Dataset Information

DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species.

ABSTRACT: Illegal selective logging of tropical timber is of increasing concern worldwide. Madagascar is a biodiversity hotspot and home to some of the world's most sought after tropical timber species. Malagasy rosewoods belong to the genus Dalbergia (Fabaceae), which is highly diverse and has a pantropical distribution, but these timber species are among the most threatened as a consequence of intensive illegal selective logging and deforestation. Reliable identification of Dalbergia species from Madagascar is important for law enforcement but is almost impossible without fertile plant material, which is often unavailable during forest inventories or when attempting to identify logged trees of cut wood. DNA barcoding has been promoted as a promising tool for species identification in such cases. In this study we tested whether DNA barcoding with partial sequences of three plastid markers (matK, rbcL and trnL (UAA)) can distinguish between Dalbergia from Madagascar and from other areas of its distributional range, and whether Malagasy species can be distinguished from one another. Phylogenetic analyses revealed that the Malagasy Dalbergia species studied form two monophyletic groups, each containing two subgroups, only one of which corresponds to a single species. We characterized diagnostic polymorphisms in the three DNA barcoding markers that allow rapid discrimination between Dalbergia from Madagascar and from other areas of its distribution range. Species identification success based on individual barcoding markers or combinations was poor, whereas subgroup identification success was much higher (up to 98%), revealing both the value and limitations of a DNA barcoding approach for the identification of closely related Malagasy rosewoods.

SUBMITTER: Hassold S

PROVIDER: S-EPMC4928830 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species.

Hassold Sonja S Lowry Porter P PP Bauert Martin R MR Razafintsalama Annick A Ramamonjisoa Lolona L Widmer Alex A

PloS one 20160630 6

Illegal selective logging of tropical timber is of increasing concern worldwide. Madagascar is a biodiversity hotspot and home to some of the world's most sought after tropical timber species. Malagasy rosewoods belong to the genus Dalbergia (Fabaceae), which is highly diverse and has a pantropical distribution, but these timber species are among the most threatened as a consequence of intensive illegal selective logging and deforestation. Reliable identification of Dalbergia species from Madaga ...[more]

PMID: 27362258

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Project description:BackgroundCITES is an international agreement between governments to ensure that international trade in specimens of wild animals and plants does not threaten their survival. Regarding spiders, all species listed in CITES are tarantulas. They are included in Appendix II, meaning that they are species that are not necessarily now threatened with extinction but that they may become so unless trade is closely controlled.Many tarantulas are legally and illegally traded in the pet market and they are one of the most traded invertebrate groups. Originally, the CITES list published in 1995 included all the current species of the genus Brachypelma Simon, 1891 plus Aphonopelma pallidum (F. O. Pickard-Cambridge, 1897) and the so-called Aphonopelma albiceps (Pocock, 1903). After that, some taxonomic changes were done, as well as descriptions of new species in the genus Brachypelma. The objective of this paper is to assess the 21 taxonomically valid spider species listed on CITES according to the IUCN criteria, study the general patterns and trends and advise on possible future conservation actions critical for the survival of endangered species.New informationAmongst all 21 species assessed, 16 had sufficient data on their distribution, ecology and threats to properly understand their current status and suggest possible conservation measures. A decline in the area of occupancy (AOO) and extent of occurrence (EOO) was inferred to almost all species, caused mostly by human activities (urbanisation, roads, agricultural and touristic activities), which often lead to the complete loss of subpopulations across their range. Hurricanes and frequent rising water, which are increasing in frequency due to climate change, can cause decline in habitat quality and consequent change in EOO and AOO of some species and should also be considered when planning conservation actions. Severe fragmentation was detected in 13 species and is therefore one of the most relevant threats to the most endangered Brachypelma species and should be made a priority aspect to deal with when proposing conservation actions for the group. Regarding the loss of individuals in wild populations, the main cause seems to be the overharvesting to meet the illegal trade.The most important conservation actions identified across species include preserving their natural habitat through protected areas, establishing management plans for both the species and their habitats and undertaking systematic monitoring to provide information about population recovery and species re-introduction programmes. In general, we propose to prioritise and support research on the population trends and distribution, as well as on the impact of land use and habitat degradation. Special attention regarding conservation actions and research plans has to be given to the central Pacific coastal area of Mexico, particularly around Guerrero State where five species of Brachypelma occur. Critically, for some of the most endangered species, such as B. baumgarteni and B. hamorii, there is no official protected area in their range of occurrence. It would therefore be highly recommended to establish at least one conservation unit which focuses on protecting each of these species in situ. In some cases, basic taxonomic research is needed before development of any appropriate conservation action can be proposed.

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Project description:Chondrichthyes - sharks, rays, skates, and chimeras, are among the most threatened and data deficient vertebrate species. Global demand for shark and ray derived products, drives unregulated and exploitative fishing practices, which are in turn facilitated by the lack of ecological data required for effective conservation of these species. Here, we describe a Next Generation Sequencing method (using the MinION, a hand-held portable sequencing device from Oxford Nanopore Technologies), and analyses pipeline for molecular ecological studies in Chondrichthyes. Using this method, the complete mitochondrial genome and nuclear intergenic and protein-coding sequences were obtained by direct sequencing of genomic DNA obtained from shark fin tissue. Recovered loci include mitochondrial barcode sequences- Cytochrome oxidase I, NADH2, 16S rRNA and 12S rRNA- and nuclear genetic loci such as 5.8S rRNA, Internal Transcribed Spacer 2, and 28S rRNA regions, which are commonly used for taxonomic identification. Other loci recovered were the nuclear protein-coding genes for antithrombin or SerpinC, Immunoglobulin lambda light chain, Preprogehrelin, selenium binding protein 1(SBP1), Interleukin-1 beta (IL-1β) and Recombination-Activating Gene 1 (RAG1). The median coverage across all genetic loci was 20x and sequence accuracy was ≥99.8% compared to reference sequences. Analyses of the nuclear ITS2 region and the mitochondrial protein-encoding loci allowed accurate taxonomic identification of the shark specimen as Carcharhinus falciformis, a CITES Appendix II species. MinION sequencing provided 1,152,211 bp of new shark genome, increasing the number of sequenced shark genomes to five. Phylogenetic analyses using both mitochondrial and nuclear loci provided evidence that Prionace glauca is nested within Carcharhinus, suggesting the need for taxonomic reassignment of P. glauca. We increased genomic information about a shark species for ecological and population genetic studies, enabled accurate identification of the shark tissue for biodiversity indexing and resolved phylogenetic relationships among multiple taxa. The method was independent of amplification bias, and adaptable for field assessments of other Chondrichthyes and wildlife species in the future.

Dataset Information

DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species.

Publications

DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species.

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