Phylogeny of Cerberus (Serpentes: Homalopsinae) and phylogeography of Cerberus rynchops: diversification of a coastal marine snake in Southeast Asia

Aim The biogeography of Southeast Asia has been greatly affected by plate tectonic events over the last 10 Myr and changing sea levels during the Quaternary. We investigated how these events may have influenced the evolution of Cerberus Cuvier, a marine coastal snake belonging to the Homalopsinae (Oriental‐Australian Rear‐fanged Water Snakes). This study is an expansion of a previous study on the biogeography and systematics of Cerberus. Location We obtained species from localities across the range of the widely distributed Cerberus: India, Sri Lanka, the Andaman islands, Myanmar, the Philippines, Borneo, Suluwesi, Sumatra, Vietnam, Thailand, Singapore and Australia. Methods We analysed mtDNA sequences (12S, ND3, ATPase, 2338 nucleotide characters) from 21 localities. The sample consisted of 65 Cerberus rynchops (Schneider), three Cerberus australis (Gray) and four Cerberus microlepis Boulenger. One Homalopsis buccata (Linnaeus), one Bitia hydroides Gray, one Enhydris enhydris (Schneider), and two Enhydris plumbea (Boie) were used as outgroups. Results We produced phylogenetic trees based on parsimony, maximum likelihood and Bayesian analysis. We did not find unambiguous support for the monophly of Cerberus. Cerberus austalis, H. buccata and all other Cerberus populations formed a three‐way basal polytomy under parsimony and C. australis formed the sister group to a clade consisting of H. buccata and all other Cerberus in likelihood and Bayesian analysis. The non‐Australian Cerberus were monophyletic and consisted of four primary biogeographical clades: Indian and Mayanmar, Philippines, Greater Sunda Islands and Suluwesi, and the Thai‐Malay peninsula and Gulf of Thailand. The range of genetic divergence between these clades and Australian Cerberus was 0.06–0.12. Genetic divergence among clades to the west of Australia was less pronounced (Thai‐Malay peninsula and Gulf of Thailand = 0.02–0.05; Sunda Islands and Suluwesi = 0.02–0.05; Philippines = 0.02–0.06; India and Myanmar = 0.04–0.06, Philippines = 0.02–0.5). Main conclusions Gyi [University of Kansas Publications, Museum of Natural History 20 (1970), 47] recognized three species of Cerberus: C. australis (from Australia), C. microlepis (known only from Lake Buhi in the Philippines), and the widely distributed C. rynchops (India to Wallacea). We did not find strong support for the monophyly of the genus. Cerberus australis is highly divergent from all other Cerberus lineages sampled from this region. The geographically widespread C. rynchops is resolved into four biogeographical clades (Indian and Myanmar, Philippines, Greater Sunda Islands and Suluwesi, and the Thai‐Malay Peninsula and Gulf of Thailand). We discuss how the dispersal biology of a salt‐water tolerant, coastal marine taxon and the complex geological history of the region (Tertiary plate tectonic movements and Quaternary sea‐level changes) could produce the observed patterns of diversification.     

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.     

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.     

West to east dispersal and subsequent rapid diversification of the mega‐diverse genus Begonia (Begoniaceae) in the Malesian archipelago

Aim The complex palaeogeography of the Malesian archipelago, characterized by the evolution of an ever‐changing mosaic of terrestrial and marine areas throughout the Cenozoic, provides the geographic backdrop for the remarkable diversification of Malesian Begonia (> 450 species). This study aimed to investigate the origin of Malesian Begonia, the directionality of dispersal events within the Malesian archipelago and the impact of ancient water gaps on colonization patterns, and to identify drivers of diversification. Location Asia, Southeast Asia, Malesia. Methods Plastid DNA sequence data of representatives of all families of the Cucurbitales and Fagales (matK, rbcL, trnL intron, trnL–F spacer, 4076 aligned positions, 92 taxa) and a sample of all major Asian Begonia sections (ndhA intron, ndhF–rpl32 spacer, rpl32–trnL spacer, 4059 aligned positions, 112 taxa) were analysed under an uncorrelated‐rates relaxed molecular clock model to estimate the age of the Begonia crown group divergence and divergence ages within Asian Begonia. Ancestral areas were reconstructed using a likelihood approach implementing a dispersal–extinction–cladogenesis model, and with a Bayesian approach to dispersal–vicariance analysis. Results The results indicated an initial diversification of Asian Begonia in continental Asia in the Miocene, and subsequent colonization of Malesia by multiple lineages. There was support for at least six independent dispersal events from continental Asia and western Malesia to Wallacea dating from the late Miocene to the Pleistocene. Begonia section Petermannia (> 270 species) originated in Western Malesia, and subsequently dispersed to Wallacea, New Guinea and the Philippines. Lineages within this section diversified rapidly since the Pliocene, coinciding with rapid orogenesis on Sulawesi and New Guinea. Main conclusions The predominant trend of Begonia dispersals between continental Asia and Malesia, and also within Malesia, has been from west to east. The water bodies separating the Sunda Shelf region from Wallacea have been porous barriers to dispersal in Begonia following the emergence of substantial land in eastern Malesia from the late Miocene onwards. We hypothesize two major drivers of the diversification of Malesian Begonia: (1) the formation of topographical heterogeneity and the promotion of microallopatry by orogenesis in the Pliocene and Pleistocene; and (2) cyclic vicariance by frequent habitat fragmentations and amalgamations due to climate and sea‐level fluctuations during the Pleistocene.     

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.     

Phylogenetic evolution and biogeography of Southeast Asian shrews (genus Crocidura: Soricidae)

Genetic variation of 20 species of shrews from the Malay peninsula, Sumatra, Java, Borneo, the Philippines and Sulawesi was assessed by allozyme electrophoresis at 32 loci. According to Mantel's tests, the genetic differentiation of these species of shrews is not a function of the geographic distance separating them (r = 0.09, NS), but is correlated to the water depth surrounding the islands where they live (r = 0.49, P < 0.01). The results are just the reverse if the correlations are computed for the Sunda Shelf taxa only. In this case, the sampled populations show an isolation-by-distance relationship (r = 0.32; P < 0.01), while no significant correlation with water depth was detected (r = 0.20; P - 0.07). Qualitative predictions based on eustatic sea level variation and water depth were formulated as a model of historic connections between the islands. This palaeogeographic model was tested through Brooks Parsimony Analysis. The assumption of a simple vicariant evolution of the shrews was rejected, but several concordant patterns indicate that the phytogeny of these mammals was indeed shaped by these events. Homoplasies demonstrated that the SE Asian species of Crocidura include composite zoogeographic histories. Sulawesi, for example, supports at least six species, five of which are closely related, while the last one, C. nigripes, is more closely related to a Bornean taxon. This pattern was interpreted as the result of a first wave of colonizers which subsequently radiated, followed by a more recent, second colonization event from Borneo. The overall small genetic distance found within the assemblage of the five old endemics (D_N= 0.151 pL 0.041) suggests that the radiation was not accompanied by extensive differentiation, although from a karyological point of view, they exhibit unusual variations when compared to other Indomalayan Crocidura. By contrast, the four species found on Sumatra are more differentiated (D_N= 0.221 pL 0.063) and never form sister-group relationships in any phylogenetic reconstruction; each one is more closely related to different taxa living outside Sumatra. This suggests that they are probably remnants of an important centre of dispersal for the entire Malay Archipelago. The standard genetic distance averaged among all Southeast Asian species (D_N= 0.235 pL 0.094) is about half that measured within Palearctic or African taxa. Such an overall lower mean level of genetic variability is consistent with the hypothesis of a relatively recent colonization of the Malay Archipelago by shrews of the genus Crocidura.     

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.     

Repeated evolution of carnivory among Indo‐Australian rodents

Convergent evolution, often observed in island archipelagos, provides compelling evidence for the importance of natural selection as a generator of species and ecological diversity. The Indo‐Australian Archipelago (IAA) is the world's largest island system and encompasses distinct biogeographic units, including the Asian (Sunda) and Australian (Sahul) continental shelves, which together bracket the oceanic archipelagos of the Philippines and Wallacea. Each of these biogeographic units houses numerous endemic rodents in the family Muridae. Carnivorous murids, that is those that feed on animals, have evolved independently in Sunda, Sulawesi (part of Wallacea), the Philippines, and Sahul, but the number of origins of carnivory among IAA murids is unknown. We conducted a comprehensive phylogenetic analysis of carnivorous murids of the IAA, combined with estimates of ancestral states for broad diet categories (herbivore, omnivore, and carnivore) and geographic ranges. These analyses demonstrate that carnivory evolved independently four times after overwater colonization, including in situ origins on the Philippines, Sulawesi, and Sahul. In each biogeographic unit the origin of carnivory was followed by evolution of more specialized carnivorous ecomorphs such as vermivores, insectivores, and amphibious rats.     

Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae: Hippocampus)

Four distinct phylogeographical patterns across Southeast Asia were observed for four species of seahorse (genus Hippocampus) with differing ecologies. For all species, genetic differentiation (based on cytochrome b sequence comparisons) was significantly associated with sample site (Phi(ST) = 0.190-0.810, P < 0.0001) and with geographical distance (Mantel's r = 0.37-0.59, P < 0.019). Geographic locations of genetic breaks were inconsistent across species in 7/10 comparisons, although some similarities across species were also observed. The two shallow-water species (Hippocampus barbouri and Hippocampus kuda) have colonized the Sunda Shelf to a lesser degree than the two deeper-water species (Hippocampus spinosissimus and Hippocampus trimaculatus). In all species the presence of geographically restricted haplotypes in the Philippines could indicate past population fragmentation and/or long-distance colonization. A nested clade analysis (NCA) revealed that long-distance colonization and/or fragmentation were likely the dominant forces that structure populations of the two shallow-water species, whereas range expansion and restricted dispersal with isolation by distance were proportionally more important in the history of the two deeper-water species. H. trimaculatus has the most widespread haplotypes [average clade distance (D(c)) of nonsingleton haplotypes = 1169 km], indicating potentially high dispersal capabilities, whereas H. barbouri has the least widespread haplotypes (average D(c) = 67 km) indicating potentially lower dispersal capabilities. Pleistocene separation of marine basins and postglacial flooding of the Sunda Shelf are extrinsic factors likely to have contributed to the phylogeographical structure observed, whereas differences among the species appear to reflect their individual ecologies.     

From Shelf to Shelf: Assessing Historical and Contemporary Genetic Differentiation and Connectivity across the Gulf of Mexico in Gag,Mycteroperca microlepis

Describing patterns of connectivity among populations of species with widespread distributions is particularly important in understanding the ecology and evolution of marine species. In this study, we examined patterns of population differentiation, migration, and historical population dynamics using microsatellite and mitochondrial loci to test whether populations of the epinephelid fish, Gag, Mycteroperca microlepis, an important fishery species, are genetically connected across the Gulf of Mexico and if so, whether that connectivity is attributable to either contemporary or historical processes. Populations of Gag on the Campeche Bank and the West Florida Shelf show significant, but low magnitude, differentiation. Time since divergence/expansion estimates associated with historical population dynamics indicate that any population or spatial expansions indicated by population genetics would have likely occurred in the late Pleistocene. Using coalescent-based approaches, we find that the best model for explaining observed spatial patterns of contemporary genetic variation is one of asymmetric gene flow, with movement from Campeche Bank to the West Florida Shelf. Both estimated migration rates and ecological data support the hypothesis that Gag populations throughout the Gulf of Mexico are connected via present day larval dispersal. Demonstrating this greatly expanded scale of connectivity for Gag highlights the influence of “ghost” populations (sensu Beerli) on genetic patterns and presents a critical consideration for both fisheries management and conservation of this and other species with similar genetic patterns.     

Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in South‐East Asia

Tropical rainforests in South‐East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag‐based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south‐western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28–0.09 million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.     

Land masses and oceanic currents drive population structure of Heritiera littoralis,a widespread mangrove in the Indo‐West Pacific

Phylogeographic forces driving evolution of sea‐dispersed plants are often influenced by regional and species characteristics, although not yet deciphered at a large spatial scale for many taxa like the mangrove species Heritiera littoralis. This study aimed to assess geographic distribution of genetic variation of this widespread mangrove in the Indo‐West Pacific region and identify the phylogeographic factors influencing its present‐day distribution. Analysis of five chloroplast DNA fragments’ sequences from 37 populations revealed low genetic diversity at the population level and strong genetic structure of H. littoralis in this region. The estimated divergence times between the major genetic lineages indicated that glacial level changes during the Pleistocene epoch induced strong genetic differentiation across the Indian and Pacific Oceans. In comparison to the strong genetic break imposed by the Sunda Shelf toward splitting the lineages of the Indian and Pacific Oceans, the genetic differentiation between Indo‐Malesia and Australasia was not so prominent. Long‐distance dispersal ability of H. littoralis propagules helped the species to attain transoceanic distribution not only across South East Asia and Australia, but also across the Indian Ocean to East Africa. However, oceanic circulation pattern in the South China Sea was found to act as a barrier creating further intraoceanic genetic differentiation. Overall, phylogeographic analysis in this study revealed that glacial vicariance had profound influence on population differentiation in H. littoralis and caused low genetic diversity except for the refugia populations near the equator which might have persisted through glacial maxima. With increasing loss of suitable habitats due to anthropogenic activities, these findings therefore emphasize the urgent need for conservation actions for all populations throughout the distribution range of H. littoralis.     

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.     

Pleistocene genetic connectivity in a widespread,open‐habitat‐adapted mosquito in the Indo‐Oriental region

Aim The environmental effect of Pleistocene climatic change in the Indo‐Oriental region has resulted in allopatric fragmentation and the generation of diversity in forest‐associated species. The aim of this study was to determine the extent to which Pleistocene climatic change has resulted in the fragmentation and speciation of an open‐habitat‐adapted mosquito, Anopheles vagus s.l., across its range. Location Anopheles vagus s.l. was sampled across the Indo‐Oriental region. Methods We generated 116 mitochondrial cytochrome c oxidase subunit I (COI) and 121 nuclear internal transcribed spacer 2 (ITS2) DNA sequences from 18 populations. Relationships between mitochondrial haplotypes were reconstructed using minimum spanning networks, and population structure was examined using analyses of molecular variance. The population history, including lineage divergence times, population expansion and gene flow, was inferred using beast and the isolation with migration (IM) model. Results There was no evidence to support the presence of the endemic Philippines species, A. limosus; instead, Philippine populations were closely related to, and derived from, A. vagus on the eastern Southeast Asian mainland. The most distinct populations were those from Java and East Timor, which differed from all other populations by all individuals having a 4‐bp insertion in the ITS2 sequence. The corresponding mitochondrial haplotypes had an estimated divergence time of 2.6 Ma [95% confidence interval (CI) 1.9–3.6 Ma]. Haplotype networks and analysis of molecular variance for COI supported western (Sri Lanka, India and Myanmar) and eastern (Thailand, Singapore, Cambodia, Vietnam and the Philippines) population groupings. This grouping structure results from the divergence of an eastern and a western mitochondrial lineage, estimated to have occurred 0.37 Ma (95% CI 0.26–0.55 Ma). Subsequent migration from the east to the west (0.16 Ma) is inferred to have created an admixture zone in Myanmar and Thailand. Main conclusions With the possible exception of populations from Java and East Timor, A. vagus appears to be one widespread genetically diverse taxon across its extensive range. The abundance of grassland during long interglacial periods may have facilitated population connectivity and range expansion across the Oriental and western Australasian regions.     

Phylogeography of the magpie-robin species complex (Aves: Turdidae: Copsychus) reveals a Philippine species, an interesting isolating barrier and unusual dispersal patterns in the Indian Ocean and Southeast Asia

Aim The oriental magpie‐robin (Copsychus saularis) of South and Southeast Asia is a phenotypically variable species that appears to be closely related to two endemic species of the western Indian Ocean: the Madagascar magpie‐robin (Copsychus albospecularis) and the Seychelles magpie‐robin (Copsychus sechellarum). This unusual distribution led us to examine evolutionary relationships in magpie‐robins, and also the taxonomic significance of their plumage variation, via a molecular phylogenetic and population genetic analysis of C. saularis and C. albospecularis. Location Southern Asia from Nepal across Indochina to southern China, and the Indian Ocean from Madagascar to the Greater Sunda and Philippine islands. Methods We sequenced 1695 nucleotides of mitochondrial DNA comprising the complete second subunit of the nicotinamide adenine dinucleotide dehydrogenase (ND2) gene and 654 bases of the cytochrome c oxidase subunit I (COI) region in 51 individuals of eight C. saularis subspecies, 10 individuals of C. albospecularis (one subspecies) and single individuals of two other Copsychus species as outgroups. The data were analysed phylogenetically, with maximum likelihood, Bayesian, relaxed clock and parsimony methods, and geographically for patterns of genetic diversity. Results Phylogenetic analysis indicated that C. albospecularis lies within the nominal C. saularis, making C. saularis polyphyletic. Malagasy and non‐Philippine Asian populations form a monophyletic group that is sister to a clade of Philippine populations. Within non‐Philippine Asian populations, two groups are evident: black‐bellied birds in the eastern Greater Sunda islands and white‐bellied birds in the western Sundas and on mainland Asia. Main conclusions The phylogeny of magpie‐robins suggests a novel pattern of dispersal and differentiation in the Old World. Ancestral magpie‐robins appear to have spread widely among islands of the Indian Ocean in the Pliocene, probably aided by their affinity for coastal habitats. Populations subsequently became isolated in island groups, notably the Philippines, Madagascar and the Greater Sundas, leading to speciation in all three areas. Isolation in the Philippines may have been aided by competitive exclusion of C. saularis from Palawan by a congener, the white‐vented shama (Copsychus niger). In the Greater Sundas, white‐bellied populations appear to have invaded Borneo and Java recently, where they hybridize with resident black‐bellied birds.     

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.     

Diversification of a ‘great speciator’ in the Wallacea region: differing responses of closely related resident and migratory kingfisher species (Aves: Alcedinidae: Todiramphus)

The Collared Kingfisher species complex is the most widespread of the ‘great speciator’ lineages of the Indo‐Pacific. They have shown a remarkable ability to spread and diversify. As a result of this rapid diversification, Todiramphus species are often found in secondary sympatry. In Southeast Sulawesi, Indonesia, two Todiramphus species are present, the breeding resident Collared Kingfisher Todiramphus chloris and the overwintering migratory Sacred Kingfisher Todiramphus sanctus. We investigated the effect of isolation on these closely related species by comparing their populations on mainland Sulawesi and its larger continental islands, with populations on the small, oceanic Wakatobi Islands. Within our wider analysis we provide further support for the distinctiveness of the Sulawesi Collared Kingfisher population, perhaps isolated by the deep water barrier of Wallace's line. Within Sulawesi we found that populations of Collared Kingfisher on the Wakatobi Islands had diverged from those on mainland Sulawesi, differing both in morphology and in mitochondrial DNA. In contrast, there was no divergence between Sacred Kingfisher populations in either morphology or mitochondrial DNA. We propose that a difference in habitat occupied by Collared Kingfisher populations between the mainland and continental islands vs. oceanic islands has caused this divergence. Mainland Collared Kingfishers are predominately found inland, whereas Wakatobi Collared Kingfishers are also found in coastal habitats. The larger body size of Wakatobi Collared Kingfisher populations may be a result of increased competition with predominantly coastal Sacred Kingfisher populations. The uniform nature of Sacred Kingfisher populations in this region probably reflects their consistent habitat choice (coastal mangrove) and their migratory nature. The demands of their breeding range are likely to have an even stronger selective influence than their Sulawesi wintering range, limiting their scope for divergence. These results provide insight into the adaptability of the widespread Todiramphus lineage and are evidence of the need for further taxonomic revision of Collared Kingfisher populations.     

A new species of Celebochoerus (Suidae,Mammalia) from the Philippines and the paleobiogeography of the genus Celebochoerus Hooijer, 1948

Celebochoerus is a unique suid having extremely large upper tusks, and which was to date only known from the Pliocene-Pleistocene of Sulawesi Island in Indonesia. Here, we report on the discovery of a canine fragment referable to Celebochoerus from the Cagayan Valley of Luzon, Northern Philippines. We name a new species, Celebochoerus cagayanensis nov. sp., which differs from the Sulawesi species Celebochoerus heekereni in having mesial and distal enamel bands on the upper canines. We see these characteristics as symplesiomorphic in suids and propose a migration route from the Philippines to Sulawesi, possibly out of Taiwan, which would have occurred independently from the better known Pleistocene migration route from India into Java.     

Taxonomic revision of shrews of the genus Crociduras from the Sunda Shelf and Sulawesi with description of two new species (Mammalia: Soricidae)

The skulls of 387 shrews of the genus Crocidura sampled in peninsular Malaysia, Sumatra, Borneo, Java and Sulawesi were submitted to principal component and stepwise discriminant analyses. These analyses helped to delineate morphological taxa in this species-rich genus of mammals. Most morphologic groups could be attributed to described species, except one taxon from Sumatra and one from Sulawesi, which are described and named as new. Most of the 21 species recognized in this paper are endemic to one major island. Although Sulawesi has never been connected to the mainland, it supports at least six species, followed by Sumatra (5–6 species), Java and the Malay Peninsula (4 spp) and Borneo (3 spp). C. monticola is apparently the only widespread species whose distribution range covers the entire Malay Archipelago except the Philippines and Sulawesi. In contrast, the continental C. fuliginosa enters only marginally into the Sunda Shelf: its southernmost record is on the Malay Peninsula. This interpretation is completely different from the classical view that C. fuliginosa is a cosmopolitan species occupying the whole of Southeast Asia. Identification keys, tables of measurements and discriminant functions provided in this work may aid in identification of the various species and subspecies of Crocidura living in the Malaya Archipelago.     

Historical biogeography of lowland species of toads (Bufo) across the Trans-Mexican Neovolcanic Belt and the Isthmus of Tehuantepec

Aim In this study, we investigate phylogeographic structure in two different species groups of lowland toads. First, we further investigate strict parapatry of the Pliocene‐vicariant Bufo valliceps/B. nebulifer species pair. Secondly, we test for similar phylogeographic structure in the distantly related toad B. marinus, a species we hypothesize will show a Pleistocene dispersal across the same area. Location The eastern extension of the Trans‐Mexican Neovolcanic Belt (TMNB) contacts the Atlantic Coast in central Veracruz, Mexico. Although it is not a massive structure at this eastern terminus, the TMNB has nonetheless effected vicariance and subsequent speciation in several groups of animals. The Isthmus of Tehuantepec unites the North American continent with Nuclear Central America and is also known to be a biogeographic barrier for many taxa. Methods We use sequence data from two mitochondrial DNA genes (c. 550 base‐pairs (bp) of 16S and c. 420 bp of cyt b) from 58 individuals of the B. valliceps/nebulifer complex, collected from 24 localities. We also present homologous sequence data from 23 individuals of B. marinus, collected from 12 localities. We conduct maximum‐parsimony, maximum‐likelihood and Bayesian analyses to investigate phylogeographic structure. We then use parsimony‐ and likelihood‐based topology tests to assess alternative phylogenetic hypotheses and use a previously calibrated molecular rate of evolution to estimate dates of divergence. Results Our results further define the parapatric contact zone across the TMNB between the Pliocene‐vicariant sister species B. valliceps and B. nebulifer. In contrast, phylogenetic structure among populations of B. marinus across the TMNB is much shallower, suggesting a more recent Pleistocene dispersal in this species. In addition, we found phylogeographic structure associated with the Isthmus of Tehuantepec in both species groups. Main conclusions The existence of a Pliocene–Pleistocene seaway across the Isthmus of Tehuantepec has been controversial. Our data depict clades on either side of the isthmus within two distinct species (B. valliceps and B. marinus), although none of the clades associated with the isthmus, for either species, are reciprocally monophyletic. In the B. valliceps/B. nebulifer complex, the TMNB separation appears to predate the isthmian break, whereas in B. marinus dispersal across the TMNB has occurred subsequent to the presence of a barrier at the Isthmus of Tehuantepec.