基于16S基因序列海南产白唇竹叶青蛇的分类地位

为研究海南产白唇竹叶青蛇分类地位,捕捉来自海南岛各地的12个白唇竹叶青蛇样本,并从GenBank下载65个竹叶青蛇的样本序列,以瘤鼻蝮蛇为外群,建立16S系统发育树。系统发育树显示,竹叶青蛇分为多个属的观点具有很大的合理性,白唇竹叶青蛇隶属于帝汶(岛屿)竹叶青蛇属。进一步验证了经典形态学和生物地理学的观点,海南岛产白唇竹叶青与其它地方产白唇竹叶青蛇不存在生殖隔离。     

Biogeography of Indonesian snakes

The islands of eastern Indonesia occupy the major zone of contact and overlap between the reptile faunas of the Asian and Australo–Papuan regions. A survey of reptiles on twenty-eight islands in eastern Indonesia between 1988 and 1993 has documented several major range extensions and many new records of species on islands. The zoogeographic affinities of the snakes of Indonesian islands are re-examined in the light of both recent surveys and taxonomic research and coupled with that published previously. The major boundary in the snake fauna of Indonesia occurs between Sulawesi and the Lesser Sunda islands to the west and the northern and southern Maluku group of islands to the east; it corresponds to the major biogeographic boundary known as Weber's Line. The biogeographic affinities of the snakes of the Tanimbar islands are equivocal. The snake fauna of islands within the Lesser Sunda group indicate that separation between islands during the Pleistocene played a role in determining current assemblages and variation within species The islands of eastern Indonesia form biogeographic subregions that have relatively high levels of endemism and evidence of incipient speciation as a consequence of changes in sea-levels and climate during the Pleistocene.     

Vicariance or dispersal? Historical biogeography of three Sunda shelf murine rodents (Maxomys surifer,Leopoldamys sabanus and Maxomys whiteheadi)

The Sunda region of south-east Asia comprises the Malay Peninsula and the islands of Java, Sumatra and Borneo, all of which lie on a shallow continental shelf projecting from Indochina. Pleistocene glacial cycles caused sea levels to drop repeatedly, exposing vast areas of the Sunda shelf and creating land bridges among the islands and mainland. These land bridges, the latest of which connected all three of the major Sunda islands to the Malay Peninsula as recently as 9500 years ago, may have enabled mammalian migrations across the Sunda shelf. Pleistocene land bridges on the Sunda shelf have been invoked to explain the current distributions of mammalian taxa occupying ranges corresponding with the Pleistocene limits of land and the appearance of new mammal species in the Pleistocene fossil record. The ability of mammals to move throughout the exposed shelf during periods of low sea level would, however, have been influenced by topographic and ecological features, which have been variously described as savanna-like or as moist tropical rain forest. Using a phylogeographical approach, we test the hypothesis that Pleistocene land bridges enabled widespread movements in three rain-forest-restricted murine rodents of the Sunda shelf: Maxomys surifer , Leopoldamys sabanus and Maxomys whiteheadi . Our results do not support the hypothesis of broad Pleistocene migrations in these taxa, but instead suggest a deep history of vicariant evolution that may correspond with the Pliocene fragmentation of the Sunda block.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 91–109.     

Recent colonization and expansion through the Lesser Sundas by seven amphibian and reptile species

The Lesser Sundas Archipelago is comprised of two parallel chains of islands that extend between the Asian continental shelf (Sundaland) and Australo‐Papuan continental shelf (Sahul). These islands have served as stepping stones for taxa dispersing between the Asian and Australo‐Papuan biogeographical realms. While the oceanic barriers have prevented many species from colonizing the archipelago, a number of terrestrial vertebrate species have colonized the islands either by rafting/swimming or by human introduction. Here, we examine phylogeographic structure within the Lesser Sundas for three snake, two lizard and two frog species that each has a Sunda Shelf origin. These species are suspected to have recently colonized the archipelago, though all have inhabited the Lesser Sundas for over 100 years. We sequenced mtDNA from 231 samples to test whether there is sufficiently deep genetic structure within any of these taxa to reject human‐mediated introduction. Additionally, we tested for genetic signatures of population expansion consistent with recent introduction and estimated the ages of Lesser Sundas clades, if any exist. Our results show little to no genetic structure between populations on different islands in five species and moderate structure in two species. Nucleotide diversity is low for all species, and the ages of the most recent common ancestor for species with monophyletic Lesser Sundas lineages date to the Holocene or late Pleistocene. These results support the hypothesis that these species entered the archipelago relatively recently and either naturally colonized or were introduced by humans to most of the larger islands in the archipelago within a short time span.     

Historical processes and contemporary ocean currents drive genetic structure in the seagrass Thalassia hemprichii in the Indo‐Australian Archipelago

Understanding spatial patterns of gene flow and genetic structure is essential for the conservation of marine ecosystems. Contemporary ocean currents and historical isolation due to Pleistocene sea level fluctuations have been predicted to influence the genetic structure in marine populations. In the Indo‐Australian Archipelago (IAA), the world's hotspot of marine biodiversity, seagrasses are a vital component but population genetic information is very limited. Here, we reconstructed the phylogeography of the seagrass Thalassia hemprichii in the IAA based on single nucleotide polymorphisms (SNPs) and then characterized the genetic structure based on a panel of 16 microsatellite markers. We further examined the relative importance of historical isolation and contemporary ocean currents in driving the patterns of genetic structure. Results from SNPs revealed three population groups: eastern Indonesia, western Indonesia (Sunda Shelf) and Indian Ocean; while the microsatellites supported five population groups (eastern Indonesia, Sunda Shelf, Lesser Sunda, Western Australia and Indian Ocean). Both SNPs and microsatellites showed asymmetrical gene flow among population groups with a trend of southwestward migration from eastern Indonesia. Genetic diversity was generally higher in eastern Indonesia and decreased southwestward. The pattern of genetic structure and connectivity is attributed partly to the Pleistocene sea level fluctuations modified to a smaller level by contemporary ocean currents.     

Biogeography of the Indonesian archipelago: mitochondrial DNA variation in the fruit bat, Eonycteris spelaea

The fruit bat, Eonycteris spelaea , occurs from India through the Philippines to the southeast limit of its distribution in the Lesser Sunda islands of Indonesia. Mitochondrial DNA (mtDNA) variation was examined in Indonesian E. spelaea island populations by amplification of the D-loop and digestion with restriction endonucleases. In addition, microgeographic variation was assessed by investigation of three cave populations within one island. A total of 24 genotypes, comprising two broad clades, was detected. The pattern of mtDNA variation reflects the colonization history of E. spelaea with estimates of haplotype and sequence diversity highest in the older western populations and lowest at the eastern periphery of the species' distribution. These findings may also be associated with an environmental cline from west to east. There is also evidence that genetic distance between populations reflects geographic relationships, especially historical connectedness, as measured by Pleistocene sea-crossing distances. At the microgeographic level, cave populations were heterogeneous and composed of diverse lineages suggesting restricted local interchange.     

Population systematics of Russell's viper: a multivariate study

A multivariate analysis of the population systematics of Russell's viper, based on scalation and colour pattern characters, reveals that the populations of this viper constitute two well-defined taxa: a western form, comprising all populations from the Indian subcontinent, and an eastern form, comprising all populations from east of the Bay of Bengal. The two forms could be considered either as subspecies of one species, or as two separate species, depending on the species concept used. Within the western form, there is no clear pattern of geographic variation. Within the eastern form, the populations from the Lesser Sunda Islands are clearly divergent from the populations of mainland Asia and Java. The conventionally recognized subspecies of Vipera russelli fail to portray this pattern of geographic variation. There is no clear relationship between the pattern of geographic variation in morphology and the pattern of geographic variation in the clinical effects of the venom in human bite victims: some populations with considerable differences in venom effects are equally distinct morphologically, whereas other populations with equally strong venom differences are morphologically very similar. The distribution of Russell's viper can be attributed to Pleistocene changes in climate and sea level, coupled with the viper's ecological requirements, which appear to include a seasonally dry climate.     

Phylogeographic structure in mitochondrial DNA of a South-east Asian freshwater fish, Hemibagrus nemurus (Siluroidei; Bagridae) and Pleistocene sea-level changes on the Sunda shelf

We postulated that the biogeographical history of South-east Asia contributed to extensive admixture during Pleistocene low sea levels of genetic groups of an obligate freshwater fish (the river catfish, Hemibagrus nemurus) isolated during periods of high sea levels. During Pleistocene glacial maxima, the sea level was lower than at present and the islands of the Sunda shelf (Sumatra, Borneo and Java) and the Asian mainland were connected by lowlands traversed by rivers. Restriction fragment length polymorphisms in mitochondrial DNA were documented for 140 putative H. nemurus analysed from 13 sampling sites resulting in the definition of 35 haplotypes. The high level of haplotype differentiation (mean P × 100 = 2.22, SD = 1.33) indicates that the subdivision of the ancestral H. netnurus group was extensive and probably occurred early in the Pleistocene. The occurrence of some genetically divergent groups of the H. netnurus complex occurring in sympatry in widely separated locations supports the proposition that low sea levels aided the dispersion and mingling of genetic groups. Based on both genetic and morphological evidence, the main H. nemurus line gave rise to three regional groups: (1) a morphologically distinct ‘Indochinese’ group composed of two mtDNA clades overlapping in east peninsular Malaysia; (2) a ‘Sundaic’ group composed of various lineages of differing morphology and genetic identity; (3) a genetically distinct ‘Sarawak’ group in west Borneo, similar in morphology to the ‘Sundaic’ and ‘Indochinese’ groups, but including a small, golden colour morph as a distinct dade. The morphologically similar Sundaic forms from west Java, Sumatra and west Borneo show some degree of genetic divergence, but their phylogenetic relationships are poorly resolved. The most genetically and morphologically distinct Sundaic dade, assigned to H. hoevenii, colonized the Kapuas river (west Borneo), east Sumatra and south peninsular Malaysia. Contrary to our original hypothesis and present biogeographical theory, little exchange of genetic groups has apparently occurred between the mainland and the Sunda Islands during recent glaciations.     

Lessons from Timor: Shells are poor taxonomic indicators in Asperitas land snails (Stylommatophora,Dyakiidae)

The limacoid land snail Asperitas Gude, 1911 encompasses several vividly coloured, yet poorly known species that are distributed throughout the Lesser Sunda Islands, Sulawesi, and the Moluccas. We examined the variation in shell morphology, including the use of geometric morphometrics, and reproductive anatomy of snails from Timor and several adjacent islands. These studies revealed that none of the taxa described from Timor and considered to be endemic to this island could be reliably distinguished from any of the others. In addition to the systematic ambiguity of morphological characteristics, we uncovered rather low amounts of genetic differentiation in the mitochondrial marker cytochrome c oxidase subunit I that was not consistent with the current taxonomy. Based on these observations, we conclude that there is just a single Asperitas species on Timor that exhibits notable variability in shell characters and body colour. This variability is ascribed to the combined effects of polymorphic colour patterns with locally varying selection in different habitats and along altitudinal gradients. Individuals from the adjacent islands of Flores, Sumbawa, Solor and Romang, which are deemed to represent distinct species-level taxa, exhibit similar amounts of variation in shell and body colour. They exhibit a consistent reproductive anatomy and overall negligible amounts of mitochondrial differentiation from the populations on Timor. Patterns in shell variation do not lend support to previously held ideas that different Sunda Islands harbour distinct radiations of polytypic Asperitas species. By contrast, we suggest that the taxonomic diversity of Asperitas has been overestimated for the over-reliance on shell features and that many presently accepted taxa are likely mere synonyms of fewer and more widespread species.     

The use of amplified fragment length polymorphism in determining species trees at fine taxonomic levels: analysis of a medically important snake, Trimeresurus albolabris

There are a huge number of phylogenetic studies based on mitochondrial DNA (mtDNA); however, these may represent gene trees that may not be congruent with the species tree. A solution to this problem is to include additional, independent, loci from the nuclear genome. At fine taxonomic levels, i.e. between populations and closely related species, previously suggested nuclear markers such as intron sequence data may not be appropriate. In this study we investigate the use of amplified fragment length polymorphisms (AFLP) to aid determination of the species tree for 24 specimens of a medically important snake, Trimeresurus albolabris. This is of particular importance for many venomous snakes as venom often varies intraspecifically. Five different primer combinations produced 434 bands and were analysed by constructing a phylogenetic tree using neighbour joining and principal component analysis. Results were similar across all methods and found distinct groupings. The results were compared with mtDNA data and a reconciled tree was constructed in order to determine the species tree for T. albolabris. We found that T. albolabris (sensu lato) is not monophyletic. Specimens from the Indonesian islands (except West Java) form a distinct clade and we propose elevation to species level. A specimen from Nepal is also distinct and suggests that this population also deserves specific status. We suggest that AFLPs may prove a valuable aid in determining species trees as opposed to gene trees at fine taxonomic levels and this should facilitate the incorporation of molecular data into such activities as antivenom production and conservation management.     

Phylogeographic patterns of Hawaiian Megalagrion damselflies (Odonata: Coenagrionidae) correlate with Pleistocene island boundaries

The Pleistocene geological history of the Hawaiian Islands is becoming well understood. Numerous predictions about the influence of this history on the genetic diversity of Hawaiian organisms have been made, including the idea that changing sea levels would lead to the genetic differentiation of populations isolated on individual volcanoes during high sea stands. Here, we analyse DNA sequence data from two closely related, endemic Hawaiian damselfly species in order to test these predictions, and generate novel insights into the effects of Pleistocene glaciation and climate change on island organisms. Megalagrion xanthomelas and Megalagrion pacificum are currently restricted to five islands, including three islands of the Maui Nui super-island complex (Molokai, Lanai, and Maui) that were connected during periods of Pleistocene glaciation, and Hawaii island, which has never been subdivided. Maui Nui and Hawaii are effectively a controlled, natural experiment on the genetic effects of Pleistocene sea level change. We confirm well-defined morphological species boundaries using data from the nuclear EF-1alpha gene and show that the species are reciprocally monophyletic. We perform phylogeographic analyses of 663 base pairs (bp) of cytochrome oxidase subunit II (COII) gene sequence data from 157 individuals representing 25 populations. Our results point to the importance of Pleistocene land bridges and historical island habitat availability in maintaining inter-island gene flow. We also propose that repeated bottlenecks on Maui Nui caused by sea level change and restricted habitat availability are likely responsible for low genetic diversity there. An island analogue to northern genetic purity and southern diversity is proposed, whereby islands with little suitable habitat exhibit genetic purity while islands with more exhibit genetic diversity.     

Relationships between morphology, genetics and geography in the cave fruit bat Eonycteris spelaea (Dobson, 1871) from Indonesia

Morphological and genetic analyses of Eonycteris spelaea from 15 islands along the Banda Arc, from Sumatra to Timor and including Kalimantan and Sulawesi, revealed considerable divergence between islands and geographical patterning. On the basis of both morphology and genetics, the populations on the large islands of Greater Sunda (Sumatra, Java, Kalimantan and Sulawesi) are generally distinct from one another and from those on the islands in Nusa Tenggara (Lombok to Timor), which form a more cohesive cluster. These differences may be the result of the Nusa Tenggara populations having been colonized more recently than those on the Greater Sunda, and probably from a single source. All biological measures of the relationships between island populations are positively associated with the extent of the sea-crossing between them, indicating the sea is an important barrier to movement. Multivariate analyses show the presence of a marked trend for body size to increase from west to east. However, individuals from Kalimantan are not consistent with this trend, being smaller than predicted, and on the two outer Banda Arc islands of Sumba and Timor animals are a little larger than predicted from the longitudinal trend. These differences could be due to the relative isolation of these populations or differing environmental conditions. There is also a negative relationship between body size and island area, but this is confounded by the longitudinal trend. No significant longitudinal trends in the genetic data were detected and the trend in body size may be an adaptive response to an environmental cline that is known to occur in this region.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79, 511–522.     

The roles of geological history and colonization abilities in genetic differentiation between mammalian populations in the Philippine archipelago

Aim To test hypotheses that: (1) late Pleistocene low sea‐level shorelines (rather than current shorelines) define patterns of genetic variation among mammals on oceanic Philippine islands; (2) species‐specific ecological attributes, especially forest fidelity and vagility, determine the extent to which common genetic patterns are exhibited among a set of species; (3) populations show reduced within‐population variation on small, isolated oceanic islands; (4) populations tend to be most highly differentiated on small, isolated islands; and (5) to assess the extent to which patterns of genetic differentiation among multiple species are determined by interactions of ecological traits and geological/geographic conditions. Location The Philippine Islands, a large group of oceanic islands in Southeast (SE) Asia with unusually high levels of endemism among mammals. Methods Starch‐gel electrophoresis of protein allozymes of six species of small fruit bats (Chiroptera, Pteropodidae) and one rodent (Rodentia, Muridae). Results Genetic distances between populations within all species are not correlated with distances between present‐day shorelines, but are positively correlated with distances between shorelines during the last Pleistocene period of low sea level; relatively little intraspecific variation was found within these ‘Pleistocene islands’. Island area and isolation of oceanic populations have only slight effects on standing genetic variation within populations, but populations on some isolated islands have heightened levels of genetic differentiation, and reduced levels of gene flow, relative to other islands. Species associated with disturbed habitat (all of which fly readily across open habitats) show more genetic variation within populations than species associated with primary rain forest (all of which avoid flying out from beneath forest canopy). Species associated with disturbed habitats, which tend to be widely distributed in SE Asia, also show higher rates of gene flow and less differentiation between populations than species associated with rain forest, which tend to be Philippine endemic species. One rain forest bat has levels of gene flow and heterozygosity similar to the forest‐living rodent in our study. Main conclusions The maximum limits of Philippine islands that were reached during Pleistocene periods of low sea level define areas of relative genetic homogeneity, whereas even narrow sea channels between adjacent but permanently isolated oceanic islands are associated with most genetic variation within the species. Moreover, the distance between ‘Pleistocene islands’ is correlated with the extent of genetic distances within species. The structure of genetic variation is strongly influenced by the ecology of the species, predominantly as a result of their varying levels of vagility and ability to tolerate open (non‐forested) habitat. Readily available information on ecology (habitat association and vagility) and geological circumstances (presence or absence of Pleistocene land‐bridges between islands, and distance between oceanic islands during periods of low sea level) are combined to produce a simple predictive model of likely patterns of genetic differentiation (and hence speciation) among these mammals, and probably among other organisms, in oceanic archipelagos.     

Geographical variation in and evolutionary history of the Sunda clouded leopard (Neofelis diardi) (Mammalia: Carnivora: Felidae) with the description of a new subspecies from Borneo

Recent morphological and molecular studies led to the recognition of two extant species of clouded leopards; Neofelis nebulosa from mainland southeast Asia and Neofelis diardi from the Sunda Islands of Borneo and Sumatra, including the Batu Islands. In addition to these new species-level distinctions, preliminary molecular data suggested a genetic substructure that separates Bornean and Sumatran clouded leopards, indicating the possibility of two subspecies of N. diardi. This suggestion was based on an analysis of only three Sumatran and seven Bornean individuals. Accordingly, in this study we re-evaluated this proposed subspecies differentiation using additional molecular (mainly historical) samples of eight Bornean and 13 Sumatran clouded leopards; a craniometric analysis of 28 specimens; and examination of pelage morphology of 20 museum specimens and of photographs of 12 wild camera-trapped animals. Molecular (mtDNA and microsatellite loci), craniomandibular and dental analyses strongly support the differentiation of Bornean and Sumatran clouded leopards, but pelage characteristics fail to separate them completely, most probably owing to small sample sizes, but it may also reflect habitat similarities between the two islands and their recent divergence. However, some provisional discriminating pelage characters are presented that need further testing. According to our estimates both populations diverged from each other during the Middle to Late Pleistocene (between 400 and 120 kyr). We present a discussion on the evolutionary history of Neofelis diardi sspp. on the Sunda Shelf, a revised taxonomy for the Sunda clouded leopard, N. diardi, and formally describe the Bornean subspecies, Neofelis diardi borneensis, including the designation of a holotype (BM.3.4.9.2 from Baram, Sarawak) in accordance with the rules of the International Code of Zoological Nomenclature.     

Population affinities of the asiatic cobra (Naja naja) species complex in south-east Asia: reliability and random resampling

The population systematics of the cobras of the genus Naja in southern Thailand, Malaysia and Indonesia are investigated, using multivariate analysis of a large number of morphological characters. These populations are found to constitute three distinct groups: a northern form, which occurs in Thailand and northern Peninsular Malaysia; an equatorial form, which occurs in southern Thailand, Peninsular Malaysia, Sumatra and Borneo; and a southern form, which occurs on Java and the Lesser Sunda Islands. The first two forms are sympatric in northern Peninsular Malaysia and southern Thailand, and therefore constitute separate species. This is of importance for the treatment of snakebite in the region. The distribution of the three forms can be related both to present ecological conditions and to Pleistocene geological and climatic events. The reliability of the results is demonstrated by the relationship between character number and congruence of patterns of geographic variation, investigated by random resampling. The pattern of geographic variation within two of the three main forms is investigated and related to current ecological conditions and Pleistocene events.     

Genetic structure of Gymnures (genus Hylomys; Erinaceidae) on continental islands of Southeast Asia: historical effects of fragmentation

Eustatic sea level changes during Pleistocene climatic fluctuations produced several cycles of connection-isolation among continental islands of the Sunda shelf. To explore the potential effects of these fluctuations, we reconstructed a model of the vicariant events that separated these islands, based on bathymetric information. Among many possible scenarios, two opposite phylogenetic patterns of evolution were predicted for terrestrial organisms living in this region: one is based on the classical allopatric speciation mode of evolution, while the other is the outcome of a sequential dispersal colonization of the archipelago. We tested the applicability of these predictions with an analysis of sequence variation of the cytochrome b gene from several taxa of Hylomys. They were sampled throughout SE-Asia and the Sunda islands. High levels of haplotype differentiation characterize the different island taxa. Such levels of differentiation support the existence of several allopatric species, as was suggested by previous allozyme and morphological data. Also in accordance with previous results, the occurrence of two sympatric species from Sumatra is suggested by their strongly divergent haplotypes. One species, Hylomys suillus maxi, is found both on Sumatra and in Peninsular Malaysia, while the other, H. parvus, is endemic to Sumatra. Its closest relative is H. suillus dorsalis from Borneo. Phylogenetic reconstructions also demonstrate the existence of a Sundaic clade composed of all island taxa, as opposed to those from the continent. Although there is no statistical support for either proposed biogeographic model of evolution, we argue that the sequential dispersal scenario is more appropriate to describe the genetic variation found among the Hylomys taxa. However, despite strong differentiation among island haplotypes, the cladistic relationships between some island taxa could not be resolved. We argue that this is evidence of a rapid radiation, suggesting that the separation of the islands may have been perceived as a simultaneous event rather than as a succession of vicariant events. Furthermore, the estimates of divergence times between the haplotypes of these taxa suggest that this radiation may actually have predated the climatic fluctuations of the Pleistocene. Further refinement of the initial palaeogeographic models of evolution are therefore needed to account for these results.     

Marine invasions by non-sea snakes, with thoughts on terrestrial-aquatic-marine transitions

Few species of snakes show extensive adaptations to aquatic environments and even fewer exploit the oceans. A survey of morphology, lifestyles, and habitats of 2552 alethenophidian snakes revealed 362 (14%) that use aquatic environments, are semi-aquatic, or aquatic; about 70 (2.7%) of these are sea snakes (Hydrophiinae and Laticaudinae). The ancient and aquatic family Acrochordidae contains three extant species, all of which have populations inhabiting brackish or marine environments, as well as freshwater. The Homalopsidae have the most ecologically diverse representatives in coastal habitats. Other families containing species exploiting saline waters with populations in freshwater environments include: the Dipsadidae of the western hemisphere, the cosmopolitan Natricidae, the African Grayinae, and probably a few Colubridae. Species with aquatic and semi-aquatic lifestyles are compared with more terrestrial (fossorial, cryptozoic, and arboreal) species for morphological traits and life histories that are convergent with those found in sea snakes; this may provide clues to the evolution of marine snakes and increase our understanding of snake diversity.     

Evidence of Sundaland’s subsidence requires revisiting its biogeography

It is widely accepted that sea level changes intermittently inundated the Sunda Shelf throughout the Pleistocene, separating Java, Sumatra and Borneo from the Malay Peninsula and from each other. On this basis, the dynamics of the biodiversity hotspot of Sundaland is consistently regarded as solely contingent on glacial sea level oscillations, with interglacial highstands creating intermittent dispersal barriers between disjunct landmasses. However, recent findings on the geomorphology of the currently submerged Sunda shelf suggest that it subsided during the Pleistocene and that, over the Late Pliocene and Quaternary, is was never submerged prior to Marine Isotope Stage 11 (MIS 11, 400 ka). This would have enabled the dispersal of terrestrial organisms regardless of sea level variations until 400 ka and hampered movements thereafter, at least during interglacial periods. Existing phylogeographic data for terrestrial organisms conform to this scenario: available divergence time estimates reveal an 8- to 9-fold increase in the rate of vicariance between landmasses of Sundaland after 400 ka, corresponding to the onset of episodic flooding of the Sunda shelf. These results highlight how reconsidering the paleogeographic setting of Sundaland challenges understanding the mechanisms generating Southeast Asian biodiversity.     

Molecular phylogeography of white‐lipped tree viper (Trimeresurus; Viperidae)

The white‐lipped tree viper (Trimeresurus albolabris) is one of the most common venomous snakes with medicine importance in South East Asia. To explore the genetic diversity, population structure and evolutionary history of Trimeresurus albolabris, we collected 98 samples from 27 localities covering its entire distribution. Two mitochondrial gene fragments (cyt‐b and ND‐4) and two nuclear genes (RAG‐1 and NT‐3) were sequenced and analysed. Bayesian inference and maximum‐likelihood methods were employed to reconstruct the phylogenetic relationships among populations based on the two mitochondrial fragments, and the median‐joining networks were depicted using nuclear genes. Divergence date and ancestral area were estimated, and the population demographic history was inferred. Both phylogenetic analyses consistently uncovered that Trimeresurus albolabris was monophyletics, with five geographically structured lineages. Divergence date and ancestral area estimation indicated that T. albolabris originated in northern Thailand and eastern Myanmar at c. 7.15 Ma. Population dynamics analyses showed the southern China lineage has experienced population expansion and contraction, but the others have not. Both the interglacial expansion and the highly heterogeneous habitats resulting from the uplift of the Plateau played a joint role in shaping the present distribution and population structure. The evolutionary history of T. albolabris can be explained by a pattern of two direction dispersal: first from North to South, and then from West to East.     

Combined next‐generation sequencing and morphology reveal fine‐scale speciation in Crocodile Skinks (Squamata: Scincidae: Tribolonotus)

Next‐generation sequencing has vast potential to revolutionize the fields of phylogenetics and population genetics through its ability to collect genomic scale data sets of thousands of orthologous loci. Despite this potential, other types of data (e.g. morphology, ecology) remain important, particularly for studies endeavouring to delimit species. Here, we integrate next‐generation sequencing with morphology to examine divergence between populations of Tribolonotus pseudoponceleti on the islands of Buka and Bougainville in the Solomon Archipelago. We used the Ion Torrent PGM to collect over 648 Mbp of sequence data for 12 samples, representing 1526 loci recovered from all samples, and 3342 were recovered from at least six samples. Genetic structure analyses strongly support the distinctiveness of these two populations, and Bayes factor delimitations decisively select speciation between Buka and Bougainville. Principal components and discriminant function analyses reveal concordant morphological divergence. Finally, demographic analyses via diffusion approximation and approximate Bayesian computation prefer a complex model of mid‐Pleistocene divergence with migration, and a later decrease or cessation of migration and population size shift, suggesting a scenario in which migration was enabled by Pleistocene merging of these two islands, and limited when isolated by higher sea levels. Further analysis of four Sanger sequenced loci in IMa2 had limited power to distinguish among models including and excluding migration, but resulted in similar population size and divergence time estimates, although with much broader confidence intervals. This study represents a framework for how next‐generation sequencing and morphological data can be combined and leveraged towards validating putative species and testing demographic scenarios for speciation.