Geographical variation in the morphology of four snake species from the Lesser Sunda Islands, eastern Indonesia

The morphology of three colubrid snakes, Elaphe subradiata, Psammodynastes pulverulentus, Lycodon aulicus capucinus , and the viper Trimeresurus albolabris , were examined from populations throughout the Lesser Sunda islands using canonical variate analysis. The Lesser Sundas form the western part of two extensive Island chains, the Banda Arcs, that lie between the large islands on the Sunda (Asian) and Sahul (Australian) continental shelves. The snakes of the Lesser Sunda islands show considerable intraspecific variation in morphology. Populations of Trimeresurus albolabris from Wetar and Psammodynastes pulverulentus from Alor show the greatest morphological separation from conspecifics. The most pronounced morphological differentiation in multidimensional space occurs between populations on islands that remained separated throughout the Pleistocene, when sea levels were about 120 m lower than present. Consensus tree evaluation of Mahalanobis distance for populations of these four species and Dendrelaphis pubis on the islands of Lombok, Sumba, Flores, Lembata and Alor, supports the finding that populations from islands that remained isolated throughout the Pleistocene by sea barriers show the greatest morphological divergence.     

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.     

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.     

First molecular evidence for the phylogenetic placement of the enigmatic snake genus Brachyorrhos (Serpentes: Caenophidia)

BrachyorrhosSchlegel, 1826a is a terrestrial-fossorial snake genus endemic to eastern Indonesia that has been assigned to six different families and subfamilies within Colubroidea (advanced snakes) over the past ~200 years. Here we report the first molecular sequences for Brachyorrhos and use them to test the position of the genus within snake phylogeny. Our Bayesian and Maximum Likelihood analyses of three mitochondrial and one nuclear gene strongly resolve Brachyorrhos within the rear-fanged semiaquatic Homalopsidae (Colubroidea), as the sister taxon to all other genera and sampled species.     

Biogeographic variation in coral species diversity on coral reefs in three regions of Indonesia

Abstract . This paper assesses variation in coral species diversity within the Indonesian archipelago, and the influence of regional species pools, geomorphology and anthropogenic pollution on coral species diversity and occurrence. We obtained transects from 33 sites on 14 reefs in three regions of Indonesia: Ambon (Moluccas), South Sulawesi and the Java Sea. We determined the within‐site species richness by using species‐sampling curves. Cluster analysis and multi‐dimensional scaling showed that land‐based pollution was the primary determinant of coral species diversity and species occurrence on reefs. Relatively unaffected reference sites in eastern Indonesia were approximately 20% more diverse than Java Sea reference sites. Rare species formed a higher proportion of the coral fauna on eastern Indonesian sites, and eastern Indonesian apparent endemic species contributed approximately 25% of the total species pool sampled. Between‐site variation in species occurrence was lower on Java Sea reefs than on eastern Indonesian reefs. A larger species pool in eastern Indonesia than in the Java Sea probably accounted for most of the difference in within‐site species diversity between eastern Indonesian and Java Sea reference sites. High fishing intensity in the Java Sea, including destructive fishing practices, may have also contributed to reduced within‐site species diversity on Java Sea reference reefs. Despite the fact that the Java Sea was exposed during Pleistocene lowstands, and was recolonized by marine organisms only within the last 10 000 years, coral species diversity and assemblage composition on the Java Sea reefs was largely similar to open ocean reefs in eastern Indonesia.     

A review of the net-winged midges (Diptera: Blephariceridae) of the West Indies,with description of a new species from Puerto Rico

ABSTRACT

The Caribbean blepharicerid fauna comprises three described species: Paltostoma palominoi Hogue and Garces, 1990, found in eastern Cuba; P. agyrocincta Curran, 1927, widespread in Puerto Rico; and P. schineri Williston, 1896, which occupies most major islands of the Lesser Antilles. In this paper, we describe P. portoricensis Hogue and Courtney, sp. n., a second species from Puerto Rico. We also provide keys to adults, pupae, and larvae of known Caribbean species, re-describe P. argyrocincta and P. schineri, and present a brief discussion of the bionomics and phylogenetic affinities of the net-winged midge fauna.     

Biogeography of Australasian flightless weevils (Curculionidae,Celeuthetini) suggests permeability of Lydekker's and Wallace's Lines

The Indo‐Australian region was formed by the collision of the Australian and Asian plates, and its fauna largely reflects this dual origin. Lydekker's and Wallace's Lines represent biogeographic transition boundaries between biotas although their permeability through geological times was rarely assessed. Here, we explore the evolutionary history of flightless weevils of the tribe Celeuthetini in this geologically highly complex region. We generated a DNA sequence data set of 2236 bp comprising two nuclear and two mitochondrial markers for 62 species of the Indo‐Australian tribe Celeuthetini. We used Bayesian Inference and Maximum Likelihood to reconstruct the first molecular phylogeny of the group. Based on this phylogenetic tree, we employed the program BioGeoBEARS to infer the biogeographical history of Celeuthetini in the region. The group's radiation begun east of Wallace's Line, probably during the mid‐Eocene. We unveil multiple transgressions of Lydekker's and Wallace's Lines mostly during the Miocene with a significant role of founder‐event speciation. The phylogeny of Celeuthetini is geographically highly structured with the first lineages occurring in New Guinea and the Moluccas, and a deep divergence between two clades largely confined to Sulawesi and their respective sister clades of the Lesser Sunda Islands. Wallace's Line was crossed once from Sulawesi and three times from the Lesser Sunda Islands to Java whilst Lydekker's Line was crossed once from New Guinea to the Moluccas. Although this beetle group shows extensive local diversification with little dispersal, the biogeographical demarcations of the Australasian region appear to have been rather porous barriers to dispersal.     

Phylogeographic analysis detects congruent biogeographic patterns between a woodland agamid and Australian wet tropics taxa despite disparate evolutionary trajectories

Aim To test the congruence of phylogeographic patterns and processes between a woodland agamid lizard (Diporiphora australis) and well‐studied Australian wet tropics fauna. Specifically, to determine whether the biogeographic history of D. australis is more consistent with a history of vicariance, which is common in wet tropics fauna, or with a history of dispersal with expansion, which would be expected for species occupying woodland habitats that expanded with the increasingly drier conditions in eastern Australia during the Miocene–Pleistocene. Location North‐eastern Australia. Methods Field‐collected and museum tissue samples from across the entire distribution of D. australis were used to compile a comprehensive phylo‐geographic dataset based on c. 1400 bp of mitochondrial DNA (mtDNA), incorporating the ND2 protein‐coding gene. We used phylogenetic methods to assess biogeographic patterns within D. australis and relaxed molecular clock analyses were conducted to estimate divergence times. Hierarchical Shimodaira–Hasegawa tests were used to test alternative topologies representing vicariant, dispersal and mixed dispersal/vicariant biogeographic hypotheses. Phylogenetic analyses were combined with phylogeographic analyses to gain an insight into the evolutionary processes operating within D. australis. Results Phylogenetic analyses identified six major mtDNA clades within D. australis, with phylogeographic patterns closely matching those seen in many wet tropics taxa. Congruent phylogeographic breaks were observed across the Black Mountain Corridor, Burdekin and St Lawrence Gaps. Divergence amongst clades was found to decrease in a north–south direction, with a trend of increasing population expansion in the south. Main conclusions While phylogeographic patterns in D australis reflect those seen in many rain forest fauna of the wet tropics, the evolutionary processes underlying these patterns appear to be very different. Our results support a history of sequential colonization of D. australis from north to south across major biogeographic barriers from the late Miocene–Pleistocene. These patterns are most likely in response to expanding woodland habitats. Our results strengthen the data available for this iconic region in Australia by exploring the understudied woodland habitats. In addition, our study shows the importance of thorough investigations of not only the biogeographic patterns displayed by species but also the evolutionary processes underlying such patterns.     

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。     

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.     

Integrating phylogenetic and taxonomic evidence illuminates complex biogeographic patterns along Huxley’s modification of Wallace’s Line

Aim Nearly 150 years ago, T. H. Huxley modified Wallace’s Line, including the island of Palawan as a component of the Asian biogeographic realm and separating it from the oceanic Philippines. Although Huxley recognized some characteristics of a transition between the regions, Palawan has since been regarded primarily as a peripheral component of the Sunda Shelf. However, several recent phylogenetic studies of Southeast Asian lineages document populations on Palawan to be closely related to taxa from the oceanic Philippines, apparently contradicting the biogeographic association of Palawan with the Sunda Shelf. In the light of recent evidence, we evaluate taxonomic and phylogenetic data in an attempt to identify the origin(s) of Palawan’s terrestrial vertebrate fauna. Location The Sunda Shelf and the Philippines. Methods We review distributional and phylogenetic data for populations of terrestrial vertebrates from Palawan. Using taxonomic data, we compare the number of Palawan taxa (species and genera) shared with the Sunda Shelf and oceanic Philippines. Among widespread lineages, we use phylogenetic data to identify the number of Palawan taxa with sister relationships to populations or species from the Sunda Shelf or oceanic Philippines. Results Although many terrestrial vertebrate taxa are shared between Palawan and the Sunda Shelf, an increasing number of species and populations are now recognized as close relatives of lineages from the oceanic Philippines. Among the 39 putative lineages included in molecular phylogenetic studies with sampling from the Sunda Shelf, Palawan and the oceanic Philippines, 17 of them reveal sister relationships between lineages from Palawan and the oceanic Philippines. Main conclusions Rather than a simple nested subset of Sunda Shelf populations, Palawan is best viewed as having played multiple biogeographic roles, including a young and old extension of the Sunda Shelf, a springboard to diversification in the oceanic Philippines, and a biogeographic component of the Philippine archipelago. Palawan has a long, complex geological history, which may explain this variation in pattern. Huxley originally noted transitional elements in Palawan’s fauna; we therefore suggest that his modification of Wallace’s Line should be recognized as a filter zone, reflecting both his original intent and available taxonomic and molecular evidence.     

Biogeography and history of the Mediterranean bird fauna

With 366 species of breeding birds, the Mediterranean region is a "hot spot" of species diversity. Many biogeographic realms contributed to the establishment of the extant fauna, which makes this region a crossroads for birds, but the two most important realms are the large forest blocks that extend today over Eurasia and the semi-arid belts of the southern and southwestern Palaearctic. The few groups that presumably differentiated within the Mediterranean basin are mostly birds of open habitats and shrublands (e.g. Sylvia spp.), whereas few species evolved in Mediterranean forests dominated by sclerophyllous evergreen tree species. We suggest this results from the history of vegetation belts and their associated faunas during the Pleistocene. On the whole, in contrast to other groups of vertebrates, the bird fauna is fairly homogeneously distributed all over the basin although there are some regional-specific trends in species assemblages, mostly on the basis of habitat selection and biogeographic origin. Many species of eastern and southeastern origin invaded the Mediterranean basin on the northern side of the sea up to the Balkan peninsula and the southern side to the Atlantic coast. The extant biogeographic patterns of the Mediterranean bird fauna are interpreted in the light of the Quaternary history shared by the biotas of the western Palaearctic in relation to the cycle of climatic changes which produced periodic huge spatiotemporal migrations of communities and populations. The severe human impact that started c. 8000-10,000 years ago resulted not so much in species extinctions as in dramatic changes in distributional patterns, complicating the reconstruction of biogeographic scenarios.     

Phylogeography of the prehensile-tailed skink Corucia zebrata on the Solomon Archipelago

The biogeography of islands is often strongly influenced by prior geological events. Corucia zebrata (Squamata: Scincidae) is endemic to the geologically complex Solomon Archipelago in Northern Melanesia. We examined the level of divergence for different island populations of C. zebrata and discussed these patterns in light of Pleistocene land bridges, island isolation, and island age. Corucia zebrata was sampled from 14 locations across the Solomon Archipelago and sequenced at two mitochondrial genes (ND2 and ND4; 1697 bp in total) and four nuclear loci (rhodopsin, an unknown intron, AKAP9, and PTPN12). Measures of genetic divergence, analyses of genetic variation, and Bayesian phylogenetic inference were used and the data assessed in light of geological information. Populations of C. zebrata on separate islands were found to be genetically different from each other, with reciprocal monophyly on mitochondrial DNA. Populations on islands previously connected by Pleistocene land bridges were marginally less divergent from each other than from populations on other nearby but isolated islands. There are indications that C. zebrata has radiated across the eastern islands of the archipelago within the last 1-4 million years. Nuclear loci were not sufficiently informative to yield further information about the phylogeography of C. zebrata on the Solomon Archipelago. Analyses of the mitochondrial data suggest that dispersal between islands has been very limited and that there are barriers to gene flow within the major islands. Islands that have been isolated during the Pleistocene glacial cycles are somewhat divergent in their mitochondrial genotypes, however, isolation by distance (IBD) and recent colonization of isolated but geologically younger islands appear to have had stronger effects on the phylogeography of C. zebrata than the Pleistocene glacial cycles. This contrasts with patterns reported for avian taxa, and highlights the fact that biogeographic regions for island species cannot be directly extrapolated among taxa of differing dispersal ability.     

Trophic divergence despite morphological convergence in a continental radiation of snakes

Ecological and phenotypic convergence is a potential outcome of adaptive radiation in response to ecological opportunity. However, a number of factors may limit convergence during evolutionary radiations, including interregional differences in biogeographic history and clade-specific constraints on form and function. Here, we demonstrate that a single clade of terrestrial snakes from Australia—the oxyuranine elapids—exhibits widespread morphological convergence with a phylogenetically diverse and distantly related assemblage of snakes from North America. Australian elapids have evolved nearly the full spectrum of phenotypic modalities that occurs among North American snakes. Much of the convergence appears to involve the recurrent evolution of stereotyped morphologies associated with foraging mode, locomotion and habitat use. By contrast, analysis of snake diets indicates striking divergence in feeding ecology between these faunas, partially reflecting regional differences in ecological allometry between Australia and North America. Widespread phenotypic convergence with the North American snake fauna coupled with divergence in feeding ecology are clear examples of how independent continental radiations may converge along some ecological axes yet differ profoundly along others.     

Local endemism and within‐island diversification of shrews illustrate the importance of speciation in building Sundaland mammal diversity

Island systems are important models for evolutionary biology because they provide convenient, discrete biogeographic units of study. Continental islands with a history of intermittent dry land connections confound the discrete definitions of islands and have led zoologists to predict (i) little differentiation of terrestrial organisms among continental shelf islands and (ii) extinction, rather than speciation, to be the main cause of differences in community composition among islands. However, few continental island systems have been subjected to well‐sampled phylogeographic studies, leaving these biogeographic assumptions of connectivity largely untested. We analysed nine unlinked loci from shrews of the genus Crocidura from seven mountains and two lowland localities on the Sundaic continental shelf islands of Sumatra and Java. Coalescent species delimitation strongly supported all currently recognized Crocidura species from Sumatra (six species) and Java (five species), as well as one undescribed species endemic to each island. We find that nearly all species of Crocidura in the region are endemic to a single island and several of these have their closest relative(s) on the same island. Intra‐island genetic divergence among allopatric, conspecific populations is often substantial, perhaps indicating species‐level diversity remains underestimated. One recent (Pleistocene) speciation event generated two morphologically distinct, syntopic species on Java, further highlighting the prevalence of within‐island diversification. Our results suggest that both between‐ and within‐island speciation processes generated local endemism in Sundaland, supplementing the traditional view that the region's fauna is relictual and primarily governed by extinction.     

Human‐mediated introduction of introgressed deer across Wallace's line: Historical biogeography of Rusa unicolor and R. timorensis

In this study we compared the phylogeographic patterns of two Rusa species, Rusa unicolor and Rusa timorensis, in order to understand what drove and maintained differentiation between these two geographically and genetically close species and investigated the route of introduction of individuals to the islands outside of the Sunda Shelf. We analyzed full mitogenomes from 56 archival samples from the distribution areas of the two species and 18 microsatellite loci in a subset of 16 individuals to generate the phylogeographic patterns of both species. Bayesian inference with fossil calibration was used to estimate the age of each species and major divergence events. Our results indicated that the split between the two species took place during the Pleistocene, ~1.8 Mya, possibly driven by adaptations of R. timorensis to the drier climate found on Java compared to the other islands of Sundaland. Although both markers identified two well‐differentiated clades, there was a largely discrepant pattern between mitochondrial and nuclear markers. While nDNA separated the individuals into the two species, largely in agreement with their museum label, mtDNA revealed that all R. timorensis sampled to the east of the Sunda shelf carried haplotypes from R. unicolor and one Rusa unicolor from South Sumatra carried a R. timorensis haplotype. Our results show that hybridization occurred between these two sister species in Sundaland during the Late Pleistocene and resulted in human‐mediated introduction of hybrid descendants in all islands outside Sundaland.     

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.     

REVISITING WALLACE'S HAUNT: COALESCENT SIMULATIONS AND COMPARATIVE NICHE MODELING REVEAL HISTORICAL MECHANISMS THAT PROMOTED AVIAN POPULATION DIVERGENCE IN THE MALAY ARCHIPELAGO

Sundaland, a biogeographic region of Southeast Asia, is a major biodiversity hotspot. However, little is known about the relative importance of Pleistocene habitat barriers and rivers in structuring populations and promoting diversification here. We sampled 16 lowland rainforest bird species primarily from peninsular Malaysia and Borneo to test the long‐standing hypothesis that animals on different Sundaic landmasses intermixed extensively when lower sea‐levels during the Last Glacial Maximum (LGM) exposed land‐bridges. This hypothesis was rejected in all but five species through coalescent simulations. Furthermore, we detected a range of phylogeographic patterns; Bornean populations are often genetically distinct from each other, despite their current habitat connectivity. Environmental niche modeling showed that the presence of unsuitable habitats between western and eastern Sundaland during the LGM coincided with deeper interpopulation genetic divergences. The location of this habitat barrier had been hypothesized previously based on other evidence. Paleo‐riverine barriers are unlikely to have produced such a pattern, but we cannot rule out that they acted with habitat changes to impede population exchanges across the Sunda shelf. The distinctiveness of northeastern Borneo populations may be underlied by a combination of factors such as rivers, LGM expansion of montane forests and other aspects of regional physiography.