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      Genetic Diversity and Structure among Isolated Populations of the Endangered Gees Golden Langur in Assam, India

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          Abstract

          Gee’s golden langur (Trachypithecus geei) is an endangered colobine primate, endemic to the semi-evergreen and mixed-deciduous forests of Indo-Bhutan border. During the last few decades, extensive fragmentation has caused severe population decline and local extinction of golden langur from several fragments. However, no studies are available on the impact of habitat fragmentation and the genetic diversity of golden langur in the fragmented habitats. The present study aimed to estimate the genetic diversity in the Indian population of golden langur. We sequenced and analyzed around 500 bases of the mitochondrial DNA (mtDNA) hypervariable region-I from 59 fecal samples of wild langur collected from nine forest fragments. Overall, genetic diversity was high ( h = 0.934, π = 0.0244) and comparable with other colobines. Populations in smaller fragments showed lower nucleotide diversity compared to the larger forest fragments. The median-joining network of haplotypes revealed a genetic structure that corresponded with the geographical distribution. The Aie and Champabati Rivers were found to be a barrier to gene flow between golden langur populations. In addition, it also established that T. geei is monophyletic but revealed possible hybridization with capped langur, T. pileatus, in the wild. It is hoped that these findings would result in a more scientific approach towards managing the fragmented populations of this enigmatic species.

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          Tracking the long-term decline and recovery of an isolated population

          Westemeier, Brawn, Simpson … (1998)
          Effects of small population size and reduced genetic variation on the viability of wild animal populations remain controversial. During a 35-year study of a remnant population of greater prairie chickens, population size decreased from 2000 individuals in 1962 to fewer than 50 by 1994. Concurrently, both fitness, as measured by fertility and hatching rates of eggs, and genetic diversity declined significantly. Conservation measures initiated in 1992 with translocations of birds from large, genetically diverse populations restored egg viability. Thus, sufficient genetic resources appear to be critical for maintaining populations of greater prairie chickens.
          Article 0 comments Cited 197 times – based on 0 reviews     Review now
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            Empirical evaluation of preservation methods for faecal DNA.

            M A Frantzen, J. Silk, J Ferguson … (1998)
            We evaluate the relative effectiveness of four methods for preserving faecal samples for DNA analysis. PCR assays of fresh faecal samples collected from free-ranging baboons showed that amplification success was dependent on preservation method, PCR-product size, and whether nuclear or mitochondrial DNA was assayed. Storage in a DMSO/EDTA/Tris/salt solution (DETs) was most effective for preserving nuclear DNA, but storage in 70% ethanol, freezing at -20 degrees C and drying performed approximately equally well for mitochondrial DNA and short (< 200 bp) nuclear DNA fragments. Because faecal DNA is diluted and degraded, repeated extractions from faeces may be necessary and short nuclear markers should be employed for genotyping. A review of molecular scatology studies further suggests that three to six faeces per individual should be collected.
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              Mitochondrial DNA variation in Chinese and Indian rhesus macaques (Macaca mulatta).

              Ryan McDonough, David Smith (2004)
              DNA was extracted from the buffy coats or serum of 212 rhesus macaques (Macaca mulatta) sampled throughout the species' geographic range. An 835 base pair (bp) fragment of mitochondrial DNA (mtDNA) was amplified from each sample, sequenced, aligned, and used to estimate genetic distances from which phylogenetic trees were constructed. A tree that included sequences from rhesus macaques whose exact origins in China are known was used to determine the regional origin of clusters of haplotypes, or haplogroups, defined by the trees. Indian rhesus sequences formed one large homogeneous haplogroup with very low levels of nucleotide diversity and no geographic structure, and a second much smaller haplogroup apparently derived from Burma. The sequences from Burma and eastern and western China were quite divergent from those in the major haplogroup of India. Each of these sequences formed separate clusters of haplotypes that exhibited far greater nucleotide diversity and/or population structure. Correspondingly, sequences from Indian rhesus macaques that are considered to represent different subspecies (based on morphological differences) were intermingled in the tree, while those from China reflected some, but not all, aspects of subspecific taxonomy. Regional variation contributed 72% toward the paired differences between sequences in an analysis of molecular variance (AMOVA), and the average differences between the populations of eastern and western China were also statistically significant. These results suggest that Indian and Chinese rhesus macaques were reproductively isolated during most, if not all, of the Pleistocene, during which time Indian rhesus macaques experienced a severe genetic bottleneck, and that some gene flow westward into India was subsequently reestablished. Samples from breeding centers in three different provinces of China included sequences from rhesus macaques that originated in both eastern (or southern) and western China, confirming anecdotal reports that regional breeding centers in China exchange breeding stock. Genetic differences among rhesus macaques (even those acquired from the same regional breeding center) that originate in different geographic regions and are employed as subjects in biomedical experiments can contribute to phenotypic differences in the traits under study. (c) 2005 Wiley-Liss, Inc.
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                Author and article information

                Contributors
                Tzen-Yuh Chiang: 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): 26 August 2016
                Publication date Collection: 2016
                Volume: 11
                Issue: 8
                Electronic Location Identifier: e0161866
                Affiliations
                [1 ]Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
                [2 ]Primate Research Centre NE India, H/N 4, Byelane 3, Ananda Nagar, Pandu, Guwahati 781012, India
                [3 ]Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore 641108, India
                National Cheng Kung University, TAIWAN
                Author notes

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

                • Conceptualization: GU JB.

                • Data curation: GU MSR SMK.

                • Formal analysis: GU MSR SMK.

                • Funding acquisition: JB.

                • Investigation: MSR SMK SN JS.

                • Methodology: GU JB MSR.

                • Project administration: GU JB.

                • Resources: GU JB.

                • Supervision: GU JB.

                • Validation: MSR SMK.

                • Writing – original draft: GU JB MSR SMK.

                • Writing – review & editing: GU JB MSR.

                Article
                Publisher ID: PONE-D-16-18849
                DOI: 10.1371/journal.pone.0161866
                PMC ID: 5001631
                PubMed ID: 27564405
                SO-VID: 8fef5326-8223-4014-a03a-05cfd426ca61
                Copyright © © 2016 Ram 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 : 17 May 2016
                Date accepted : 13 August 2016
                Page count
                Figures: 4, Tables: 3, Pages: 15
                Funding
                Funded by: Department of Science and Technology, Government of India
                Award ID: SERB project # SR/SO/ AS - 17/2012
                Award Recipient :
                This work was supported by the Department of Science and Technology, Government of India, Science and Engineering Research Board, grant # SR/SO/ AS - 17/2012 to JB. The funder 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: Evolutionary Biology
                Subject: Population Genetics
                Subject: Haplotypes
                Subject: Biology and Life Sciences
                Subject: Genetics
                Subject: Population Genetics
                Subject: Haplotypes
                Subject: Biology and Life Sciences
                Subject: Population Biology
                Subject: Population Genetics
                Subject: Haplotypes
                Subject: Biology and Life Sciences
                Subject: Evolutionary Biology
                Subject: Population Genetics
                Subject: Biology and Life Sciences
                Subject: Genetics
                Subject: Population Genetics
                Subject: Biology and Life Sciences
                Subject: Population Biology
                Subject: Population Genetics
                Subject: Biology and Life Sciences
                Subject: Molecular Biology
                Subject: Molecular Biology Techniques
                Subject: Molecular Biology Assays and Analysis Techniques
                Subject: Phylogenetic Analysis
                Subject: Research and Analysis Methods
                Subject: Molecular Biology Techniques
                Subject: Molecular Biology Assays and Analysis Techniques
                Subject: Phylogenetic Analysis
                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: Sequencing techniques
                Subject: Sequence analysis
                Subject: DNA sequence analysis
                Subject: Research and analysis methods
                Subject: Molecular biology techniques
                Subject: Sequencing techniques
                Subject: Sequence analysis
                Subject: DNA sequence analysis
                Subject: Biology and Life Sciences
                Subject: Biogeography
                Subject: Phylogeography
                Subject: Ecology and Environmental Sciences
                Subject: Biogeography
                Subject: Phylogeography
                Subject: Earth Sciences
                Subject: Geography
                Subject: Biogeography
                Subject: Phylogeography
                Subject: Biology and Life Sciences
                Subject: Evolutionary Biology
                Subject: Population Genetics
                Subject: Phylogeography
                Subject: Biology and Life Sciences
                Subject: Genetics
                Subject: Population Genetics
                Subject: Phylogeography
                Subject: Biology and Life Sciences
                Subject: Population Biology
                Subject: Population Genetics
                Subject: Phylogeography
                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: Biology and Life Sciences
                Subject: Molecular Biology
                Subject: Molecular Biology Techniques
                Subject: Artificial Gene Amplification and Extension
                Subject: Polymerase Chain Reaction
                Subject: Research and Analysis Methods
                Subject: Molecular Biology Techniques
                Subject: Artificial Gene Amplification and Extension
                Subject: Polymerase Chain Reaction
                Custom metadata
                Data Availability All sequences are available from the GenBank database (accession number(s) KX189494-KX189516).

                ScienceOpen disciplines: Uncategorized
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                ScienceOpen disciplines: Uncategorized

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