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The islands of Southeast Asia comprise one of the most geologically and biogeographically complex areas in the world and are a centre of exceptional floristic diversity, harbouring 45,000 species of flowering plants. Cyrtandra, with over 800 species of herbs and shrubs, is the largest genus in the family Gesneriaceae and is one of the most emblematic and species-rich genera of the Malesian rainforest understorey. The high number of species and tendency to narrow endemism make Cyrtandra an ideal genus for examining biogeographic patterns. We sampled 128 Cyrtandra taxa from key localities across Southeast Asia to evaluate the geo-temporal patterns and evolutionary dynamics of this clade. One nuclear and four chloroplast regions were used for phylogenetic reconstruction, molecular dating, and ancestral range estimation. Results from the dating analysis suggest that the great diversity of Cyrtandra seen in the Malesian region results from a recent radiation, with most speciation taking place in the last five million years. Borneo was recovered as the most likely ancestral range of the genus, with the current distribution of species resulting from a west to east migration across Malesia that corresponds with island emergence and mountain building. Lastly, our investigation into the biogeographic history of the genus indicates high levels of floristic exchange between the islands on the Sunda shelf and the important role of the Philippines as a stepping stone to Wallacea and New Guinea. These patterns underlie much of the plant diversity in the region and form an emerging paradigm in Southeast Asian plant biogeography.

Foraminiferal geochemistry applies geochemical elements embedded in foraminiferal calcites through bioaccumulation to interpret and reconstruct past oceanic climate histories. Due to its extensive variability and abundance, foraminifera is the easiest to retrieve and the best indicator of marine productivity and ocean temporal changes. In this review, we discuss the development of foraminiferal geochemistry studies in Southeast Asia, analyzing its current status and potential areas to be developed, namely, the Sunda Shelf. The Sunda Shelf is one of the world’s largest low-latitude shelves, bordered by marginal seas and sensitive to sea-level changes. The shelf response towards changes in ocean salinity affected the isotopic signals in foraminiferal calcites, which can indicate sea-level changes ideally. The Sunda Shelf has the potential to be developed as a study area for eustatic sea-level changes as it is located far from major glaciation centers; hence through this review, we aim to highlight the potential of exploring the application of geochemical elements in foraminifera as an indicator for sea-level changes. To date, literature on foraminiferal geochemistry in this region is very limited, thus inhibiting progress in such studies. A comprehensive summary of past studies in this region is provided to give a general overview of the direction of foraminiferal geochemistry studies and serve as guidelines for future research. [ABSTRACT FROM AUTHOR]

Phenacostethus sikat, new species, is described from coastal drainages of Kalimantan Selatan, the southeastern province of Indonesian Borneo, that flow into the Java Sea and the Straits of Makassar. This discovery and description brings the number of valid species of priapiumfishes, the atheriniform subfamily Phallostethinae, to 24 and extends the known distribution of the phallostethines to drainages on the eastern margin of the modern Sunda Shelf. Phenacostethus sikat differs from congeners in features of the priapium, the complex bilaterally asymmetric, subcephalic copulatory organ of males, and is readily distinguished by a unique, brush-shaped seminal papilla in males, as opposed to a simpler, ruffled seminal papilla in Phe. smithi, its inferred sister species based on morphology, and a smooth seminal papilla in males of Phe. posthon and Phe. trewavasae. Males of Phe. sikat and Phe. smithi are either sinistral or dextral, the hooked toxactinium arises on the right or left side of the head and curves strongly under the head towards the aproctal side of the body. Males of Phe. posthon and Phe. trewavasae are exclusively dextral or sinistral, respectively. Males of Phe. sikat have an ossified inner pulvinular bone which is cartilaginous or absent in Phe. smithi. Males of Phe. sikat and Phe. smithi have a curved and pointed or blunt second ctenactinium as opposed to a highly reduced second ctenactinium in males of Phe. posthon and Phe. trewavasae. Females of the new species lack rudimentary pelvic fins which are present in adult females of Phe. smithi, Phe. posthon, and Phallostethus. The new species is also diagnosed by a colour pattern with few or no melanophores along the horizontal septum anterior to the anal-fin origin. The mtCOI sequences of Phe. sikat differ from those of congeners by 13.85-24.23%, with an average of 21.54%, an extraordinarily high level of divergence comparable to that of other diminutive fishes. Like congeners, Phe. sikat is a miniature species. The largest specimen known is an adult female just 15.3 mm SL. [ABSTRACT FROM AUTHOR]

Although Borneo has received more attention from biologists than most other islands in the Malay Archipelago, many questions regarding the systematic relationships of Bornean mammals remain. Using next-generation sequencing technology, we obtained mitochondrial DNA sequences from the holotype of Suncus ater, the only known specimen of this shrew. Several shrews collected recently in Sarawak are closely aligned, both morphologically and mitochondrially, with the holotype of S. ater. Phylogenetic analyses of mitochondrial sequences indicate that the S. ater holotype and new Sarawak specimens do not belong to the genus Suncus, but instead are most closely related to Palawanosorex muscorum. Until now Palawanosorex has been known only from the neighboring Philippine island of Palawan. Additional sequences from nuclear ultra-conserved elements from the new Sarawak specimens strongly support a sister relationship to P. muscorum. We therefore transfer ater to Palawanosorex. The new specimens demonstrate that P. ater is more widespread in northern Borneo than previously recorded. Continued sampling of Bornean mammal diversity and reexamination of type material are critical in understanding the evolutionary history of the biologically rich Malay Archipelago. [ABSTRACT FROM AUTHOR]

Long‐term organic carbon (OC) burial on continental shelves has been widely recognized for regulating atmospheric CO2 (pCO2) and the global climate. However, quantitatively assessing shelf OC burial's role and process in prominent climate transitions is challenging. Using 367 drilling sites, we evaluated the impact of OC burial on the Sunda Shelf, the world's largest tropical shelf, on the middle Miocene carbon perturbation and climate change. Comparing the Miocene Climatic Optimum (MCO) and the Middle Miocene Climate Transition (MMCT) results demonstrated that OC was buried faster during the MMCT with an increment of 0.07–0.14 × 103 GtC/Myr. This would cause an additional 34.77–69.16 ppm pCO2 sequestration, contributing at least one‐sixth of the global pCO2 reduction. We found OC burial regulated the long‐standing Monterey carbon isotope excursion via negative and positive feedbacks during the MCO and MMCT, respectively. Expanded terrestrial carbon reservoirs and enhanced burial efficiency were key steps in the latter positive feedback. Plain Language Summary: The organic carbon (OC) formed by the photosynthesis of marine and terrestrial organisms consumes atmospheric CO2 (pCO2). Its long‐term burial in marine environments, especially on continental shelves, could influence the global carbon cycle and induce climate change. However, precisely assessing how much OC has been buried on shelves and quantifying how it affected climate change in the geological past is challenging. This is mainly due to the difficulty of obtaining complete spatial‐temporal records buried deeply on shelves and the complexity of climate feedbacks involving OC burial. To fill this gap to a certain extent, we calculated the middle Miocene OC burial of the Sunda Shelf, the world's largest tropical shelf, using 367 drilling sites and evaluated its impact on the profound carbon perturbation and climate transition of this period. We found that more OC was buried during the greenhouse period, but a faster burial rate occurred after polar cooling. The accelerated OC burial on the Sunda Shelf would cause an additional 34.77–69.16 ppm pCO2 sequestration, accounting for at least one‐sixth of the global pCO2 reduction of the middle Miocene. Efficient OC burial on the shelf was promoted by drainage system progradation and vegetation expansion arose along with sea level drop. Key Points: Organic carbon (OC) burial on the Sunda Shelf is essential to the global carbon cycle during the middle MioceneThe OC burial rate of the Middle Miocene Climate Transition (MMCT) was faster than that of the Miocene Climatic OptimumExpanded terrestrial carbon reservoirs and enhanced organic matter burial efficiency promoted the MMCT [ABSTRACT FROM AUTHOR]

Abstract Impending anthropogenic climate change will severely impact coastal organisms at unprecedented speed. Knowledge on organisms’ evolutionary responses to past sea‐level fluctuations and estimation of their evolutionary potential is therefore indispensable in efforts to mitigate the effects of future climate change. We sampled tens of thousands of genomic markers of ~300 individuals in two of the four extant horseshoe crab species across the complex archipelagic Singapore Straits. Carcinoscorpius rotundicauda Latreille, a less mobile mangrove species, has finer population structure and lower genetic diversity compared with the dispersive deep‐sea Tachypleus gigas Müller. Even though the source populations of both species during the last glacial maximum exhibited comparable effective population sizes, the less dispersive C. rotundicauda seems to lose genetic diversity much more quickly because of population fragmentation. Contra previous studies’ results, we predict that the more commonly sighted C. rotundicauda faces a more uncertain conservation plight, with a continuing loss in evolutionary potential and higher vulnerability to future climate change. Our study provides important genomic baseline data for the redirection of conservation measures in the face of climate change and can be used as a blueprint for assessment and mitigation of the adverse effects of impending sea‐level rise in other systems.

This paper documents a database of fossil foraminiferal occurrences from a core sample (2 m) retrieved from offshore southeastern Peninsular Malaysia, in 1993, with additional data on their modern distribution from published source. Five sub-samples were analysed for foraminiferal studies (0.1 m, 0.4 m, 0.6 m, 1.2 m, and 2.0 m), alongside with their diversity indices values. In addition, we also present the lithological description of the core sediment, together with the radiocarbon age of our sample. These data are potentially be reused in other paleoceanography related research, such as reconstructing paleo environments, and for future research on the Late-Quaternary/Holocene sedimentary and sea-level history of Sunda Shelf.

Impending anthropogenic climate change will severely impact coastal organisms at unprecedented speed. Knowledge on organisms' evolutionary responses to past sea‐level fluctuations and estimation of their evolutionary potential is therefore indispensable in efforts to mitigate the effects of future climate change. We sampled tens of thousands of genomic markers of ~300 individuals in two of the four extant horseshoe crab species across the complex archipelagic Singapore Straits. Carcinoscorpius rotundicauda Latreille, a less mobile mangrove species, has finer population structure and lower genetic diversity compared with the dispersive deep‐sea Tachypleus gigas Müller. Even though the source populations of both species during the last glacial maximum exhibited comparable effective population sizes, the less dispersive C. rotundicauda seems to lose genetic diversity much more quickly because of population fragmentation. Contra previous studies' results, we predict that the more commonly sighted C. rotundicauda faces a more uncertain conservation plight, with a continuing loss in evolutionary potential and higher vulnerability to future climate change. Our study provides important genomic baseline data for the redirection of conservation measures in the face of climate change and can be used as a blueprint for assessment and mitigation of the adverse effects of impending sea‐level rise in other systems. [ABSTRACT FROM AUTHOR]

High-resolution records of grain size, major and trace elements, and Sr-Nd isotopes of Core K17 from the western Sunda Shelf were investigated to evaluate the response of weathering and terrigenous input to climatic changes and human activities over the past 7400 years. Sr-Nd isotopic results indicate that the Kelantan River is the main source of sedimentary material in the study core since the mid-Holocene. Chemical weathering levels are represented by the chemical index of alteration (CIA), αAlNa, and K2O/Al2O3 ratios; and geochemical and grain size proxies (including TiO2/CaO, Rb/Sr ratios, and grain size end-member) were used to establish variations of terrigenous input into the study core since 7400 cal yr BP. Based on these records, the evolution of weathering and terrigenous input processes in the western Sunda Shelf can be divided into four stages. During stage 1 (7400–3700 cal yr BP), increasing precipitation and decreasing temperature jointly balanced the relatively stable weathering and terrigenous sediment supply. Dramatically decreasing weathering rates were consistent with less rainfall and lower temperatures during stage 2 (3700–2600 cal yr BP). Heavy rainfall played a more important role than low temperature in controlling weathering and erosion, leading to increasing terrigenous input in stage 3 (2700–1600 cal yr BP). Because of the decoupling between weathering, erosion, and climate in the late Holocene (stage 4, since 1600 cal yr BP), increasing agriculture and related human activities likely dominated weathering and erosion relative to climate changes. Furthermore, the initial time at which human activity overwhelmed natural processes in the southern South China Sea (SCS) is similar to that in the northern SCS. Our results highlight that human activities during the past 1600 years have gradually overwhelmed natural climatic controls on weathering and erosion processes in the western Sunda Shelf.

This paper documents a database of fossil foraminiferal occurrences from a core sample (2 m) retrieved from offshore southeastern Peninsular Malaysia, in 1993, with additional data on their modern distribution from published source. Five sub-samples were analysed for foraminiferal studies (0.1 m, 0.4 m, 0.6 m, 1.2 m, and 2.0 m), alongside with their diversity indices values. In addition, we also present the lithological description of the core sediment, together with the radiocarbon age of our sample. These data are potentially be reused in other paleoceanography related research, such as reconstructing paleo environments, and for future research on the Late-Quaternary/Holocene sedimentary and sea-level history of Sunda Shelf. [ABSTRACT FROM AUTHOR]

Shifts in phytoplankton phenology were observed in the Strait of Malacca (SM) and Sunda Shelf (SS), which were speculated to be potentially related to global warming and climate anomaly events. Such interactions between phytoplankton structure and physico-chemical factors were less known in narrow straits. Therefore, the spatial distribution pattern and diversity of surface phytoplankton assemblage, local hydrology, and nutrient regimes were investigated over the SM and SS (South China Sea, SCS) during 2017 and 2018 pre-monsoon season (spring). Diatoms, dinoflagellates, and cyanobacteria were representatives of microphytoplankton in the survey area. Total phytoplankton abundance peaked near Singapore Strait (SGS) and diminished toward SS. From the lower ratio of diatoms to dinoflagellates (

Pollen analysis has been conducted on a 90 cm gravity core taken from the Karimata Strait to reveal pollen facies in marine sediment and Late Holocene environmental changes in the central Sunda Shelf region. The core site is at 32 m water depth and located about 170 km northwest of Bangka Island. Indonesia. Ten samples were collected at 10 cm intervals through the core. The total number of pollen grains counted in the samples varies between very low (<50 grains) to abundant (>200 grains). High frequencies (50 - 70%) of mangrove pollen are found at 90 to 40 cm indicating that pollen facies in offshore marine sediment may be comparable with those in mangrove forest floor sediment. The core site has been in a neritic environment since its early deposition ca. 1.800 yr B.P. (~150 A.D.) when mangroves vastly grew on the tidal flats of the surrounding islands and they persisted to ca. 700 yr B.P. (~1,250 A.D.). In the middle of this period, a catastrophic event speculatively due to the 535 A.D. Krakatau eruption might have responsible for the decrease of mangroves and the disappearance of benthic foraminifers. The deposition of silicious materials (tephra) due to tins eruption might have provided an opportunity for benthic foraminifers to increase their population subsequently. From ca. 700 yr B.P. (~ 1.250 A.D.) mangroves declined, as indicated by lower frequencies of pollen grain in samples from 30 cm deep upward. It occurred simultaneously with the deposition of coarser sediment and the increase of benthic foraminifer abundance. Interplay of anthropogenic activities, strengthening ENSO cycle, and lowering erosion base level might have been responsible for these environmental changes. [ABSTRACT FROM AUTHOR]

Abstract: Aim: The genetics of organisms currently isolated in refugia has received little attention compared to post‐glacial expansions. We study the population history and connectivity of a rat endemic to montane habitat in Borneo to better understand the history and potential of populations in interglacial mountain refugia. Location: Sabah, Borneo, Malaysia. Methods: We performed a field survey of the summit rat (Rattus baluensis) on two mountains, Mt. Kinabalu and Mt. Tambuyukon, its entire known distribution. We sequenced mitogenomes and 27 introns (19 of which were polymorphic) in 49 individuals from both populations. We analysed their current genetic structure and diversity, and inferred their demographic history with approximate Bayesian computation. Results: Summit rats were tightly associated with mountain mossy forest and scrubland above 2,000 m, facilitating the prediction of their past and future distributions. The genetic analysis supports a Holocene fragmentation of a larger population into smaller ones that are now isolated in interglacial refugia on mountaintops. These findings are consistent with climatic reconstructions and the retreat of upland forest to higher elevations after the Last Glacial Maximum (LGM), ~21 kya. Main conclusions: The two isolated populations of summit rats formed through the upland shift of their habitat after the LGM. The current trend of global warming will likely lead to diminishing suitable upland habitat and result in the extinction of the population on Mt. Tambuyukon. The population on Mt. Kinabalu, the higher peak, could persist at higher elevations, highlighting the singular value of high tropical mountains as reservoirs of biodiversity during past and ongoing climate change. [ABSTRACT FROM AUTHOR]

Although Borneo has received more attention from biologists than most other islands in the Malay Archipelago, many questions regarding the systematic relationships of Bornean mammals remain. Using next-generation sequencing technology, we obtained mitochondrial DNA sequences from the holotype of Suncusater , the only known specimen of this shrew. Several shrews collected recently in Sarawak are closely aligned, both morphologically and mitochondrially, with the holotype of S.ater . Phylogenetic analyses of mitochondrial sequences indicate that the S.ater holotype and new Sarawak specimens do not belong to the genus Suncus , but instead are most closely related to Palawanosorexmuscorum . Until now Palawanosorex has been known only from the neighboring Philippine island of Palawan. Additional sequences from nuclear ultra-conserved elements from the new Sarawak specimens strongly support a sister relationship to P.muscorum . We therefore transfer ater to Palawanosorex . The new specimens demonstrate that P.ater is more widespread in northern Borneo than previously recorded. Continued sampling of Bornean mammal diversity and reexamination of type material are critical in understanding the evolutionary history of the biologically rich Malay Archipelago., (Jonathan A. Nations, Thomas C. Giarla, Muhd Amsyari Morni, Julius William Dee, Mark T. Swanson, Anna E. Hiller, Faisal Ali Anwarali Khan, Jacob A. Esselstyn.)

Knowledge of the diversity and relationships of species in many groups of plants and animals in Southeast Asia is severely limited, preventing an integrative understanding of evolutionary and ecological processes in island archipelagos. We generated a 3-locus DNA sequence data set to estimate phylogenetic relationships among species and populations of Maxomys, a genus of rodents endemic to Southeast Asia. Our inclusion of Crunomys as a potential outgroup supported the monophyly of Crunomys, but the genus was deeply nested within Maxomys. Because of the relatively ancient divergences (mean uncorrected p-distances up to 0.15 in cytochrome-b sequences) among species of Maxomys and short branch lengths among basal lineages of the phylogeny, we obtained little support for the oldest relationships in Maxomys + Crunomys. However, our analyses revealed unrecognized diversity in the form of divergent populations both between and within islands and the presence of 2 potentially undescribed species from Sulawesi. The Maxomys and Crunomys of Sulawesi belonged to 4 clades sister to extralimital species, suggesting that repeated overwater dispersal between Sundaland--Philippines and Sulawesi was an important isolating mechanism in the history of this group. [ABSTRACT FROM AUTHOR]

Long celebrated for its spectacular landscapes and strikingly high levels of endemic biodiversity, the Philippines has been studied intensively by biogeographers for two centuries. Concentration of so many endemic land vertebrates into a small area and shared patterns of distribution in many unrelated forms has inspired a search for common mechanisms of production, partitioning, and maintenance of life in the archipelago. In this review, we ( a) characterize an ongoing renaissance of species discovery, ( b) discuss the changing way biogeographers conceive of the archipelago, ( c) review the role molecular phylogenetic studies play in understanding the evolutionary history of Philippine vertebrates, and ( d) describe how a 25-year Pleistocene island connectivity paradigm continues to provide some explanatory power, but has been augmented by increased understanding of the archipelago's geological history and ecological gradients. Finally, we ( e) review new insights provided by studies of adaptive versus nonadaptive radiation and phylogenetic perspectives on community ecology. [ABSTRACT FROM AUTHOR]

A new cassid species of the genus Phalium Link, 1807 is described from material trawled in the Sunda Shelf. Phalium pseudobandatum, new species, is superficially close to P. bandatum (Perry, 1811) because of similarities in shell colour and markings. However, the new species can be separated from P. bandatum by conchological characteristics. The position of the posterior sinus in the new species is at or extends above the shoulder, accompanied by a low spire with a side profile that is smooth and not step-like. It also has a less rotund body whorl with a more angular shoulder compared to P. bandatum. A distinct groove on the parietal shield where it adjoins the body whorl is also present on shells of the new species. In addition, the thickened middle part of the outer lip is not seen in similarly sized specimens of P. bandatum. The siphonal canal of the new species is not pigmented, and the crenulations at the anterior edge of the outer lip are more numerous but less distinct than in P. bandatum. We also suggest that P. exaratum (Reeve, 1848) is a distinct Indian Ocean species rather than a geographical subspecies of P. bandatum. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Given its complex zoogeography and large number of islands insular Southeast Asia makes an excellent subject for studying the interrelationships of species richness, island area and isolation. The islands are merely highpoints of an immense shallow continental shelf which during Pleistocene glacial periods was exposed periodically as dry land connecting the now isolated islands with one another. The area is home to a large number of primate taxa, including many endemic to the region (Nasalis, Presbytis, Pongo, Symphalangus, Simias, Tarsius). Worldwide, the number of described (extant) species of primates has doubled in the last two decades partially as a result of applying a different species concept (viz. Phylogenetic Species Concept PSC as opposed to the Biological Species Concept BSC). According to Isaac et al. (Trends in Ecology and Evolution 19: 464-469, 2004) this 'taxonomic inflation' will influence the outcome of macroecological studies. We studied the species-area relationships in Primates on 118 islands in insular Southeast Asia, and used two taxonomies (PSC and BSC). The number of primate species (PSC 37 species, BSC 23 species) is highly significantly related to surface area of the islands, and the slope of the curve is similar for both PSC and BSC species (z = 0.13). Species 'newly' described under the PSC are not only from large islands but also smaller ones hence affecting neither intercept nor the slope of the curve. Area alone was a much better predictor for primate species richness than models that included other macroecological variables (latitude, longitude, altitude, distance to mainland, greatest depth between island and mainland, distance to neighbouring islands). Degree of isolation has little influence on species number but both longitude and latitude are inversely correlated with the number of species per island, suggesting that species numbers decrease in a northerly and easterly direction. The low z-values suggest that for primates the islands of Southeast Asia are perhaps less isolated than previously recognised. [ABSTRACT FROM AUTHOR]

Aims Insular Southeast Asia and adjacent regions are geographically complex, and were dramatically affected by both Pliocene and Pleistocene changes in climate, sea level and geology. These circumstances allow the testing of several biogeographical hypotheses regarding species distribution patterns and phylogeny. Avian species in this area present a challenge to biogeographers, as many are less hindered by barriers that may block the movements of other species. Widely distributed Southeast Asian avian lineages, of which there are many, have been generally neglected. Ficedula flycatchers are distributed across Eurasia, but are most diverse within southern Asia and Southeast Asian and Indo-Australian islands. We tested the roles of vicariance, dispersal and the evolution of migratory behaviours as mechanisms of speciation within the Ficedula flycatchers, with a focus on species distributed in insular Southeast Asia. Methods Using a published molecular phylogeny of Ficedula flycatchers, we reconstructed ancestral geographical areas using dispersal vicariance analysis, weighted ancestral area analysis, and a maximum likelihood method. We evaluated the evolution of migratory behaviours using maximum likelihood ancestral character state reconstruction. Speciation timing estimates were calculated via local molecular clock methods. Results Ficedula originated in southern mainland Asia, c. 6.5 Ma. Our analyses indicate that two lineages within Ficedula independently and contemporaneously colonized insular Southeast Asia and Indo-Australia, c. 5 Ma. The potential impact of vicariance due to rising sea levels is difficult to assess in these early colonization events because the ancestral areas to these clades are reconstructed as oceanic islands. Within each of these clades, inter-island dispersal was critical to species’ diversification across oceanic and continental islands. Furthermore, Pliocene and Pleistocene climatic change may have caused the disjunct island distributions between several pairs of sister taxa. Both vicariance and dispersal shaped the distributions of continental species. Main conclusions This study presents the first evaluation, for Ficedula, of the importance of vicariance and dispersal in shaping distributions, particularly across insular Southeast Asia and Indo-Australia. Although vicariant speciation may have initially separated the island clades from mainland ancestors, speciation within these clades was driven primarily by dispersal. Our results contribute to the emerging body of literature concluding that dynamic geological processes and climatic change throughout the Pliocene and Pleistocene have been important factors in faunal diversification across continental and oceanic islands. [ABSTRACT FROM AUTHOR]

Aim To test the potential of two contrasting biogeographical hypotheses (Indian/Pacific Ocean Basin' vs. 'Wallace's Line') to explain the distribution of genetic diversity among populations of a marine fish in Southeast Asia. Location The marine waters of Asia and Southeast Asia: from India to Japan, and east to the Indonesian islands of Sulawesi and Flores. Methods We sequenced a 696 base pair fragment of cytochrome b DNA of 100 individuals of Hippocampus trimaculatus Leach 1814 (three-spot seahorse), obtained from across its range. We tested our hypotheses using phylogenetic reconstructions and analyses of molecular variance. Results Significant genetic divergence was observed among the specimens. Two distinct lineages emerged that diverged by an average of 2.9%. The genetic split was geographically associated, but surprisingly it indicated a major east-west division similar to the terrestrial Wallace's Line (ΨST = 0.662, P < 0.00 1) rather than one consistent with an Indian-Pacific ocean basin separation hypothesis (PsT = 0.023, P = 0.153). Samples from east of Wallace's Line, when analysed separately, however, were consistent with an Indian/Pacific Ocean separation (ΨST = 0.461, P = 0.005). The degree of genetic and geographical structure within each lineage also varied. Lineage A, to the west, was evolutionarily shallow (star-like), and the haplotypes it contained often occurred over a wide area. Lineage B to the east had greater genetic structure, and there was also some evidence of geographical localization of sublineages within B. Main conclusions Our results indicate that the genetic diversity of marine organisms in Southeast Asia may reflect a more complex history than the simple division between two major ocean basins that has been proposed by previous authors. In particular, the east-west genetic division observed here is novel among marine organisms examined to date. The high hap lotype, but low nucleotide diversity to the west of Wallace's Line is consistent with post-glacial colonization of the Sunda Shelf. Additional data are needed to test the generality of these patterns. [ABSTRACT FROM AUTHOR]

The discovery of the first complete skeleton of a fossil orang-utan from the Hoa Binh province in Vietnam brings original information about the evolution of these asiatic apes. Dental morphology and morphometry of the adult individual are compared with those of known taxa (modern and fossil), whereas its body proportions are compared with those of the two modern subspecies, from Borneo (Pongo pygmaeus pygmaeus) and from Sumatra (Pongo pygmaeus abelii). Hypothetical causes for the extinction of orangs-utans on the continent are mentioned.

Thirty-nine surface sediment samples collected from the western Sunda Shelf off the Malay Peninsula (WSSMP) in the southern South China Sea (SCS) were analysed for grain size, major and trace elemental compositions, and light/heavy mineral contents to trace the sediment sources and their transport mechanisms in the study area. In the WSSMP, the surface sediments are relatively poorly sorted but transportable. A principal component analysis of 37 elements and grain size fractions indicates that the surface sediments can be grouped into four major assemblages in the study area. Integrating with the light/heavy minerals data in the 63–125 μm fractions of the surface sediment samples, to better trace the sediment sources of the coarse-grained components in the marine environment, the study area can be further divided into four sediment provinces. Province I is located in the northwestern part of the study area. The concentrations of TiO2, Na2O, garnet, siderite, and glauconite in Province I were higher than in the other provinces. The main sediment source for this province originated from the Kelantan River and the Gulf of Thailand transported by the northeastern monsoon current. Province II is located offshore of the Pahang and Endau Rivers. The percentages of TiO2, rare earth elements, Al2O3, quartz, plagioclase, hypersthene, and magnetite in the surface sediments were typically higher in this province than in the other provinces. The Pahang and Endau rivers provide most of the sediments to this province, which are transported by southward coastal currents. Province III is located in the northeastern and eastern parts of the study area, where the coarse-grained sediment fraction had relatively high hornblende and biotite contents. Sediments in this province are mostly transported from the Mekong River during the northeastern monsoon. The other parts of the study area belong to Province IV, where the surface sediment elemental and mineral concentrations were mostly between those of the other three provinces. Therefore, we suggest that Province IV has a mixed source due to inputs from the surrounding rivers. [ABSTRACT FROM AUTHOR]

Wallace's Line demarcates the transition between the differentiated regional faunas of Asia and Australia. However, while patterns of biotic differentiation across these two continental landmasses and the intervening island groups (Wallacea) have been extensively studied, patterns of long-term dispersal and diversification across this region are less well understood. Frogmouths (Aves: Podargidae) are a relictual family of large nocturnal birds represented by three extant genera occurring, respectively, in Asia, 'Sahul' (Australia and New Guinea) and the Solomon Islands, thus spanning Wallace's Line. We used new mitochondrial genomes from each of the extant frogmouth genera to estimate the timeline of frogmouth evolution and dispersal across Wallace's Line. Our results suggest that the three genera diverged and dispersed during the mid-Cenozoic between approximately 30 and 40 Mya. These divergences are among the oldest inferred for any trans-Wallacean vertebrate lineage. In addition, our results reveal that the monotypic Solomons frogmouth ( Rigidipenna inexpectata ) is one of the most phylogenetically divergent endemic bird lineages in the southwest Pacific. We suggest that the contemporary distribution of exceptionally deep divergences among extant frogmouth lineages may be explained by colonization of, and subsequent long-term persistence on, island arcs in the southwest Pacific during the Oligocene. These island arcs may have provided a pathway for biotic dispersal out of both Asia and Australia that preceded the formation of extensive emergent landmasses in Wallacea by at least 10 million years.