all cpDNA haplotypes (c. 0.37-0.48 mya), together with paleogeological evidence, strongly rejects paleo-drainage formation as a mechanism underlying allopatric fragmentation, whereas mountain glaciers following the ridges of the MSD during glacials (and possible interglacials) could have been responsible. This study thus indicates an important role for mountain glaciers in driving (incipient) allopatric speciation across the MSD in the HHM region by causing vicariant lineage divergence and acting as barriers to post-divergence gene flow.     

Phylogeography of Rhodiola kirilowii (Crassulaceae): A Story of Miocene Divergence and Quaternary Expansion

The evolution and current distribution of the Sino-Tibetan flora have been greatly affected by historical geological events, such as the uplift of the Qinghai-Tibetan Plateau (QTP), and Quaternary climatic oscillations. Rhodiola kirilowii, a perennial herb with its distribution ranging from the southeastern QTP and the Hengduan Mountains (HM) to adjacent northern China and central Asia, provides an excellent model to examine and disentangle the effect of both geological orogeny and climatic oscillation on the evolutionary history of species with such distribution patterns. We here conducted a phylogeographic study using sequences of two chloroplast fragments (trnL-F and trnS-G) and internal transcribed spacers in 29 populations of R. kirilowii. A total of 25 plastid haplotypes and 12 ITS ribotypes were found. Molecular clock estimation revealed deep divergence between the central Asian populations and other populations from the HM and northern China; this split occurred ca. 2.84 million year ago. The majority of populations from the mountains of northern China were dominated by a single haplotype or ribotype, while populations of the HM harbored both high genetic diversity and high haplotype diversity. This distribution pattern indicates that HM was either a diversification center or a refugium for R. kirilowii during the Quaternary climatic oscillations. The present distribution of this species on mountains in northern China may have resulted from a rapid glacial population expansion from the HM. This expansion was confirmed by the mismatch distribution analysis and negative Tajima''s D and Fu''s F _S values, and was dated to ca. 168 thousand years ago. High genetic diversity and population differentiation in both plastid and ITS sequences were revealed; these imply restricted gene flow between populations. A distinct isolation-by-distance pattern was suggested by the Mantel test. Our results show that in old lineages, populations may harbour divergent genetic forms that are sufficient to maintain or even increase overall genetic diversity despite fragmentation and low within-population variation.     

Reevaluation of a classic phylogeographic barrier: new techniques reveal the influence of microgeographic climate variation on population divergence

We evaluated the mtDNA divergence and relationships within Geomys pinetis to assess the status of formerly recognized Geomys taxa. Additionally, we integrated new hypothesis‐based tests in ecological niche models (ENM) to provide greater insight into causes for divergence and potential barriers to gene flow in Southeastern United States (Alabama, Florida, and Georgia). Our DNA sequence dataset confirmed and strongly supported two distinct lineages within G. pinetis occurring east and west of the ARD. Divergence date estimates showed that eastern and western lineages diverged about 1.37 Ma (1.9 Ma–830 ka). Predicted distributions from ENMs were consistent with molecular data and defined each population east and west of the ARD with little overlap. Niche identity and background similarity tests were statistically significant suggesting that ENMs from eastern and western lineages are not identical or more similar than expected based on random localities drawn from the environmental background. ENMs also support the hypothesis that the ARD represents a ribbon of unsuitable climate between more suitable areas where these populations are distributed. The estimated age of divergence between eastern and western lineages of G. pinetis suggests that the divergence was driven by climatic conditions during Pleistocene glacial–interglacial cycles. The ARD at the contact zone of eastern and western lineages of G. pinetis forms a significant barrier promoting microgeographic isolation that helps maintain ecological and genetic divergence.     

Molecular phylogeography and intraspecific divergence of Spiraea alpina (Rosaceae) distributed in the Qinghai-Tibetan Plateau and adjacent regions inferred from nrDNA

The Qinghai-Tibetan plateau (QTP) uplift had a decisive effect on climatic and eco-environmental evolution in East Asia during the Quaternary. In the current study phylogeographic structure and diversification history of Spiraea alpina across the QTP were investigated for the first time based on nuclear internal transcribed spacer. The nuclear internal transcribed spacers (ITS_1a–ITS₄) were generated for a total of 284 individuals distributed within 31 natural populations. A clear phylogeographic structure was found for S. alpina. The results showed that this species colonized in three different glacial refugia during the Quaternary extensive glaciation and expanded during the Interglacial period. Analysis of molecular variance (AMOVA) showed 74.13% genetic diversity among populations and 25.87% genetic variation within populations with distinct phylogeographic structure (F_ST = 0.741*). The estimated divergence time revealed that the main lineages of S. alpina diversified during the Quaternary 1.2–0.6 million years ago. The study concluded that severe climatic oscillations during Quaternary and the uplift of QTP had a profound effect on intraspecific divergence of S. alpina.     

Comparative biogeography of the congener lilies Lilium distichum and Lilium tsingtauense in Korea

The main Korean mountain range (the so-called “Baekdudaegan”), which stretches from north to south across most of the Peninsula, has been thought to harbor glacial refugia for boreal and temperate plant species, where they likely found relatively stable habitats and maintained large population sizes. Under this scenario, high levels of genetic variation for plant populations can be anticipated. To test this hypothesis, we examined levels of allozyme diversity in the boreal herb Lilium distichum, which in Korea occurs largely along the Baekdudaegan and in its closely related congener L. tsingtauense, a temperate species that can occur from the coastal islands to high-altitude mountains in the Baekdudaegan. As expected, L. distichum harbored high levels of genetic variation within populations, and we found significant correlations between percentage of polymorphic loci (and allelic richness) and elevation. For L. tsingtauense we found moderate genetic variation, with its populations showing a significantly positive correlation between intra-population expected heterozygosity and elevation. Our results suggest that populations/species that occur within or near the main ridge of the Baekdudaegan probably endured the glacial periods in macrorefugia, whereas those populations/species located at low elevations (far away from mid- and high-elevation mountains) did it in microrefugia. Palaeodistribution modelling is in agreement with genetic data, indicating that the Baekdudaegan was suitable habitat for both species during the glacial (LGM) and interglacial periods (like the present). This study as well as the data from other studies compiled here provides strong evidence that the Baekdudaegan was a major refugial area for the East Asian flora throughout the Quaternary and, thus, meriting high priority for conservation biogeography.     

Shennongjia–Wushan Mountains—One cryptic glacial refugium introduced by the phylogeographical study of the Geometridae moth Ourapteryx szechuana Wehrli

The origin and evolution of biodiversity in the Shennongjia and Wushan Mountains, located in central China, are little known. In this study, we used Ourapteryx szechuana, which is widely distributed in China and northern Nepal, to explore whether these mountains acted as glacial refugia during climate oscillations of the Quaternary. In total, 192 samples of O. szechuana were collected throughout much of the distribution range. Phylogenetic analysis, molecular dating, demographic history reconstructions, and MAXENT were used to investigate the evolutionary history and differentiation mechanisms and predict the potential species distributions during four different periods. The phylogenetic tree and the star‐like median‐joining network strongly supported two reciprocally monophyletic and allopatric lineages. Lineage I was restricted to the Shennongjia and Wushan Mountains. The divergence time of O. szechuana from its sister species O. thibetaria was approximately 1.94 Ma. The differentiation processes of the two intraspecific lineages occurred at approximately 0.47 Ma. The demographic history reconstruction and the ecological niche model suggested that Lineage II experienced an expansion after the LGM (Last Glacial Maximum), whereas Lineage I did not experience any expansion. Our results suggested the Naynayxungla glaciation promoted the divergence of the two lineages by restricting them to different refugia. The valleys of the Shennongjia–Wushan Mountains may have kept stable and warm (thus ice‐free) environments during Quaternary glaciations, allowing this region to act as a glacial refugia. Our studies show that the Shennongjia and Wushan Mountains are likely to be important but little studied glacial refugia for the insect and thus worthy of more attention.

The Naynayxungla Glaciation promoted the divergence of the two lineages by restricting them to different refugia. The Shennongjia and Wushan Mountains are one important and easily neglected refugia for the insect groups and are worthy of more attention.     

Shaped by uneven Pleistocene climate: mitochondrial phylogeographic pattern and population history of white wagtail Motacilla alba (Aves: Passeriformes)

We studied the phylogeography and population history of the white wagtail Motacilla alba, which has a vast breeding range, covering areas with different Pleistocene climatic histories. The mitochondrial NADH dehydrogenase subunit II gene (ND2) and Control Region (CR) were analyzed for 273 individuals from 45 localities. Our data comprised all nine subspecies of white wagtail. Four primary clades were inferred (M, N, SW and SE), with indications of M. grandis being nested within M. alba. The oldest split was between two haplotypes from the endemic Moroccan M. a. subpersonata (clade M) and the others, at 0.63–0.96 Mya; other divergences were at 0.31–0.38 Mya. The entire differentiation falls within the part of the Pleistocene characterized by Milankovitch cycles of large amplitudes and durations. Clade N was distributed across the northern Palearctic; clade SW in southwestern Asia plus the British Isles and was predicted by Ecological niche models (ENMs) to occur also in central and south Europe; and clade SE was distributed in central and east Asia. The deep divergence within M. a. subpersonata may reflect retention of ancestral haplotypes. Regional differences in historical climates have had different impacts on different populations: clade N expanded after the last glacial maximum (LGM), whereas milder Pleistocene climate of east Asia allowed clade SE a longer expansion time (since MIS 5); clade SW expanded over a similarly long time as clade SE, which is untypical for European species. ENMs supported these conclusions in that the northern part of the Eurasian continent was unsuitable during the LGM, whereas southern parts remained suitable. The recent divergences and poor structure in the mitochondrial tree contrasts strongly with the pronounced, well defined phenotypical differentiation, indicating extremely fast plumage divergence.     

Interglacial refugia preserved high genetic diversity of the Chinese mole shrew in the mountains of southwest China

The mountains of southwest China (MSC) harbor extremely high species diversity; however, the mechanism behind this diversity is unknown. We investigated to what degree the topography and climate change shaped the genetic diversity and diversification in these mountains, and we also sought to identify the locations of microrefugia areas in these mountains. For these purposes, we sampled extensively to estimate the intraspecific phylogenetic pattern of the Chinese mole shrew (Anourosorex squamipes) in southwest China throughout its range of distribution. Two mitochondrial genes, namely, cytochrome b (CYT B) and NADH dehydrogenase subunit 2 (ND2), from 383 archived specimens from 43 localities were determined for phylogeographic and demographic analyses. We used the continuous-diffusion phylogeographic model, extensive Bayesian skyline plot species distribution modeling (SDM) and approximate Bayesian computation (ABC) to explore the changes in population size and distribution through time of the species. Two phylogenetic clades were identified, and significantly higher genetic diversity was preserved in the southern subregion of the mountains. The results of the SDM, continuous-diffusion phylogeographic model, extensive Bayesian skyline plot and ABC analyses were congruent and supported that the Last Interglacial Maximum (LIG) was an unfavorable period for the mole shrews because of a high degree of seasonality; A. squamipes survived in isolated interglacial refugia mainly located in the southern subregion during the LIG and rapidly expanded during the last glacial period. These results furnished the first evidence for major Pleistocene interglacial refugia and a latitudinal effect in southwest China, and the results shedding light on the higher level of species richness in the southern subregion.     

New Zealand endemic open-habitat specialist,the Black-fronted Tern (Chlidonias albostriatus), experienced population expansion during Pleistocene glaciation and recent decline

Understanding how climatic and environmental changes, as well as human activities, induce changes in the distribution and population size of avian species refines our ability to predict future impacts on threatened species. Using multilocus genetic data, we show that the population of a threatened New Zealand endemic open-habitat specialist, the Black-fronted Tern Chlidonias albostriatus – in contrast to forest specialists – expanded during the last glacial period. The population has decreased subsequently despite the availability of extensive open habitat after human arrival to New Zealand. We conclude that population changes for open habitat specialists such as Black-fronted Terns in pre-human New Zealand were habitat-dependent, similar to Northern Hemisphere cold-adapted species, whereas post-human settlement populations were constrained by predators independent of habitat availability, similar to other island endemic species.     

Molecular phylogeography and population structure of a mid-elevation montane frog Leptobrachium ailaonicum in a fragmented habitat of southwest China

Leptobrachium ailaonicum is a vulnerable anuran restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes at mid-elevations (approximately 2000–2600 m) in the subtropical Mount Wuliang and Mount Ailao ranges in southwest China (Yunnan Province) and northern Vietnam. Given high habitat specificity and lack of suitable habitat in lower elevations between these ranges, we hypothesized limited gene flow between populations throughout its range. We used two mitochondrial genes to construct a phylogeographic pattern within this species in order to test our hypothesis. We also examined whether this phylogeographic pattern is a response to past geological events and/or climatic oscillations. A total of 1989 base pairs were obtained from 81 individuals of nine populations yielding 51 unique haplotypes. Both Bayesian and maximum parsimony phylogenetic analyses revealed four deeply divergent and reciprocally monophyletic mtDNA lineages that approximately correspond to four geographical regions separated by deep river valleys. These results suggest a long history of allopatric separation by vicariance. The distinct geographic distributions of four major clades and the estimated divergence time suggest spatial and temporal separations that coincide with climatic and paleogeographic changes following the orogeny and uplift of Mount Ailao during the late Miocene to mid Pliocene in southwest China. At the southern distribution, the presence of two sympatric yet differentiated clades in two areas are interpreted as a result of secondary contact between previously allopatric populations during cooler Pleistocene glacial cycles. Analysis of molecular variance indicates that most of the observed genetic variation occurs among the four regions implying long-term interruption of maternal gene flow, suggesting that L. ailaonicum may represent more than one distinct species and should at least be separated into four management units corresponding to these four geographic lineages for conservation.     

Patterns of Diversity,Areas of Endemism,and Multiple Glacial Refuges for Freshwater Crabs of the Genus Sinopotamon in China (Decapoda: Brachyura: Potamidae)

Previous research has shown that the geographical distribution patterns of freshwater fishes and amphibians have been influenced by past climatic oscillations in China resulting from Pleistocene glacial activity. However, it remains unknown how these past changes have impacted the present-day distribution of Chinese freshwater crabs. This work describes the diversity and endemism of freshwater crabs belonging to Sinopotamon, a highly speciose genus endemic to China, and evaluates its distribution in terms of topography and past climatic fluctuations. Species diversity within Sinopotamon was found to be concentrated in an area from the northeastern edge of the Yunnan-Guizhou Plateau to the Jiangnan Hills, and three areas of endemism were identified. Multiple regression analysis between current climatic variables and Sinopotamon diversity suggested that regional annual precipitation, minimum temperature in the coldest month, and annual temperature range significantly influenced species diversity and may explain the diversity patterns of Sinopotamon. A comparison of ecological niche models (ENMs) between current conditions and the last glacial maximum (LGM) showed that suitable habitat for Sinopotamon in China severely contracted during the LGM. The coincidence of ENMs and the areas of endemism indicated that southeast of the Daba Mountains, and central and southeastern China, are potential Pleistocene refuges for Sinopotamon. The presence of multiple Pleistocene refuges within the range of this genus could further promote inter- and intraspecific differentiations, and may have led to high Sinopotamon species diversity, a high endemism rate and widespread distribution.     

Multilocus sequence analysis of homologous recombination and diversity in Arthrobacter sensu lato named species and glacier-inhabiting strains

Members of the bacterial genus Arthrobacter sensu lato are Gram-positive actinomycetes distributed worldwide and found in numerous environments including soil, water, glacier ice, and sewage. Homologous recombination is an important driving force in bacterial evolution, but its impact on Arthrobacter sensu lato evolution is poorly understood. We evaluated homologous recombination among 41 Arthrobacter sensu lato named species, using multilocus sequence analysis (MLSA). A high level of recombination was found, associated with strong diversification and a reticulate evolutionary pattern of Arthrobacter sensu lato. We also collected a total of 31 cold-adapted Arthrobacter sensu lato strains from two cold glaciers located in northwest China and two temperate glaciers in southwest China, and evaluated their diversity and population structure by MLSA. The glacier strains displayed high diversity, but rates of recombination among the four glacier groups were quite low, indicating that barriers to homologous recombination formed in the past among the populations on different glaciers. Our findings indicate that historical glaciation events shaped the contemporary distributions, taxonomic relationships, and phylogeographic patterns of Arthrobacter sensu lato species on glaciers.     

Importance of demographic history for phylogeographic inference on the arctic–alpine plant Phyllodoce caerulea in East Asia

Arctic–alpine plants have enormous ranges in the Northern Hemisphere. Phylogeographic studies have provided insights into their glacial survival as well as their postglacial colonization history. However, our understanding of the population dynamics of disjunct alpine populations in temperate regions remains limited. During Pleistocene cold periods, alpine populations of arctic–alpine species in East Asia were either connected to an ice-free Beringia refugium or they persisted with prolonged isolation after their establishment. To estimate which of these scenarios is more likely, we elucidated the genetic structure of Phyllodoce caerulea (Ericaceae) in Beringia and northern Japan, East Asia. Sequence variation in multiple nuclear loci revealed that P. caerulea can be distinguished into northern and southern groups. A demographic analysis demonstrated that the north–south divergence did not predate the last glacial period and detected introgression from Phyllodoce aleutica, relative widely distributed in East Asia, exclusively into the southern group. Therefore, although there has been genetic divergence between northern Japan and Beringia in P. caerulea, the divergence is unlikely to have resulted from their prolonged geographic separation throughout several cycles of glacial and interglacial periods. Instead, our study suggests that the introgression contributed to the genetic divergence of P. caerulea and that the range of P. caerulea was plausibly connected between northern Japan and Beringia during the last glacial period. Overall, our study not only provides a biogeographic insight into alpine populations of arctic–alpine plants in East Asia but also emphasizes the importance of careful interpretation of genetic structure for inferring phylogeographic history.     

Different trends and divergent responses to climate factors in the radial growth of Abies georgei along elevations in the central Hengduan Mountains

Climate change has been unprecedented in the last half-century. Tree growth dynamics and responses to climate warming at different elevations vary by study area due to regional diversity in site-specific climatic conditions in the central Hengduan Mountains. A. georgei is the dominant species in high-elevation montane forests in the central Hengduan Mountains. To study the response of A. georgei radial growth to climate and identify tree growth trends at different elevations, tree-ring width chronologies at four elevations across the subalpine A. georgei forest belt were built and growth-climate relationships were analyzed. The primary findings of this study were as follows: (1) radial growth rates of A. georgei decreased with elevation; (2) warming alleviated the limitation of low temperatures and abundant precipitation on tree radial growth at the highest sampling site; and (3) unlike at other elevations, the trend of trees basal area increment (BAI) at the lowest sampling site showed a significant decline over the past 20 years. This suggests the presence of an elevational inflection point, likely between 3800 m and 4000 m, where tree growth trends diverge. These results confirmed that A. georgei at higher elevation in the central Hengduan Mountains currently benefits from higher temperatures. However, the effects of drought on A. georgei at lower elevations would cause radial growth to decrease with climate warming. Therefore, it is critical to establish effective management strategies based on how A. georgei responds to climate change at various elevations.     

Profound climatic effects on two East Asian black-throated tits (Ave: Aegithalidae), revealed by ecological niche models and phylogeographic analysis

Although a number of studies have assessed the effects of geological and climatic changes on species distributions in East Asian, we still have limited knowledge of how these changes have impacted avian species in south-western and southern China. Here, we aim to study paleo-climatic effects on an East Asian bird, two subspecies of black-throated tit (A. c. talifuensis-concinnus) with the combined analysis of phylogeography and Ecological Niche Models (ENMs). We sequenced three mitochondrial DNA markers from 32 populations (203 individuals) and used phylogenetic inferences to reconstruct the intra-specific relationships among haplotypes. Population genetic analyses were undertaken to gain insight into the demographic history of these populations. We used ENMs to predict the distribution of target species during three periods; last inter-glacial (LIG), last glacial maximum (LGM) and present. We found three highly supported, monophyletic MtDNA lineages and different historical demography among lineages in A. c. talifuensis-concinnus. These lineages formed a narrowly circumscribed intra-specific contact zone. The estimated times of lineage divergences were about 2.4 Ma and 0.32 Ma respectively. ENMs predictions were similar between present and LGM but substantially reduced during LIG. ENMs reconstructions and molecular dating suggest that Pleistocene climate changes had triggered and shaped the genetic structure of black-throated tit. Interestingly, in contrast to profound impacts of other glacial cycles, ENMs and phylogeographic analysis suggest that LGM had limited effect on these two subspecies. ENMs also suggest that Pleistocene climatic oscillations enabled the formation of the contact zone and thus support the refuge theory.     

The Past and Present of an Estuarine-Resident Fish,the “Four-Eyed Fish” Anableps anableps (Cyprinodontiformes,Anablepidae), Revealed by mtDNA Sequences

Historical events, such as changes in sea level during the Pleistocene glacial cycles, had a strong impact on coastal habitats, limiting connectivity and promoting the genetic divergence of various species. In this study, we evaluated the influence of climate oscillations and the possibility of estuary function as a barrier to gene flow among populations of the four-eyed fish, Anableps anableps. This species is fully estuarine-resident, has internal fertilization, is viviparous and does not migrate across long distances. These features make the four-eyed fish an excellent model for the study of evolutionary processes related to genetic differentiation of species and populations in estuaries. The evolutionary history of A. anableps was inferred from phylogeographic and population analyses using sequences of the mitochondrial DNA Control Region of 13 populations distributed in the Amazon and Northeast Coast of Brazil from Calcoene (Amapa) to Parnaiba (Piaui). The 83 retrieved haplotypes show a pattern of four distinct mitochondrial lineages, with up to 3.4% nucleotide divergence among them. The evolutionary reconstruction suggests that these lineages diverged recently in the late Pleistocene/early Holocene after the Atlantic Ocean reaching current levels. Analysis of variability, neutrality and the genetic expansion pattern revealed that the lineages have distinct characteristics, which were shaped by the different geomorphological features of coastal regions combined with sea level oscillations over a very long period of time. Only few neighboring populations show a discreet gene flow. This study may also be helpful for designing new experiments to better understand the geomorphological evolutionary history of the estuaries of the Amazon and the Northeast Coast of Brazil using estuarine-resident species as a model.     

The impact of Quaternary climate oscillations on divergence times and historical population sizes in Thylamys opossums from the Andes

Climate oscillations during the Quaternary altered the distributions of terrestrial animals at a global scale. In mountainous regions, temperature fluctuations may have led to shifts in range size and population size as species tracked their shifting habitats upslope or downslope. This creates the potential for both allopatric speciation and population size fluctuations, as species are either constrained to smaller patches of habitat at higher elevations or able to expand into broader areas at higher latitudes. We considered the impact of climate oscillations on three pairs of marsupial species from the Andes (Thylamys opossums) by inferring divergence times and demographic changes. We compare four different divergence dating approaches, using anywhere from one to 26 loci. Each pair comprises a northern (tropical) lineage and a southern (subtropical to temperate) lineage. We predicted that divergences would have occurred during the last interglacial (LIG) period approximately 125 000 years ago and that population sizes for northern and southern lineages would either contract or expand, respectively. Our results suggest that all three north–south pairs diverged in the late Pleistocene during or slightly after the LIG. The three northern lineages showed no signs of population expansion, whereas two southern lineages exhibited dramatic, recent expansions. We attribute the difference in responses between tropical and subtropical lineages to the availability of ‘montane‐like’ habitats at lower elevations in regions at higher latitudes. We conclude that climate oscillations of the late Quaternary had a powerful impact on the evolutionary history of some of these species, both promoting speciation and leading to significant population size shifts.     

Species reassessment congruent with the phylogeographical study of the Biston falcata species group

The Himalaya, Hengduan, and Qinling mountains are very important mountain systems in China. Because they are geographically adjacent, species distributed in these three mountains usually have close relationships, but species/populations distributed in the first two mountain systems have higher genetic diversity and more complex phylogenetic structures than those found in the Qinling Mountains. In this study, we used molecular and morphological methods to explore the phylogeographical structure, species differentiation, and evolutionary history of the Biston falcata species group, which is widely distributed in the Himalaya, Hengduan, and Qinling mountains. Five species were identified; B. quercii is distributed in the Qinling Mountains and its adjacent areas, and the other four species are mainly distributed in the Himalaya and Hengduan Mountains. Four gradual species differentiation events occurred at approximately 3.07, 1.75, 1.50, and 1.30 Ma, corresponding to the stage with strong geological movements of the Qinghai‐Tibet Plateau. The low land between the Qinling and the northern Hengduan Mountains, the Sichuan Basin, the low land between the eastern and central Himalaya Mountains and the Mekong‐Salween Divide are four geographical barriers that resulted in multiple speciations. In addition, long‐range dispersal as another mechanism for speciation is non‐negligible. In spite of failing to confirm the ancestral area, our study provided direct evidence of the speciation induced by the geographical barriers and adaptation to the plateau.     

Continental Refugium in the Mongolian Plateau during Quaternary Glacial Oscillations: Phylogeography and Niche Modelling of the Endemic Desert Hamster,Phodopus roborovskii

The Mongolian Plateau (MP), which is situated in the interior of Asia and possesses a typical continental climate, experienced harsh climatic conditions during the Quaternary glacial fluctuations. Although these events likely had huge impacts on the local animal populations, the current effects have hardly been explored. To investigate whether the MP supported a refugium along an oceanic-continental gradient (ROCG), and whether this refugium was glacial or interglacial, we investigated the demographic and phylogeographic history of an endemic mammal species, the desert hamster Phodopus roborovskii. We reconstructed the demographic variation, the phylogeographic diffusion, and modelled the potential habitat during historical periods. The genetic diversity in the MP was the highest among all the localities, and the MP was a suitable habitat throughout the modelled historical periods. A phylogeographic diffusion analysis emphasized the importance of the MP as the centre of origin, preservation and spread for P. roborovskii. The homogeneous landscape provided the opportunity for a wide gene flow, which resulted in low resolution of the phylogenetic relationships. Moreover, P. roborovskii was favoured by the interglacial condition, with both its demographical and geographical ranges expanded within the interglacial periods. The range variation from the Last Glacial Maximum to the current condition reflects a distinct longitudinal shift, while both ranges largely contracted from that of the Last Interglacial. Our results support that the MP served as a refugium and spread centre for P. roborovskii during the Quaternary climate fluctuations. The interglacial expansion and the longitudinal shifts highlighted the important effects of precipitations on the distribution range of species adapted to arid and semi-arid during glacial oscillations.