基因组时代的新视野: 东南亚哺乳动物类群在第四纪冰河时期多样性的起源与分化

东南亚地区东起菲律宾群岛, 西至印度次大陆, 北及中国中部, 南至巽他群岛, 涵盖了世界上25个最重要的生物多样性热点地区之中的6个, 具有极其重要的全球生物多样性保护的战略意义。该地区复杂的地质地貌和气候历史使其动植物的种类和数量都极为丰富。经典的生物地理分界线华莱士线和克拉地峡将该地区进一步划分出包括部分巽他群岛和马来半岛在内的南部巽他区和北部印度支那区两个生物多样性热点地区。主要基于形态学的生物地理学研究认为巽他区和印度支那区通过马来半岛陆地相连, 并且第四纪大部分时间海平面下降形成大陆桥, 直到一万年前该地区的众多岛屿仍与大陆连接, 促进了哺乳动物的种群迁徙与基因交流, 因此物种种群间的差别将很细微。然而近来分子遗传学研究表明, 由于其他生态因素制约, 哺乳动物的迁移能力可能比以往认为的低, 大陆桥的存在并不一定导致迁徙的发生, 许多种群的隔离早在200万年前便已形成, 并且没有因为后来冰川期海平面降低而恢复种群交流, 而距今7.3万年前发生的苏门答腊多巴超级火山爆发也可能进一步影响了物种间和物种内多样性的形成和分化。通过已有的东南亚哺乳动物种群遗传学研究结果, 我们认为物种间或种群间的差异主要表现为三个层次: 巽他区种群与印度支那区种群间约百万年尺度的分化, 巽他区不同岛屿种群间约数十万年尺度的分化, 以及发生于晚更新世的分化事件。已有的东南亚种群遗传学研究主要采用线粒体及核基因多位点数据进行分析, 而种群基因组学分析则使得获得详尽的种群历史动态成为可能, 并使我们可以进一步了解东南亚哺乳动物类群所经历的物种形成过程。     

Tail length variation inMacaca fascicularis andM. mulatta

Based on collectors' measurements of 1,040 specimens, variation of relative tail length [RTL = (tail length/head and body length) × 100] has been studied inMacaca fascicularis andM. mulatta, two closely related species that replace one another in tropical Asia and subtropical Asia, respectively. RTL usually is greater than 90 inM. fascicularis and usually is less than 60 inM. mulatta; intermediate values occur in only 3.5% of specimens studied. Within each species, RTL is approximately equal in females and males. From infancy to adulthood, RTL tends to decline in both species. InM. fascicularis, RTL generally decreases with increasing latitude; inM. mulatta, RTL is approximately constant latitudinally. Where the geographic ranges of these two species meet at ca. 15°N in the Indochinese Peninsula, a few specimens have been collected in which RTL and dorsal pelage color are intermediate between those inM. fascicularis andM. mulatta. The observed pattern of variation suggests that the ranges ofM. fascicularis andM. mulatta formerly were separated by a zoogeographic barrier — perhaps during a Pleistocene glacial interval. After disappearance of the postulated barrier, the ranges of these two species apparently became contiguous and limited hybridization has occurred.     

Morphological and Body Color Variation in Thai <Emphasis Type="Italic">Macaca fascicularis fascicularis</Emphasis> North and South of the Isthmus of Kra

Long-tailed macaques (Macaca fascicularis fascicularis) are widely distributed in Southeast Asia and are morphologically and genetically (Tosi et al. in International Journal of Primatology 23:161–178, 2002) distinguishable on either side of the Isthmus of Kra (ca. 10.5°N). We compared the somatometry and body color of 15 local populations of long-tailed macaques in Thailand distributed over areas from 6.5°N to 16.3°N and also a Thai rhesus macaque population at 17.2°N. Limb proportions and body color variation follow the geographical trend. However, contrary to a previous report, body size does not decrease with latitude in the northern group and also in the southern (southerly distributed) rhesus macaque. Relative tail length (RTL) and color contrast in yellow between the back and thigh are the sole traits that distinctively separate the 2 groups: the southern group has a long relative tail length (RTL >125%) and small color contrast, whereas the northern group has a short RTL (<120%) and large color contrast. The southern rhesus macaques appear to have somatometric and body color traits that follow the geographical trend in long-tailed macaques, though they maintain their distinctive species-specific traits of shorter RTL (ca. 55%), shorter relative facial length, and a bipartite body color pattern. Researchers assume that the northern group of long-tailed macaques and the southern rhesus macaques had undergone partial introgression with each other. Montane refugia present during the glacial period are localities in which introgression occurred in long-tailed macaques.     

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.     

Biogeographic variation in skull morphology across the Kra Isthmus in dusky leaf monkeys

Despite the growing literature on the underlying factors of geographical phenotypic variation, little is known about how and to what extent biogeographic barriers in South‐East Asia have shaped morphological variation in primates. We aimed to investigate the geographical variations in skull morphology in dusky leaf monkeys by decomposing them into clinal (latitudinal), non‐clinal spatial (discrete difference between regions north and south of the Isthmus of Kra), and environment‐related components. We applied geometric morphometrics to measure 53 adult male specimens from 36 localities, covering the regions both north and south of the Isthmus of Kra. A linear model was used to test the effects of region (north vs. south of the Isthmus of Kra), latitude, and environmental factors (temperature and rainfall) on the size and shape of skulls. A part of variation in skull shape differed moderately between the regions in the north and south of the Isthmus of Kra, and this difference cannot be explained by latitudinal and environmental factors. However, for size and the majority of variations in shape, we detected limited contributions of region and the two environmental factors. Shape differentiation that was unexplained by latitudinal and environmental factors suggests that dusky leaf monkeys may have experienced a population division due to habitat constriction around the Isthmus of Kra. However, this divergence probably has been obscured by subsequent gene flow between populations after habitat recovery.     

The Indochinese–Sundaic zoogeographic transition: a description and analysis of terrestrial mammal species distributions

Aim We describe the distributions of mammal species between the Indochinese and Sundaic subregions and examine the traditional view that the two faunas show a transition near the Isthmus of Kra on the Thai–Malay peninsula. Location Species distributions are described along a 2000‐km transect from 20° N (northernmost Thailand) to 1° N (Singapore). Methods For the 325 species of native non‐marine mammals occurring along the transect we used published records to provide a database of their distributional records by degree of latitude. Results Along the transect we found 128 Indochinese species with southern range limits, 121 Sundaic species with northern range limits, four un‐assignable endemics and 72 widespread species. In total, 152 southern and 147 northern range limits were identified, and their distribution provides no evidence for a narrow faunal transition near the Isthmus of Kra (10°30′ N) or elsewhere. Range limits of both bats and non‐volant mammals cluster in northernmost peninsular Malaysia (5° N) and 800 km further north, where the peninsula joins the continent proper (14° N). The clusters of northern and southern range limits are not concordant but overlap by 100–200 km. Similarly, the range limits of bats and non‐volant mammals cluster at slightly different latitudes. There are 30% fewer species and range limits in the central and northern peninsula (between 6 and 13° N), and 35 more widely distributed species have range gaps in this region. In addition, we found 70 fewer species at the southern tip of the peninsula (1° N) than at 3–4° N. Main conclusions The deficiencies of both species and species range limits in the central and northern peninsula are attributed to an area effect caused by repeated sea‐level changes. Using a new global glacioeustatic curve developed by Miller and associates we show that there were > 58 rapid sea‐level rises of > 40 m in the last 5 Myr that would have resulted in significant faunal compression and local population extirpation in the narrow central and northern parts of the peninsula. This new global sea‐level curve appears to account for the observed patterns of the latitudinal diversity of mammal species, the concentration of species range limits north and south of this area, the nature and position of the transition between biogeographical subregions, and possibly the divergence of the faunas themselves during the Neogene. The decline of species diversity at the southern end of the transect is attributed to a peninsula effect similar to that described elsewhere.     

Y-Chromosome and Mitochondrial Markers in Macaca fascicularis Indicate Introgression with Indochinese M. mulatta and a Biogeographic Barrier in the Isthmus of Kra

This is the first report of Y-chromosome introgression between primate species. We sequenced 3.1 Kb of Y-chromosome DNA and 1.5 Kb of mtDNA for 27 macaques of Fooden's (Folia Primatol. [1976] 25: 225–236) fascicularis species group and 5 outgroup taxa (Macaca sylvanus, Papio hamadryas, Theropithecus gelada, Allenopithecus nigroviridis, and Cercopithecus mona). Phylogenies constructed separately for the paternal and maternal data sets show a Y-chromosome paraphyly among lineages of Macacafascicularis, but a mitochondrial monophyly for the same individuals. The Y-chromosome topology depicts Indochinese Macaca fascicularis haplotypes joining with those of M. mulatta, followed by M. cyclopis and M. fuscata, before clustering with a clade of lineages of M. fascicularis from peninsular Malaysia, Indonesia, and the Philippines. These contrasting patterns of mitochondrial and Y-chromosome DNA, evaluated in the context of the evolutionary consequences of macaque sex-biased dispersal, present strong evidence for contemporary hybridization between Macaca fascicularis and M. mulatta in Indochina and a biogeographic barrier in the Isthmus of Kra.     

Explaining the causes of the zoogeographic transition around the Isthmus of Kra: using bats as a case study

Aim  The causes of a zoogeographic divide in peninsular Thailand around the Isthmus of Kra have not been adequately resolved. We explored climatic, historical and geological perspectives to gain insights into factors that may have contributed to the development and maintenance of this zoogeographic transition, and to determine whether a faunal transition occurs for bats. Location  Southeast Asia, focusing on the Thai Peninsula. Methods  Spatial principal components analysis was used to determine the relationship between climate and species distribution patterns. We studied bats (order Chiroptera) because of their ability to bypass small‐scale geophysical barriers. Spatial data on bat species distributions on the Thai Peninsula were analysed in relation to multivariate measures of climate to determine the possible influence of climatic zonation on distribution patterns. We assessed the effects of the interaction of climatic zonation with the highly dynamic environmental conditions the area has undergone in relation to species distribution patterns. Results  A zoogeographic transition was found, with 44 species (out of 127) restricted to the north of the Isthmus of Kra and 29 restricted to the south, although there were relatively few abrupt changes in distribution at the exact position of the isthmus. Northern and southern species were associated with specific climatic conditions. Major transitions in the distribution of bat species exist at 6–6.5° N and 13–13.5° N, with a smaller peak at 11.0° N. These major peaks fall in the same areas as the borders of climatic zones, and the 6–6.5° N peak falls in the same area as a floristic divide (the Kangar–Pattani Line). Main conclusions  On the mainland, climatic zones cause gradual changes in species distributions. However, in addition to climatic factors, repeated changes in the breadth of the Sunda Shelf during recent glacial cycles may have caused locally high extinction rates at narrow points on the peninsula, exacerbating transitions in species distribution patterns along the region, in the context of a peninsula effect that reduces opportunities for recolonization.     

Evolutionary history of the Paradoxurus palm civets – a new model for Asian biogeography

Aim Using molecular data and dental features, we investigated the genetic and morphological diversity among species of palm civets in the genus Paradoxurus, with a focus on the common palm civet, Paradoxurus hermaphroditus (Carnivora, Viverridae), in order to address biogeographic scenarios and provide recommendations for a taxonomic revision. Location Asia: Pakistan to the Lesser Sunda Islands. Methods We investigated the genetic diversity within Paradoxurus using two mitochondrial (cytochrome b, control region) and one nuclear (intron 7 of the β‐fibrinogen) markers. We used samples from 85 individuals of P. hermaphroditus (including 20 museum specimens) and one representative of each of the other species in the genus Paradoxurus: Paradoxurus jerdoni and Paradoxurus zeylonensis. DNA sequences were analysed using phylogenetic and haplotype network methods, and divergence dates were estimated for the clades retrieved. Furthermore, we examined dental characters from a large series of specimens and compared the morphological variation with the molecular data. Results Our phylogenetic analyses revealed that P. hermaphroditus is paraphyletic. We identified three major lineages distributed: (1) in the Indian subcontinent, south China, Hainan and in areas above 200 m in Indochina; (2) in Peninsular Malaysia, Java, Sumatra and in areas below 200 m in Indochina; and (3) in Borneo, the Philippines and the Mentawai archipelago. Our morphological observations were congruent with these three molecular lineages. Divergence date estimates inferred a Pliocene origin for Paradoxurus (2.8–5.7 Ma), with the three main clades diversifying from the mid–Early Pliocene to the end of the Pliocene. We suggest that the flooding of the Isthmus of Kra during the Pliocene was a major event shaping the diversification of Paradoxurus palm civets. We also hypothesize that the elevational segregation of the two lineages on the mainland could have resulted from the vegetational changes that were induced by Late Pliocene glacial episodes. Main conclusions The Isthmus of Kra is a major boundary between two major lineages of P. hermaphroditus. There is a need for a taxonomic revision for P. hermaphroditus, and we suggest that this species should be split into at least three species.     

Mammals of south-east Asian islands and their Late Pleistocene environments

Aim The environments that existed in south‐east Asian islands during the last glacial are poorly known, limiting our understanding of mammalian biogeography in the region. The objective of this research is to investigate the ecological characteristics of mammal faunas on small islands, and to see whether the habitat requirements of the species in those faunas can be used to deduct the vegetation types that existed on islands before becoming isolated by rising sea levels. Location The maps presented here cover the small islands of tropical south‐east Asia, including the Burmese, Thai and Cambodian islands in the north, the islands off the coast of west Sumatra in the west, the islands around Java in the south, and the islands off the east coast of Borneo in the east, including the Philippine islands of Palawan and those in the Sulu Archipelago. Methods The presence records of mammal species on 215 small islands in the region were compiled, and the habitat requirements for each of these species was assessed (species that had probably been introduced by humans were excluded from the analysis). For each island location (longitude and latitude), maximum altitude of the island, total area, depth to nearest land, distance to nearest island, and distance to nearest mainland were assessed. Geographical and statistical analyses were used to investigate patterns of mammalian habitat requirements. Results The geographical analysis showed that forest‐dependent species, i.e. species that are only found in primary forest (lowland and mountainous), appear to be concentrated on islands off west Sumatra, in the Lingga and Riau Archipelagos, around Palawan, and around Bunguran Island; they are absent mostly from the islands of the Java Sea, those off the east coast of eastern Borneo, from most islands in the Sunda Strait, several islands in the northern South China Sea, and from all islands off the west coast of the Malay/Thai Peninsula and in the Gulf of Thailand. Species that generally occur outside primary forest, that is those in secondary forest, gardens, plantations and open areas mostly occurred on islands where the forest‐dependent species were absent. The statistical analysis showed that latitude and size of islands were important factors that determined the absence and presence of forest‐dependent species on small islands. Main conclusions The data suggest that during the last glacial there were several areas in the Sundaic region that remained forest covered: west of Sumatra, north‐west of Borneo, the Malacca Straits and around Palawan. Other areas may have been covered by more open vegetation types like tree savanna, or open deciduous forest: on and to the east of the Malay/Thai Peninsula, the Java Sea area, including the Sunda Strait, and eastern Borneo.     

The Indochinese–Sundaic faunal transition at the Isthmus of Kra: an analysis of resident forest bird species distributions

Aim  To establish the geographical position of the biogeographical transition between Indochinese and Sundaic faunas using distributional data for the best-documented taxon, the birds.
Methods  Distributional data of 544 resident forest and forest edge bird species of Thailand and the Thai–Malay peninsula were examined at 45 sites spanning 15° of latitude from northern-most Thailand to the southern peninsular Malaysia. Sites were grouped into 23 degree or half-degree latitudinal zones and avifaunal similarity coefficients were calculated between each zone.
Results  A Mantel test revealed a significant transition between northern Indochinese and southern Sundaic (Indomalay) avifauna assemblages just north of the Isthmus of Kra (10°30' N). Northern and southern range limits of 152 species (> 269 species and subspecies combined) lie between 11° and 13° N.
Main conclusions  This transition between zoogeographical subregions is not coincident with the widely recognized transition between floristic provinces which is traditionally placed 400–500 km further south at the Kangar–Pattani line, but is associated with a change from wet seasonal evergreen dipterocarp rain forest to mixed moist deciduous forest north of the Isthmus of Kra in the northern Thai–Malay peninsula. Climatological and ecological factors associated with the distribution of forest types today are reviewed and it is hypothesized that the avian transition tracks the northern phytogeographical boundary. Palaeogeographical factors, including hypothetical Neogene seaways, which may account for the historical development of both phytogeographical and avifaunal transitions are also described.     

Wallace's Line and plant distributions: two or three phytogeographical areas and where to group Java?

Wallace's Line or its variants divide the Malay Archipelago or Malesia into a western and eastern area, but is this suitable for plant distributions? Indeed, all boundaries satisfactorily divide Malesia into two parts, stopping far more species east or west of a line than disperse over the boundary. However, phenetic analyses (principal components analysis, nonmetric multidimensional scaling analysis and the unweighted pair group method with arithmetic mean) of 7340 species distributions revealed a stronger partitioning of Malesia into three instead of two regions: the western Sunda Shelf minus Java (Malay Peninsula, Sumatra, Borneo), central Wallacea (Philippines, Sulawesi, Lesser Sunda Islands, Moluccas, with Java), and the eastern Sahul Shelf (New Guinea). Java always appears to be part of Wallacea, probably because of its mainly dry monsoon climate. The three phytogeographic areas equal the present climatic division of Malesia. An everwet climate exists on the Sunda and Sahul Shelves, whereas most of Wallacea has a yearly dry monsoon. During glacial maxima, the Sunda and Sahul Shelves became land areas connected with Asia and Australia, respectively, whereas sea barriers remained within Wallacea. Consequently, the flora of the two shelves is more homogeneous than the Wallacean flora. Wallacea is a distinct area because it comprises many endemic, drought tolerant floristic elements. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 531–545.     

The effect of island area on body size in a primate species from the Sunda Shelf Islands

Aim  We examine the effect of island area on body dimensions in a single species of primate endemic to Southeast Asia, the long-tailed macaque ( Macaca fascicularis ). In addition, we test Allen's rule and a within-species or intraspecific equivalent of Bergmann's rule (i.e. Rensch's rule) to evaluate body size and shape evolution in this sample of insular macaques.
Location  The Sunda Shelf islands of Southeast Asia.
Methods  Body size measurements of insular macaques gathered from the literature were analysed relative to island area, latitude, maximum altitude, isolation from the mainland and other islands, and various climatic variables using linear regression.
Results  We found no statistically significant relationship between island area and body length or head length in our sample of insular long-tailed macaques. Tail length correlated negatively with island area. Head length and body length exhibited increases corresponding to increasing latitude, a finding seemingly consistent with the expression of Bergmann's rule within a single species. These variables, however, were not correlated with temperature, indicating that Bergmann's rule is not in effect. Tail length was not correlated with either temperature or increasing latitude, contrary to that predicted by Allen's rule.
Main conclusions  The island rule dictating that body size will covary with island area does not apply to this particular species of primate. Our study is consistent with results presented in the literature by demonstrating that skull and body length in insular long-tailed macaques do not, strictly speaking, conform to Rensch's rule. Unlike previous studies, however, our findings suggest that tail-length variation in insular macaques does not support Allen's rule.     

Piecing together an integrative taxonomic puzzle: microsatellite,wing shape and aedeagus length analyses of Bactrocera dorsalis s.l. (Diptera: Tephritidae) find no evidence of multiple lineages in a proposed contact zone along the Thai/Malay Peninsula

Bactrocera dorsalis (Hendel) and B. papayae Drew & Hancock represent a closely related sibling species pair for which the biological species limits are unclear; i.e. it is uncertain if they are truely two biological species, or one biological species which has been incorrectly split taxonomically. The geographical ranges of the two taxa are thought to abut or overlap on or around the Isthmus of Kra, a recognised biogeographic barrier located on the narrowest portion of the Thai Peninsula. We collected fresh material of B. dorsalis s.l. (i.e. B. dorsalis s.s.+ B. papayae) in a north–south transect down the Thai Peninsula, from areas regarded as being exclusively B. dorsalis s.s., across the Kra Isthmus, and into regions regarded as exclusively B. papayae. We carried out microsatellite analyses and took measurements of male genitalia and wing shape, both used previously to separate the taxa. No significant population structuring was found in the microsatellite analysis, consistent with one, predominantly panmictic population. Both morphological datasets showed consistent, clinal variation along the transect, without disjunction. No evidence supported historical vicariance driven by the Isthmus of Kra, and no dataset supported the current taxonomy of two species. Rather, within and across the area of range overlap or abutment between the two species, only continuous morphological and genetic variation was recorded. Recognition that morphological traits previously used to separate these taxa are continuous, and that there is no genetic evidence for population segregation in the region of suspected species overlap, is consistent with a growing body of literature that reports no evidence of biological differentiation between these taxa.     

Phylogeographic evidence for the existence of an ancient biogeographic barrier: the Isthmus of Kra Seaway

Biogeographic boundaries are characterised by distinct faunal and floral assemblages restricted on either side, but patterns among groups of taxa often vary and may not be discrete. Historical biogeography as a consequence, while providing crucial insights into the relationship between biological diversity and earth history, has some limitations. Patterns of intraspecific molecular variation, however, may show unambiguous evidence for such historical divides, and can be used to test competing biogeographic hypotheses (often based on the dispersal-vicariance debate). Here, we utilise this method to test the hypothesis that a major biogeographic transition zone between the Sundaic and Indochinese biotas, located just north of the Isthmus of Kra in SE Asia, is the result of Neogene marine transgressions that breached the Isthmus in two locations for prolonged periods of time (>1 million year duration). Phylogeographic analyses of a freshwater decapod crustacean, the giant freshwater prawn Macrobrachium rosenbergii, strongly supports the historical existence of the more northerly postulated seaway. Results presented here highlight the power of utilising intraspecific molecular variation in testing biogeographical hypotheses.     

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.     

Phylogeography of Asian weaver ants, Oecophylla smaragdina

The phylogeography of Oecophylla smaragdina was studied using the mitochondrial cytochrome b gene (Cytb), cytochrome oxidase subunit I (COI), and nuclear long-wavelength opsin gene (LW Rh). Weaver ants were collected from 35 localities and from one to nine colonies per locality. Neighbor-joining trees inferred from 647 bp of Cytb and 1,026 bp of COI using Oecophylla longinoda as an outgroup indicated that the haplotypes of O. smaragdina were clearly separated into seven groups: group 1 of India excluding West Bengal; group 2 of Bengal, Indochinese Peninsula, Malay Peninsula and Greater Sunda Islands, including Lombok and Sumbawa; group 3 of the Philippines; group 4 of Flores; group 5 of Sulawesi; group 6 of Halmahera; and group 7 of New Guinea and Australia. This grouping was also supported by a strict consensus tree derived from maximum parsimony and maximum likelihood trees. In addition, two haplotypes of LW Rh were found in O. smaragdina: one in group 2 and another in all the other groups. Comparison to haplotypes in other hymenopteran species suggests that group 2 is younger than other groups of O. smaragdina. The clustering of the seven groups was coincident with geological evidence of the distribution of continents, islands, and seas during glacial periods.     

Neogene marine transgressions, palaeogeography and biogeographic transitions on the Thai–Malay Peninsula

Aim The aim of this review is to contribute to our understanding of the origination of the Sundaic and Indochinese biotas in Southeast Asia. Numerous unsolved problems surround the origination of the differences between these biotas and the determinants of the breadth and current position of the transition between them. Location Literature reviews show that phytogeographical and zoogeographical transitions between the Sundaic and Indochinese subregions lie on the Thai–Malay peninsula just north of the Isthmus of Kra. A second, more widely recognized botanical transition lies 500 km further south at the Kangar–Pattani line near the Thai–Malay border. Results The phytogeographical transition involves 575 genera of plants, and a change from wet seasonal evergreen dipterocarp rain forest to moist mixed deciduous forest. The zoogeographical transition is best characterized for forest birds, and more than half the species present in this region have species boundaries north of the Isthmus of Kra, at 11–13° N latitude. Although the phytogeographical transition is climate‐related today, and the avifaunal transition is viewed as being associated with the vegetation change, there is no obvious present day geological, physiographical or environmental feature to account for the origination of the provincial biotas. Similarly, known Neogene palaeoenvironmental changes on the tectonically stable peninsula, including those associated with periods of lower sea levels and the emergence of Sundaland, fail to account for either the origination of the provincial differences or the current position of the transition. Main conclusions Contrary to earlier palaeogeographical reconstructions, it is suggested that Neogene marine transgressions flooded the peninsula in two areas and created circumstances leading to the biogeographical patterns of the present day. The Vail global eustatic curve, supported by the oxygen isotope record, indicates that sea levels were c. 100 m above the present‐day level during the early/middle Miocene (24–13 Ma) and again during the early Pliocene (5.5–4.5 Ma). Present topography suggests such high sea stands would have created 30–100‐km wide seaways north and south of the Nakhon si Thammarat Range in the central peninsula (southern Thailand). Geological, palaeontological and phylogenetic evidence for such hypothetical seaways is scant (there have been no focussed searches) but does not preclude their occurrence. The role of such Neogene highstands in explaining present day biogeographical patterns in Southeast Asia and elsewhere requires assessment.     

The distribution of the Malay civet Viverra tangalunga (Carnivora: Viverridae) across Southeast Asia: natural or human‐mediated dispersal?

The Malay civet Viverra tangalunga Gray, 1832 is a fairly large viverrid that has a wide distribution in both the Sundaic and Wallacea regions of Southeast Asia. We investigated the genetic diversity of V. tangalunga by analysing the mitochondrial DNA of 81 individuals throughout its range in order to elucidate the evolutionary history of this species and to test the hypotheses of natural dispersal and/or potential human introductions to some islands and regions. Our phylogenetic analyses revealed that V. tangalunga has a low matrilinear genetic diversity and is poorly structured geographically. Borneo is likely to have served as the ancestral population source from which animals dispersed during the Pleistocene. Viverra tangalunga could have naturally dispersed to Peninsular Malaysia, Sumatra, and Belitung, and also to several other Sunda Islands (Bangka, Lingga, and Bintang in the Rhio Archipelago), and to Palawan, although there is possible evidence that humans introduced V. tangalunga to the latter islands. Our results strongly suggested that V. tangalunga was transported by humans across Wallace's Line to Sulawesi and the Moluccas, but also to the Philippines and the Natuna Islands. Our study has shown that human‐mediated dispersal can be an important factor in understanding the distribution of some species in this region. © 2014 The Linnean Society of London     

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.