No abstract

Wildlife trade has been considered one of the largest threats to biodiversity in Southeast Asia. Many vertebrates, such as pangolins, elephants and turtles have been heavily hunted as a result of high demand from emerging markets in China and other countries in the region. In Vietnam, over-exploitation of turtles over several decades to supply the international trade has extirpated numerous populations and driven several species to the brink of extinction. To reverse this trend, conservation measures, such as re-introduction of confiscated or captive-bred animals to their native habitats, should be implemented to recover severely declined local populations. For species with a complex phylogeographic structure, however, it is crucial to understand geographic patterns of genetically-distinct populations to avoid releasing animals of unknown origin to wrong localities. In this study, we investigate the phylogeographic pattern of the Four-eyed Turtle (Sacalia quadriocellata), a widely traded species, which occurs in southern China, northern and central Laos and much of Vietnam, using samples with known localities and those collected from the local trade. Our range-wide phylogenetic and network study, based on the complete mitochondrial cytochrome b gene, recovered at least three major clades and seven subclades within the species range. Amongst these, two subclades, one from northern Annamites, Vietnam and the other from north-eastern Laos, are newly discovered. The fine scale phylogeographic analysis helped us to assign misidentified sequences from GenBank and those from confiscated animals with unknown origin to well-defined geographic populations. The results highlight the importance of incorporating samples collected from the local trade and the wild in genetic analyses to support both ex-situ and in-situ conservation programmes of highly-threatened species in accordance with the IUCN’s One Plan Approach.

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The mode of development of marine invertebrates has major effects on dispersal and population structure. Species without a feeding larval stage (direct developers) are generally more genetically subdivided than species with planktotrophic (swimming and feeding) development. Evidence of the re-evolution of planktotrophy from a direct-developing ancestor has been accumulating within marine invertebrates. However, it remains unclear whether such evolutionary transitions are rare or common. The Bembicium genus (Gastropoda: Littorinidae) provides an additional opportunity to examine the re-evolution of planktotrophy. The genus includes two species with planktotrophic development (Bembicium auratum and Bembicium nanum) and three species with direct development (Bembicium vittatum, Bembicium melanostoma and Bembicium flavescens). Phylogenetic analyses based on sequences of two mitochondrial markers (COI and 16S rRNA) and one nuclear marker (ANT) provide evidence for a switch from direct development back to planktotrophy. Also, pairwise genetic distances between haplotypes reveal that the two planktotrophic species have greater genetic diversity (at the species level) than the direct developers, and the three direct-developing species are genetically structured based on geographical distance. Our study adds to growing evidence for the re-evolution of planktotrophy and suggests that the genetic basis for a switch between modes of development might be simple in marine snails.

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Edited by Haruki NakamuraSequencing of individual human genomes enables studying relationship among nucleotide variations, amino acid substitutions, effect on protein structures and diseases. Many studies have found general tendencies, for instance, that pathogenic variations tend to be found in the buried regions of the protein structures, that benign variations tend to be found on the surface of the proteins, and that variations on evolutionary conserved residues tend to be pathogenic. These tendencies were deduced from globular proteins with standard evolutionary changes in amino acid sequences. In this study, we investigated the variation distribution on actin, one of the highly conserved proteins. Many nucleotide variations and three-dimensional structures of actin have been registered in databases. By combining those data, we found that variations buried inside the protein were rather benign and variations on the surface of the protein were pathogenic. This idiosyncratic distribution of the variation impact is likely ascribed to the extensive use of the surface of the protein for protein-protein interactions in actin.

No abstract

Otter clam farming in Vietnam has recently encountered difficulties due to swollen-siphon disease. Here, we report the metagenome sequences of microorganisms extracted from the siphon tissue of infected otter clams. The data comprised bacterial and viral sequences which likely include those derived from the disease-causing agent.