Niche divergence promotes rapid diversification of East African sky island white‐eyes (Aves: Zosteropidae)

The Eastern Afromontane biodiversity hotspot composed of highly fragmented forested highlands (sky islands) harbours exceptional diversity and endemicity, particularly within birds. To explain their elevated diversity within this region, models founded on niche conservatism have been offered, although detailed phylogeographic studies are limited to a few avian lineages. Here, we focus on the recent songbird genus Zosterops, represented by montane and lowland members, to test the roles of niche conservatism versus niche divergence in the diversification and colonization of East Africa's sky islands. The species‐rich white‐eyes are a typically homogeneous family with an exceptional colonizing ability, but in contrast to their diversity on oceanic islands, continental diversity is considered depauperate and has been largely neglected. Molecular phylogenetic analysis of ~140 taxa reveals extensive polyphyly among different montane populations of Z. poliogastrus. These larger endemic birds are shown to be more closely related to taxa with divergent habitat types, altitudinal distributions and dispersal abilities than they are to populations of restricted endemics that occur in neighbouring montane forest fragments. This repeated transition between lowland and highland habitats over time demonstrate that diversification of the focal group is explained by niche divergence. Our results also highlight an underestimation of diversity compared to morphological studies that has implications for their taxonomy and conservation. Molecular dating suggests that the spatially extensive African radiation arose exceptionally rapidly (1–2.5 Ma) during the fluctuating Plio‐Pleistocene climate, which may have provided the primary driver for lineage diversification.     

Geographical differentiation of the Euchiloglanis fish complex (Teleostei: Siluriformes) in the Hengduan Mountain Region,China: Phylogeographic evidence of altered drainage patterns

The uplift of the Tibetan Plateau caused significant ecogeographical changes that had a major impact on the exchange and isolation of regional fauna and flora. Furthermore, Pleistocene glacial oscillations were linked to temporal large‐scale landmass and drainage system reconfigurations near the Hengduan Mountain Region and might have facilitated speciation and promoted biodiversity in southwestern China. However, strong biotic evidence supporting this role is lacking. Here, we use the Euchiloglanis fish species complex as a model to demonstrate the compound effects of the Tibetan Plateau uplift and Pleistocene glacial oscillations on species formation in this region. The genetic structure and geographical differentiation of the Euchiloglanis complex in four river systems within the Hengduan Mountain Region were deduced using the cytochrome b (cyt b) gene and 10 microsatellite loci from 360 to 192 individuals, respectively. The results indicated that the populations were divided into four independently evolving lineages, in which the populations from the Qingyi River and Jinsha River formed two sub‐lineages. Phylogenetic relationships were structured by geographical isolation, especially near drainage systems. Divergence time estimation analyses showed that the Euchiloglanis complex diverged from its sister clade Pareuchiloglanis sinensis at around 1.3 Million years ago (Ma). Within the Euchiloglanis complex, the divergence time between the Dadu–Yalong and Jinsha–Qingyi River populations occurred at 1.0 Ma. This divergence time was in concordance with recent geological events, including the Kun‐Huang Movement (1.2–0.6 Ma) and the lag time (<2.0 Ma) of river incision in the Hengduan Mountain Region. Population expansion signals were detected from mismatched distribution analyses, and the expansion times were concurrent with Pleistocene glacier fluctuations. Therefore, current phylogeographic patterns of the Euchiloglanis fish complex in the Hengduan Mountain Region were influenced by the uplift event of the Tibetan Plateau and were subsequently altered by paleo‐river transitions during the late Pleistocene glacial oscillations.     

Genetic variation and geographical structure of five mouse-sized opossums (Marsupialia, Didelphidae) throughout the Guiana Region

Aim and location To study the patterns of genetic variation and geographical structure of five forest‐dwelling didelphid species distributed throughout the Guiana Region (Marmosops parvidens, M. pinheiroi, Monodelphis brevicaudata, Marmosa murina, Micoureus demerarae) and place the results for wide‐ranging species (M. murina, M. demerarae) in the broader geographical context of the rest of the taxon ranges based on published data. Methods Variation in the mitochondrial cytochrome b gene were analysed in order to assess intra‐specific sequence divergence as well as haplotypic and nucleotide diversity among populations. Relationships between haplotypes were inferred by cladistic (maximum parsimony) and probabilistic (maximum likelihood) approaches, allowing comparisons between tree topologies and patterns of populations geographical distribution. Results Phylogenetic analysis of the Guiana Region populations suggest the lack of common patterns of geographical structure among mouse‐sized opossums except for both Marmosops species. Marmosops parvidens and M. pinheiroi showed individuals from Surinam strongly related with those from Guyana, and haplotypes from French Guiana having a basal position. Concerning Micoureus demerarae, haplotypes from Venezuela were positioned as ancestral, in contrast with Monodelphis brevicaudata, whose French Guiana haplotypes were clustered in a basal position. No evidence of geographical structure was observed for Marmosa murina. Genetic variation within Guiana Region populations fluctuated between 1% for M. murina and 7% in the case of M. brevicaudata. Regarding the widely distributed species, phylogeographical structure at the scale of the Amazon Basin suggests that Guiana Region populations are the sister group of south‐eastern Amazonian and Atlantic Forest populations, thus resulting in an eastern clade well separated from the western Amazonian regions. Main conclusions Monophyly of mouse‐sized opossums haplotypes over the Guiana Region confirms the presence of a well‐differentiated zoogeographical area relative to other Amazonia bioregions. Low genetic diversity among Guiana Region samples suggests a relatively recent origin of populations dating from later Miocene and Pleistocene periods. Moreover, nucleotide and haplotypic diversity values suggest an evolutionary scenario of rapid population growth and dispersal over the Guiana territory, from an ancestral population with small effective size. Dispersal events – rather than vicariance – seem to be responsible for the present genetic and phylogeographical patterns observed in the Guiana Region.     

Habitat fragmentation affects genetic diversity and differentiation of the Yarkand hare

The Yarkand hare, Lepus yarkandensis, is an endemic, endangered species restricted to the Tarim Basin of the Xinjiang Uygur Autonomous Region, China. The Yarkand hare is distributed in scattered oases which are physically isolated by the desert. Its natural fragmentation habitat makes it an ideal object for studying effect of habitat fragmentation on its genetic structure. To evaluate the effects of habitat fragmentation on genetic diversity of the species, we assessed genetic diversity for 20 sampling populations based on control region and Cytb markers. Relatively low levels of gene diversity are found in most of isolated populations in the southern margin of the Taklamakan Desert. Furthermore, a positive correlation is found between gene diversity and the size of historical effective population. Significant genetic differentiation is detected among most populations by pairwise F_ST analyses, which is characterized by an isolation by distance pattern. Additionally, the AMOVA results show highly significant population structure among seven geographical groups. High migration rates are found among continuous populations, while very low levels of migration rates are found among the relatively isolated populations, suggesting that the desert may make an effective barrier against gene flow. Finally, the control region shows four clades by the phylogenetic analyses, three of which are present in nearly all sampling populations. The observed pattern of the lineage mixing, also shown by the Cytb data, may be caused by extensive gene flow among populations, and could be explained by possible demographical expansion of the Yarkand hare during the late Pleistocene interglacial period.     

The DNA history of a lonely oak: Quercus humboldtii phylogeography in the Colombian Andes

The climatic and geological changes that occurred during the Quaternary, particularly the fluctuations during the glacial and interglacial periods of the Pleistocene, shaped the population demography and geographic distribution of many species. These processes have been studied in several groups of organisms in the Northern Hemisphere, but their influence on the evolution of Neotropical montane species and ecosystems remains unclear. This study contributes to the understanding of the effect of climatic fluctuations during the late Pleistocene on the evolution of Andean mountain forests. First, we describe the nuclear and plastidic DNA patterns of genetic diversity, structure, historical demography, and landscape connectivity of Quercus humboldtii, which is a typical species in northern Andean montane forests. Then, these patterns were compared with the palynological and evolutionary hypotheses postulated for montane forests of the Colombian Andes under climatic fluctuation scenarios during the Quaternary. Our results indicated that populations of Q. humboldtii have high genetic diversity and a lack of genetic structure and that they have experienced a historical increase in connectivity from the last glacial maximum (LGM) to the present. Furthermore, our results showed a dramatic reduction in the effective population size followed by an expansion before the LGM, which is consistent with the results found by palynological studies, suggesting a change in dominance in Andean forests that may be related to ecological factors rather than climate change.     

中国近海细鳞鯻线粒体控制区的遗传多样性

通过线粒体控制区序列的分析,研究采自中国南海及东海5个群体102尾细鳞鯻的遗传多样性。发现在962 bp序列中有205个变异位点,其中135个为简约信息位点,共定义102个单倍型。中国近海细鳞鯻总体呈现出较高的遗传多样性特征(Hd=1.000,Pi=0.022),其中博鳌最高(Hd=1.000,Pi=0.028),平潭最低(Hd=1.000,Pi=0.014)。不同地理群体间无明显分化,基因交流频繁(Fst=-0.014—0.041,P0.05);中性检验均为显著负值,推测在16.9万年—5.06万年前,即中-晚更新世出现种群扩张。系统邻接树和单倍型网络图均出现3个显著分化的谱系(谱系间Fst=0.508—0.698,P0.001;净遗传距离Da=0.024—0.031),且各谱系中均有不同地理来源的群体。3个谱系间分歧时间大约在1.07百万年—0.24百万年前,推测可能是更新世冰期边缘海的出现导致群体隔离而产生分化。谱系A(Lineage A)包含85.3%的个体,其总体遗传多样性较高(Hd=1.000,Pi=0.012),其中平潭最高(Hd=1.000,Pi=0.014),合浦最低(Hd=1.000,Pi=0.010);群体间Fst在-0.021—0.068之间,P0.005;AMOVA分析显示只有1.97%的变异来自于种群间,表明群体间也无明显分化;中性检验均为显著负值,推测在25.4万年—7.6万年前出现种群扩张。中国近海细鳞鯻主要受到中-晚更新世海侵和海退的影响而出现种群扩张使得谱系间发生二次接触,最终形成具有显著谱系结构但无地理分化的情况。     

Genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River (upper Mekong)

The genus Schizothorax (Cyprinidae), one of the most diverse genera of ichthyofauna of the Qinghai‐Tibetan Plateau (QTP), is a good candidate for investigating patterns of genetic variation and evolutionary mechanisms. In this study, sequences from the mitochondrial control region, the cytochrome b gene, and two nuclear genes were used to re‐examine the genetic diversity and investigate the evolutionary history of the Schizothorax species complex inhabiting the Lancang River. Three maternal clades were detected in the Schizothorax species complex, but frequent nuclear allele sharing also occurred among the three maternal clades. A discrepancy between topologies of mitochondrial and nuclear loci might result from introgression or/and incomplete lineage sorting. The divergence of the clades of the Schizothorax species complex was closely related to the Late Pliocene and Early Pleistocene orogenesis of the QTP and Southwest Mountains of China. Demographic analyses indicated that the species complex subsequently persisted in situ with stable populations during Pleistocene glacial cycling, which suggested that Pleistocene climate changes did not exert a remarkable influence on the species complex. Our study provides a comprehensive analysis of the genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River.     

Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai‐Tibetan plateau

Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Pleistocene for the Qinghai‐Tibetan (Tibetan) plateau, a region where glaciation was not synchronous with the North Hemisphere ice sheet maxima, remains poorly understood. Here, we compared the phylogeographical patterns of five avian species on the Qinghai‐Tibetan plateau by three mitochondrial DNA fragments: the Tibetan snow finch (Montifringilla adamsi), the Blanford’s snow finch (Pyrgilauda blanfordi), the horned lark (Eremophila alpestris), the twite (Carduelis flavirostris) and the black redstart (Phoenicurus ochruros). Our results revealed the three species mostly distributed on the platform region of the plateau that experienced population expansion following the retreat of the extensive glaciation period (0.5–0.175 Ma). These results are at odds with the results from avian species of Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023–0.018 Ma). A single refugium was identified in a restricted semi‐continuous area around the eastern margin of the plateau, instead of multiple independent refugia for European and North American species. For the other two species distributed on the edges of the plateau (the twite and black redstart), populations were maintained at stable levels. Edge areas are located on the eastern margin, which might have had little or no ice cover during the glaciation period. Thus, milder climate may have mitigated demographic stresses for edge species relative to the extremes experienced by platform counterparts, the present‐day ranges of which were heavily ice covered during the glaciation period. Finally, various behavioural and ecological characteristics, including dispersal capacities, habitat preference and altitude specificity along with evolutionary history might have helped to shape different phylogeographical structures appearing in these five species.     

The role of repeated sea-level fluctuations in the generation of shrew (Soricidae: Crocidura) diversity in the Philippine Archipelago

Repeated sea-level fluctuations during and prior to the Pleistocene had a dramatic effect on the distribution of land and connection among islands between the Asian and Australian continents. These cycles of connection and isolation have long been recognized as an important factor determining the distribution and organization of biodiversity in the Philippines. However, surprisingly few studies have tested for predicted patterns of genetic diversity derived from a Pleistocene sea-level model of geography. Here, we examine evidence for fit to such a model in a widely distributed lineage of shrews (Crocidura). The topology of relationships among Crocidura from the Philippines is concordant with a Pleistocene sea-level model, but (1) AMOVAs reveal that genetic diversity is explained at least as well by modern islands as by Pleistocene islands; (2) Mantel tests reveal a significant influence of isolation by distance; and (3) the degree of genetic divergence between some populations connected by dry land during the last glacial maximum reveals isolation that almost certainly predates the most recent glacial activity. We further employ multiple strategies for inferring time-calibrated phylogenies, but these result in widely varying time estimates for the invasion of SE Asian islands by shrews. Overall, our results suggest Pleistocene sea-level fluctuations have been an important, but not dominant factor shaping shrew diversity.     

Deep intra‐island divergence of a montane forest endemic: phylogeography of the Puerto Rican frog Eleutherodactylus portoricensis (Anura: Eleutherodactylidae)

Aim Hypotheses proposed for lineage diversification of tropical montane species have rarely been tested within oceanic islands. Our goal was to understand how basin barriers and Pleistocene climatic fluctuations shaped the distribution of diversity in Eleutherodactylus portoricensis (Eleutherodactylidae), a frog endemic to the montane rain forests of Puerto Rico. Location The north‐eastern (Luquillo) and south‐eastern (Cayey) mountains of Puerto Rico. Methods We generated mitochondrial DNA (mtDNA) control region sequences (c. 565 bp) from 144 individuals of E. portoricensis representing 16 localities, and sequenced 646 bp of cytochrome b and 596 bp of nuclear DNA (nDNA) rhodopsin exon and intron 1 from a subset of individuals. We conducted a phylogenetic analysis on the mtDNA sequence data and explored population substructure with maximum parsimony networks, a spatial analysis of molecular variance, and pairwise F_ST analysis. Coalescent simulations were performed to test alternative models of population divergence in response to late Pleistocene interglacial periods. Historical demography was assessed through coalescent analyses and Bayesian skyline plots. Results We found: (1) two highly divergent groups associated with the disjunct Luquillo and Cayey Mountains, respectively; (2) a shallow mtDNA genetic discontinuity across the La Plata Basin within the Cayey Mountains; (3) phylogeographic congruence between nDNA and mtDNA markers; (4) divergence dates for both mtDNA and nDNA pre‐dating the Holocene interglacial (c. 10 ka), and nDNA suggesting divergence in the penultimate interglacial (c. 245 ka); and (5) historical demographic stability in both lineages. Main conclusions The low‐elevation Caguas Basin is a long‐term barrier to gene flow between the two montane frog populations. Measures of genetic diversity for mtDNA were similar in both lineages, but lower nDNA diversity in the Luquillo Mountains lineage suggests infrequent dispersal between the two mountain ranges and colonization by a low‐diversity founder population. Population divergence began prior to the Holocene interglacial. Stable population sizes over time indicate a lack of demonstrable demographic response to climatic changes during the last glacial period. This study highlights the importance of topographic complexity in promoting within‐island vicariant speciation in the Greater Antilles, and indicates long‐term persistence and lineage diversification despite late Pleistocene climatic oscillations.     

Geographic patterns of genetic diversity in Poulsenia armata (Moraceae): implications for the theory of Pleistocene refugia and the importance of riparian forest

Abstract. Tropical forests are species-diverse communities, but we know very little about the geographical distribution of genetic diversity within a species. During the late Pleistocene, lower temperatures and rainfall reduced the distribution of tropical wet forests, and in Central America lowland species may have been limited to riparian habitats. Approximately 12,000 years bp , temperature and rainfall increased in Central America, the distribution of wet forest species expanded, and today the distribution of some species extends into southern Mexico. The distribution of genetic diversity, based on RAPD markers, among ten populations of Poulsenia armata (Miq.) Standl. (Moraceae) suggests that these populations did not originate from a single refugium or region in the late Pleistocene. The Central American populations had high genetic diversity and unique bands giving support to the hypothesis that populations of P. armata occurred in Central American during the late Pleistocene. The majority of genetic diversity was partitioned among populations and there was no geographical relationship among populations, suggesting that these populations were isolated for a long period and there has been little gene flow. Populations of P. armata may have persisted in riparian zones along the Caribbean coast during the late Pleistocene. Given that riparian forest can support high levels of biodiversity in ecological time, and they have played an important role during periods of climate change over geological time, their conservation is of utmost importance particularly with the threat of a rapid shift in climatic patterns.     

Evolution and maintenance of divergent lineages in an endangered freshwater fish, <Emphasis Type="Italic">Macquaria australasica</Emphasis>

Variable hydrological regimes and habitat availability are factors that affect the distribution of freshwater dependent species and are expected to influence their levels of genetic diversity. Although geologically relatively stable, the south eastern region of Australia has experienced significant changes in hydrological conditions during the Quaternary. This area has also been recently affected by anthropogenic activities, resulting in dramatic population declines of Macquarie Perch (Macquaria australasica). We conducted a range-wide phylogeographic study of this endangered fish to assess the relationship between landscape and freshwater fish evolution in south eastern Australia and infer levels of genetic diversity and population structure. Surprisingly, we detected high genetic diversity, with 46 mtDNA control region haplotypes found across 37 sampling locations. Some lineages were remarkably divergent; one represents a putative undescribed species that probably went extinct during the period of this study. Our reconstruction of population history using a combination of coalescent and phylogenetic methods indicates that the species originated on the coast, east of the Great Dividing Range (GDR), with subsequent colonisation of the Murray-Darling basin, west of the GDR. Nested clade and IM analyses inferred a series of range expansions and fragmentations across the species range consistent with the history of climatic oscillations in south eastern Australia during the Pleistocene. We conclude that the unexpected high levels of diversity and divergence observed in M. australasica may be due to specific habitat requirements, localised recruitment, and Pleistocene climate fluctuations. Under expectations of a drier climate and increased sea levels due to global warming, populations of this and other freshwater species may be expected to experience increased habitat fragmentation and loss of genetic diversity. Conservation management should focus on habitat protection, the maintenance of genetic diversity and taxonomic review.     

Climate change drives speciation in the southern rock agama (Agama atra) in the Cape Floristic Region, South Africa

Aim Vicariance has played a major role in the evolution of the southern rock agama, Agama atra (Reptilia: Agamidae), and it is hypothesized that habitat shifts will affect small‐scale patterns of gene flow. The Cape Floristic Region (CFR) is known for high levels of diversity and endemism; thus we set out to investigate whether genetic structuring of CFR populations of A. atra corresponds to regional environmental shifts. Location Cape Fold Mountains and the Cape Floristic Region of South Africa. Methods The phylogeographical structure of 116 individuals of A. atra was determined by making use of 988 characters derived from two mitochondrial DNA fragments (control region and the NADH dehydrogenase subunit 2 coding region, ND2). Most animals originated from the CFR, but to gain a better understanding of the processes and patterns of dispersal within the species, 17 additional specimens from outside the CFR were also included and analysed in a phylogenetic context. Results Parsimony and Bayesian analyses revealed four distinct CFR clades (Cape clades) associated with geography. Phylogenetic analyses suggest that populations of A. atra in the CFR region are not entirely isolated from other populations, because some individuals from outside the CFR were nested within the four main Cape clades. The combined mitochondrial DNA data set revealed 59 distinct haplotypes in the CFR. Analysis of molecular variance (amova ) confirmed the high degree of genetic structure among the Cape clades, with more than 75% of the genetic variation found among the geographical areas. A spatial amova suggested that a ‘central clade’ originally defined as one of the four Cape clades may contain several additional populations. The main cladogenesis of A. atra within the CFR is estimated to have taken place c. 0.64–2.36 Ma. Main conclusions Agama atra shows at least four distinct genetic provinces within the CFR region, which highlights the conservation importance of this biologically diverse area. The dates of separation among the clades coincide well with the documented Pleistocene climate fluctuations, which might have contributed towards the isolation among lineages; the congruent genetic structure of A. atra with other CFR taxa further supports vicariance as a main isolating factor.     

Phylogeography of the narrow‐headed vole Lasiopodomys (Stenocranius) gregalis (Cricetidae,Rodentia) inferred from mitochondrial cytochrome b sequences: an echo of Pleistocene prosperity

A species‐wide phylogeographic study of the narrow‐headed vole Lasiopodomys (Stenocranius) gregalis was performed using the mitochondrial (mt) cytochrome b gene. We examined 164 specimens from 50 localities throughout the species distribution range. Phylogeographic pattern clearly demonstrates the division into four major mtDNA lineages with further subdivision. The level of genetic differentiation between them was found to be extremely high even for the species level: about 6–11%. The most striking result of our study is extremely high mutation rate of cytb in L. gregalis. Our estimates suggested its value of 3.1 × 10^?5 that is an order of magnitude higher than previous estimates for Microtus species. The mean estimated time of basal differentiation of the narrow‐headed vole is about 0.8 Mya. This time estimate is congruent with the known paleontological record. The greatest mitochondrial diversity is found in Southern Siberia where all four lineages occur; therewith, three of them are distributed exclusively in that area. The lineage that is distributed in south‐eastern Transbaikalia is the earliest derivate and exhibits the highest genetic divergence from all the others (11%). It is quite probable that with further research, this lineage will turn out to represent a cryptic species. Spatial patterns of genetic variation in populations of the narrow‐headed vole within the largest mt lineage indicate the normal or stepping stone model of dispersal to the north and south‐west from the Altay region in Middle Pleistocene. Both paleontological data and genetic diversity estimates suggest that this species was very successful during most of the Pleistocene, and we propose that climate humidification and wide advance of tree vegetation at the Pleistocene–Holocene boundary promoted range decrease and fragmentation for this typical member of tundra‐steppe faunistic complex. However, we still observe high genetic diversity within isolated fragments of the range.     

Multilocus phylogeography of the sea snake Hydrophis curtus reveals historical vicariance and cryptic lineage diversity

The Indo‐Australian archipelago (IAA) supports the world's highest diversity of marine fish, invertebrates and reptiles. Many of the marine fish and invertebrates show congruent phylogeographic patterns, supporting a view that the region's complex geo‐climatic history has played an important role in generating its exceptional biodiversity. Here, we examine population genetic structure of the viviparous sea snake, Hydrophis curtus, to assess how past and present barriers to gene flow in the IAA have contributed to genetic and species diversity in a fully marine reptile. Mitochondrial and anonymous nuclear sequences and ten microsatellite loci were used to identify patterns of historical genetic structure and population expansion, reconstruct dated genealogies and assess levels of recent gene flow. These markers revealed strong concordant geographic structure within H. curtus with a prominent genetic break between populations broadly distributed in the Indian Ocean and the West Pacific. These populations were estimated to have diverged in the late Pliocene or early Pleistocene, and microsatellite admixture analyses suggested limited recent gene flow between them despite the current lack of barriers to dispersal, indicating possible cryptic species. Subsequent divergence in the mid–late Pleistocene was detected within the West Pacific clade among the populations in the Phuket‐Thailand region, South‐East Asia and Australia, and two of these populations also showed genetic signals of recent range expansions. Our results show that climatic fluctuations during the Plio‐Pleistocene generated high levels of cryptic genetic diversity in H. curtus, and add to similar findings for diverse other marine groups in the IAA.     

Lasting through the ice age: The role of the proglacial refugia in the maintenance of genetic diversity,population growth,and high dispersal rate in a widespread freshwater crustacean

1. The severe climatic changes during the Pleistocene ice ages have shaped the genetic structure and distribution of biota in Europe. We aimed to reveal in detail the genetic diversity, geographical population structure, historical and present demography, migration patterns, and the presence of possible glacial refugia within the nominative subspecies Asellus aquaticus aquaticus.
2. We analysed DNA sequences of the mitochondrial cytochrome c oxidase subunit I gene and nuclear noncoding internal transcribed spacer II region, from populations inhabiting post-glacial Europe (from the British Isles and Scandinavia to the northern Mediterranean and Black Sea coasts).
3. The origin of the taxon, including establishment in the Dinaric Western Balkans, dates to the Middle/Late Pliocene, but most of its genetic diversity emerged during the Middle/Late Pleistocene before the Last Glacial Maximum.
4. Despite the general absence of spatial genetic structure with population growth, we discovered two different phylogeographic stories across 11 clusters revealed by a coalescent approach. Firstly, the periglacial cluster group—spatially restricted mainly to the northern Balkans, Pannonian Basin, and Pontic Region—is older and more divergent. It apparently retained a relatively stable population size during the glacial-interglacial cycles. Conversely, the proglacial cluster group—widely distributed in areas close to the glacier margins (north of the Alps, Sudetes, Carpathians) and in the Pannonian Basin—is younger and composed of closely related individuals. It originated in Pleistocene and lasted continuously through the Last Glacial Maximum in numerous high latitude refugia. This was probably due to the vast network of proglacial lakes and rivers, which played a crucial role in the maintenance of genetic diversity, population growth, and high dispersal rate.
5. The evolutionary history of A. a. aquaticus reveals unexpected patterns and is an important lesson when making predictions for other aquatic taxa. Our results suggest that we should stop perceiving the proglacial habitats as lifeless ice desert.

     

Population genomic evidence for multiple Pliocene refugia in a montane‐restricted harvestman (Arachnida,Opiliones, Sclerobunus robustus) from the southwestern United States

The integration of ecological niche modelling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis‐based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of nonrefugial populations are corroborated with empirical data. In this study, we focus on a montane‐restricted cryophilic harvestman, Sclerobunus robustus, distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double‐digest RAD‐seq data and conducted population‐level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid‐latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades of S. robustus. Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades pre‐dates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model‐based coalescent approaches, we find support for postdivergence migration between clades from separate refugia.     

Phylogeography of the pademelons (Marsupialia: Macropodidae: Thylogale) in New Guinea reflects both geological and climatic events during the Plio‐Pleistocene

Aim Alternative hypotheses concerning genetic structuring of the widespread endemic New Guinean forest pademelons (Thylogale) based on current taxonomy and zoogeography (northern, southern and montane species groupings) and preliminary genetic findings (western and eastern regional groupings) are investigated using mitochondrial sequence data. We examine the relationship between the observed phylogeographical structure and known or inferred geological and historical environmental change during the late Tertiary and Quaternary. Location New Guinea and associated islands. Methods We used primarily museum specimen collections to sample representatives from Thylogale populations across New Guinea and three associated islands. Mitochondrial cytochrome b and control region sequence data were used to construct phylogenies and estimate the timing of population divergence. Results Phylogenetic analyses indicated subdivision of pademelons into ‘eastern’ and ‘western’ regional clades. This was largely due to the genetic distinctiveness of north‐eastern and eastern peninsula populations, as the ‘western’ clade included samples from the northern, southern and central regions of New Guinea. Two tested island groups were closely related to populations north of the Central Cordillera; low genetic differentiation of pademelon populations between north‐eastern New Guinea and islands of the Bismarck Archipelago is consistent with late Pleistocene human‐mediated translocations, while the Aru Islands population showed divergence consistent with cessation of gene flow in the mid Pleistocene. There was relatively limited genetic divergence between currently geographically isolated populations in subalpine and nearby mid‐montane or lowland regions. Main conclusions Phylogeographical structuring does not conform to zoogeographical expectations of a north/south division across the cordillera, nor to current species designations, for this generalist forest species complex. Instead, the observed genetic structuring of Thylogale populations has probably been influenced by geological changes and Pleistocene climatic changes, in particular the recent uplift of the north‐eastern Huon Peninsula and the lowering of tree lines during glacial periods. Low sea levels during glacial maxima also allowed gene flow between the continental Aru Island group and New Guinea. More work is needed, particularly multi‐taxon comparative studies, to further develop and test phylogeographical hypotheses in New Guinea.     

Globorotalia puncticulata: Population divergence, dispersal and extinction related to Pliocene–Quaternary water masses

The isolating effect of water mass partitioning of populations on the morphology, stratigraphic distribution and extinction of planktonic foraminifera is assessed from the Pliocene–Quaternary record of Globorotalia puncticulata. Southern Hemisphere, Mediterranean and North Atlantic data on these aspects of its history are examined and appear consistent with a limited dispersal biogeographic model wherein populations are largely confined by hydrographic barriers.Earliest populations appeared during the latest Miocene in Southern Hemisphere middle latitude water masses. However, morphometric analysis shows that significant differentiation in the axial shape of shells had developed by 4 Ma between Southwest Pacific populations from ODP Site 1123 (temperate water) and ODP Site 1119 (subantarctic water). These sites are in close proximity but separated by the Subtropical Front. At Site 1123 inflation of late-formed chambers and reduction in the number included in the outer whorl created shell profiles that anticipated the globose form of Globorotalia inflata. The latter's gradual evolution from G. puncticulata s.s. took place in this temperate water mass, with the earliest morphotypes with three chambers in the outer whorl present by 4.1 Ma. In contrast, subantarctic populations at Site 1119 retained four chambers but their axial shape was modified. The development of a large, highly arched aperture and increase in the number of chambers in the outer whorl in Mediterranean–North Atlantic Globorotalia puncticulata bononiensis is an example of population differentiation later in the Pliocene.Chronostratigraphy shows that the northward expansion of central temperate water populations commenced with their occupation of Southwest Pacific subtropical water about 4.8 Ma. The rather abrupt entry of substantial populations into Mediterranean and North Atlantic water at 4.5 Ma marked a major biogeographic expansion and established G. puncticulata as a bipolar species. It was widely distributed about 3 Ma, with major populations in several water masses during a period of middle Pliocene warmth.After this acme North Atlantic and Mediterranean G. puncticulata bononiensis populations collapsed as late Pliocene Northern Hemisphere glacials intensified. They were extinguished in MIS 96 (2.4 Ma). Concurrently, G. puncticulata s.s became extinct in the warm subtropical Southwest Pacific. Subantarctic populations persisted but in turn were decimated in severe glacials during the Middle Pleistocene Transition. Most had disappeared by MIS 16 (0.66 Ma). However, at Sites 594 and 1119 there was a small Lazarus-like revival in MIS 11 (0.41 Ma). The highest known occurrence is in MIS 9 (0.33 Ma) at Site 1119. Confinement of the species to subantarctic water in the Pleistocene may have raised its vulnerability to extinction.While stable isotope data indicate that the lineage's evolution is related to depth habitat selection about the thermocline, its biogeography suggests that hydrographic barriers significantly isolated populations and probably facilitated speciation. Eddies such as the North Brazil Current rings provide conduits for inter-water mass transfer of populations but the history of G. puncticulata suggests that such mechanisms seldom operated successfully.The morphology of the lectotype of G. puncticulata s.s., from beach sand at Rimini, Italy, is consistent with a lower Pliocene source. Reports of living occurrences are poorly documented and the species is considered to be extinct.     

Biochemical genetic variability in brown hares (Lepus europaeus) from Greece

Allozyme variability of 91 brown hares (Lepus europaeus) from seven regions in Greece was compared to existing data of Bulgarian populations to test the hypothesis of the occurrence of specific alleles in Greece, likely stemming from an isolated Late Pleistocene refugial population in the southern Balkans. This hypothesis is particularly suggested by some subfossil Late Pleistocene hare remains in Greece and the reported high mtDNA diversity in Greek hares. Allozymic diversity could be higher in Greek hares than in hares from neighboring regions as a result of the accumulation of variants in a long-lasting Pleistocene refugium. Conversely, Greek hares could exhibit reduced genetic diversity because of long-lasting low effective population sizes during the Late Glacial Maximum and a lower chance of postglacial gene flow from other populations into this rather marginal part in the southern Balkans. Horizontal starch gel electrophoresis of proteins from 35~loci revealed three alleles (Es-1 ^–162, Pep-2 ¹¹⁴, Mpi ⁸⁸) at low frequencies, which were not found in Bulgarian or any other brown hare population. In contrast, some alleles from the populations from Bulgaria and other regions of Europe were absent in the Greek samples. Population genetic statistics indicated only a slight tendency of increased gene pool diversity in Greek hares, little substructuring in Greek and Bulgarian populations, respectively, as well as an only slightly lower level of gene flow between the two neighboring regions, as compared to the gene flow within each region. The results conform to the hypothesis of a Late Pleistocene refugial population in the southern Balkans, with some few specific nuclear gene pool characteristics, but little effect on the overall genetic differentiation between Greek and Bulgarian hares.