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      A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library

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          Abstract

          Several published checklists of bat species have covered Peninsular Malaysia as part of a broader region and/or in combination with other mammal groups. Other researchers have produced comprehensive checklists for specific localities within the peninsula. To our knowledge, a comprehensive checklist of bats specifically for the entire geopolitical region of Peninsular Malaysia has never been published, yet knowing which species are present in Peninsular Malaysia and their distributions across the region are crucial in developing suitable conservation plans. Our literature search revealed that 110 bat species have been documented in Peninsular Malaysia; 105 species have precise locality records while five species lack recent and/or precise locality records. We retrieved 18 species from records dated before the year 2000 and seven species have only ever been recorded once. Our search of Barcode of Life Datasystems (BOLD) found that 86 (of the 110) species have public records of which 48 species have public DNA barcodes available from bats sampled in Peninsular Malaysia. Based on Neighbour-Joining tree analyses and the allocation of DNA barcodes to Barcode Index Number system (BINs) by BOLD, several DNA barcodes recorded under the same species name are likely to represent distinct taxa. We discuss these cases in detail and highlight the importance of further surveys to determine the occurences and resolve the taxonomy of particular bat species in Peninsular Malaysia, with implications for conservation priorities.

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          Cryptic species as a window on diversity and conservation.

          David P. Bickford, David Lohman, Navjot Sodhi … (2007)
          The taxonomic challenge posed by cryptic species (two or more distinct species classified as a single species) has been recognized for nearly 300 years, but the advent of relatively inexpensive and rapid DNA sequencing has given biologists a new tool for detecting and differentiating morphologically similar species. Here, we synthesize the literature on cryptic and sibling species and discuss trends in their discovery. However, a lack of systematic studies leaves many questions open, such as whether cryptic species are more common in particular habitats, latitudes or taxonomic groups. The discovery of cryptic species is likely to be non-random with regard to taxon and biome and, hence, could have profound implications for evolutionary theory, biogeography and conservation planning.
          Article 0 comments Cited 1035 times – based on 0 reviews     Review now
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            The Role of DNA Barcodes in Understanding and Conservation of Mammal Diversity in Southeast Asia

            Charles M. Francis, Alex Borisenko, Natalia V. Ivanova … (2010)
            Background Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats. However, many aspects of this diversity, even for relatively well-known groups such as mammals, are poorly known, limiting ability to develop conservation plans. This study examines the value of DNA barcodes, sequences of the mitochondrial COI gene, to enhance understanding of mammalian diversity in the region and hence to aid conservation planning. Methodology and Principal Findings DNA barcodes were obtained from nearly 1900 specimens representing 165 recognized species of bats. All morphologically or acoustically distinct species, based on classical taxonomy, could be discriminated with DNA barcodes except four closely allied species pairs. Many currently recognized species contained multiple barcode lineages, often with deep divergence suggesting unrecognized species. In addition, most widespread species showed substantial genetic differentiation across their distributions. Our results suggest that mammal species richness within the region may be underestimated by at least 50%, and there are higher levels of endemism and greater intra-specific population structure than previously recognized. Conclusions DNA barcodes can aid conservation and research by assisting field workers in identifying species, by helping taxonomists determine species groups needing more detailed analysis, and by facilitating the recognition of the appropriate units and scales for conservation planning.
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              Applying the Bootstrap in Phylogeny Reconstruction

              Douglas E Soltis, Pamela Soltis (2003)
              Article 0 comments Cited 79 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Voon-Ching Lim:
                ORCID: http://orcid.org/0000-0002-2722-4771
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Rosli Ramli: Role: Formal analysisRole: Writing – original draft
                Subha Bhassu: Role: Formal analysisRole: Writing – original draft
                John-James Wilson: Role: ConceptualizationRole: Formal analysisRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Sharon Swartz: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date (Electronic): 25 July 2017
                Publication date Collection: 2017
                Volume: 12
                Issue: 7
                Electronic Location Identifier: e0179555
                Affiliations
                [1 ] Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
                [2 ] International College Beijing, China Agricultural University, Beijing, P. R. China
                Brown University, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                ‡ VCL and JJW designed the review, and RR and SB provided suggestions to improve the draft on this work.

                Author information
                http://orcid.org/0000-0002-2722-4771
                Article
                Publisher ID: PONE-D-17-04279
                DOI: 10.1371/journal.pone.0179555
                PMC ID: 5526618
                PubMed ID: 28742835
                SO-VID: 870ff1c3-eaf7-47ea-bfcf-7a26c661e32e
                Copyright © © 2017 Lim et al
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 2 February 2017
                Date accepted : 30 May 2017
                Page count
                Figures: 6, Tables: 0, Pages: 65
                Funding
                Funded by: Institut Pengurusan dan Pemantauan Penyelidikan, Universiti Malaya (MY)
                Award ID: PG060-2016A
                Award Recipient :
                ORCID: http://orcid.org/0000-0002-2722-4771
                This project was supported by a grant under the University of Malaya Postgraduate Research Fund (PG060-2016A). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Research Article
                Subject: Biology and Life Sciences
                Subject: Ecology
                Subject: Ecosystems
                Subject: Forests
                Subject: Ecology and Environmental Sciences
                Subject: Ecology
                Subject: Ecosystems
                Subject: Forests
                Subject: Ecology and Environmental Sciences
                Subject: Terrestrial Environments
                Subject: Forests
                Subject: Biology and life sciences
                Subject: Molecular biology
                Subject: Molecular biology techniques
                Subject: DNA barcoding
                Subject: Research and analysis methods
                Subject: Molecular biology techniques
                Subject: DNA barcoding
                Subject: Biology and life sciences
                Subject: Evolutionary biology
                Subject: Evolutionary systematics
                Subject: Molecular systematics
                Subject: DNA barcoding
                Subject: Biology and life sciences
                Subject: Taxonomy
                Subject: Evolutionary systematics
                Subject: Molecular systematics
                Subject: DNA barcoding
                Subject: Computer and information sciences
                Subject: Data management
                Subject: Taxonomy
                Subject: Evolutionary systematics
                Subject: Molecular systematics
                Subject: DNA barcoding
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Animals
                Subject: Animal Types
                Subject: Wildlife
                Subject: Biology and Life Sciences
                Subject: Zoology
                Subject: Animal Types
                Subject: Wildlife
                Subject: People and Places
                Subject: Geographical Locations
                Subject: Asia
                Subject: Malaysia
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Animals
                Subject: Vertebrates
                Subject: Amniotes
                Subject: Mammals
                Subject: Bats
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Plants
                Subject: Trees
                Subject: Biology and life sciences
                Subject: Genetics
                Subject: DNA
                Subject: Forms of DNA
                Subject: Mitochondrial DNA
                Subject: Biology and life sciences
                Subject: Biochemistry
                Subject: Nucleic acids
                Subject: DNA
                Subject: Forms of DNA
                Subject: Mitochondrial DNA
                Subject: Earth Sciences
                Subject: Geomorphology
                Subject: Topography
                Subject: Landforms
                Subject: Caves
                Custom metadata
                Data Availability All of the data (i.e. DNA barcodes) were obtained from Barcode of Life Data Systems at http://v4.boldsystems.org/. DNA barcodes which were included in the manuscript were publicly available. We also included some of the data as Supporting Information. Barcode of Life Data Systems is a public data repository. However, some of the data maybe not be publicly available if the owner of the dataset privatised it. Some of the data (e.g. checklists) are only available to registered users due to the restriction imposed by the Barcode of Life Data Systems.

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