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Zhao X, Qiu Q, Li C, Fu D, Hu X, Gao S, Zhu Y, Mu H, Wang R, Yang H, Li B. Genome-based development of 15 microsatellite markers in fluorescent multiplexes for parentage testing in captive tigers. PeerJ 2020; 8:e8939. [PMID: 32411512 PMCID: PMC7210807 DOI: 10.7717/peerj.8939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/18/2020] [Indexed: 11/20/2022] Open
Abstract
As one of the most endangered species, tiger (Panthera tigris) inbreeding has become an urgent issue to address. Using a microsatellite (short tandem repeat, STR) identification system, paternity testing may be helpful to avoid inbreeding in captive breeding programs. In this study, we developed a genome-based identification system named tiger pedigree identification multiplex system (TPI-plex). By analyzing the entire tiger genome, 139,967 STR loci were identified and 12.76% of these displayed three to six alleles among three re-sequenced individual tiger genomes. A total of 204 candidate STRs were identified and screened with a reference population containing 31 unrelated captive tigers. Of these, 15 loci were chosen for inclusion in the multiplex panel. The mean allele number and mean expected heterozygosity (He) were 7.3333 and 0.7789, respectively. The cumulative probability of exclusion (CPE) and total probability of discrimination power (TDP) reached 0.999999472 and 0.999999999999995, respectively. The results showed that the TPI-plex system can be applied in routine pedigree identification for captive tigers. We also added a sex identification marker named TAMEL into the TPI-plex for sex determination.
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Affiliation(s)
- Xiao Zhao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Forensics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Qiguan Qiu
- Changsha Ecological Zoo, Changsha, China
| | - Chang Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Dongke Fu
- Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Forensics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Xuesong Hu
- Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Shengjie Gao
- Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Yugang Zhu
- Changsha Sanzhen Tiger Park, Changsha, China
| | - Haofang Mu
- Center of Forensic Sciences, BGI, Beijing, China
| | - Runping Wang
- BGI Shaanxi Xixian new area Institute of Forensic Science, Xi'an, China
| | - Huanming Yang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Bo Li
- BGI-Shenzhen, Shenzhen, China
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Li B, Wu D, Cai Y, Vladimir G M, Zhang W, Xu Y. Genetic individualization of sable ( Martes zibellina L. 1758) using microsatellites. Anim Cells Syst (Seoul) 2018; 22:253-258. [PMID: 30460105 PMCID: PMC6138352 DOI: 10.1080/19768354.2018.1494039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 05/22/2018] [Accepted: 06/21/2018] [Indexed: 10/28/2022] Open
Abstract
Genetic individualization based on non-invasive sampling is crucial for estimating the numbers of individuals in endangered mammalian populations. In sable (Martes zibellina)-poaching cases, identifying the number of animals involved is critical for determining the penalty. In addition, investigating animal numbers for wild sable populations requires genetic individualization when collecting several samples in neighboring regions. Microsatellites have been demonstrated to be reliable markers for individual identification. Thirty-three microsatellite loci derived from Mustelidae were selected to develop a genetic individualization method for sable. Three reference populations containing 54 unrelated sables were used to calculate allele number, allelic frequencies, and the polymorphic information content of each locus. The data were subsequently used to assess the validity of a combination of twelve loci for sable individualization. We defined twelve polymorphic loci that were easy to be amplified and genotyped. Four significant deviations from Hardy-Weinberg equilibrium were observed among the 12 loci in the three populations. The match probability of an individual from the reference populations with a random individual based on the 12 loci was 1.37 × 10-13. Using the combination of the twelve loci provides sufficient power to individualize sables considering the levels of microsatellite polymorphism observed. These loci were successfully applied to a case of sable poaching and provided valid evidence to determine the penalty. The genetic individualization of sable based on these loci might also be useful to investigate the numbers of animals in wild populations.
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Affiliation(s)
- Bo Li
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China.,State Forestry Administration Detecting Center of Wildlife Resources, Harbin, People's Republic of China
| | - Dan Wu
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China.,College of Biotechnology and Engineering, West Yunnan University, Lincang, People's Republic of China
| | - Yingying Cai
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China
| | - Monakhov Vladimir G
- Institute of Plant and Animal Ecology, Ural Division of RAS, Yekaterinburg, Russia
| | - Wei Zhang
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China.,State Forestry Administration Detecting Center of Wildlife Resources, Harbin, People's Republic of China
| | - Yanchun Xu
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China.,State Forestry Administration Detecting Center of Wildlife Resources, Harbin, People's Republic of China
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Karmacharya D, Sherchan AM, Dulal S, Manandhar P, Manandhar S, Joshi J, Bhattarai S, Bhatta TR, Awasthi N, Sharma AN, Bista M, Silwal NR, Pokharel P, Lamichhane RR, Sharma N, Llewellyn B, Wultsch C, Kelly MJ, Gour D, Waits L, Hero JM, Hughes J. Species, sex and geo-location identification of seized tiger (Panthera tigris tigris) parts in Nepal-A molecular forensic approach. PLoS One 2018; 13:e0201639. [PMID: 30138352 PMCID: PMC6107122 DOI: 10.1371/journal.pone.0201639] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/19/2018] [Indexed: 11/19/2022] Open
Abstract
Tiger (Panthera tigris) populations are in danger across their entire range due to habitat loss, poaching and the demand for tiger parts. The Bengal tiger (Panthera tigris tigris) is an endangered apex predator with a population size estimated to be less than 200 in Nepal. In spite of strict wildlife protection laws, illegal trade of tiger parts is increasing; and Nepal has become one of the major sources and transit routes for poached wildlife parts. Identification of wildlife parts is often challenging for law enforcement officials due to inadequate training and lack of available tools. Here, we describe a molecular forensic approach to gain insight into illegally trafficked tiger parts seized across Nepal. We created Nepal's first comprehensive reference genetic database of wild tigers through the Nepal Tiger Genome Project (2011-2013). This database has nuclear DNA microsatellite genotype and sex profiles, including geo-spatial information, of over 60% (n = 120) of the wild tigers of Nepal. We analyzed 15 putative cases of confiscated poached tiger parts and all were confirmed to be of tiger. Ten samples were identified as male and five were female. We determined probable geo-source location for 9 of the 14 samples with 6-8 nuclear DNA microsatellite loci using inferences from four different statistical assignment methods. Six samples were assigned to Bardia National Park and one of these was an exact match to a female tiger previously profiled in our fecal DNA reference database. Two tiger samples were assigned to Shuklaphanta Wildlife Reserve and one to Chitwan National Park. We are unable to definitively assign five tiger samples which could be offspring dispersers or might have come from tiger population outside of Nepal. Our study revealed that the western region, particularly Bardia National Park, is a poaching hotspot for illegal tiger trade in Nepal. We present feasibility of using molecular forensic based evidence to incriminate criminals in a court of law in the fight against wildlife crime.
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Affiliation(s)
- Dibesh Karmacharya
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
- School of Environment, Griffith University, Gold Coast, Queensland, Australia
| | | | - Santosh Dulal
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Prajwol Manandhar
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | | | - Jyoti Joshi
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Susmita Bhattarai
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Tarka R. Bhatta
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Nagendra Awasthi
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Ajay N. Sharma
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Manisha Bista
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Nawa R. Silwal
- Central Investigation Bureau (CIB), Pillar 4, Nepal Police, Kathmandu, Nepal
| | - Pravin Pokharel
- Central Investigation Bureau (CIB), Pillar 4, Nepal Police, Kathmandu, Nepal
| | - Rom R. Lamichhane
- Bio-Diversity Section, Ministry of Forest and Soil Conservation, Kathmandu, Nepal
| | - Netra Sharma
- Environment Team, U.S. Agency for International Development (USAID), Kathmandu, Nepal
| | - Bronwyn Llewellyn
- Environment Team, U.S. Agency for International Development (USAID), Kathmandu, Nepal
| | - Claudia Wultsch
- Sackler Institute for Comparative Genomics, American Natural History Museum, New York, New York, United States of America
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Digpal Gour
- Laboratory for Ecological, Evolutionary and Conservation Genetics, University of Idaho, Moscow, Idaho, United States of America
| | - Lisette Waits
- Laboratory for Ecological, Evolutionary and Conservation Genetics, University of Idaho, Moscow, Idaho, United States of America
| | - Jean-Marc Hero
- School of Science and Engineering, University of the Sunshine Coast, Sunshine Coast, Queensland, Australia
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, United Kingdom
| | - Jane Hughes
- School of Environment, Griffith University, Gold Coast, Queensland, Australia
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Iyengar A. Forensic DNA analysis for animal protection and biodiversity conservation: A review. J Nat Conserv 2014. [DOI: 10.1016/j.jnc.2013.12.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Sharma S, Dutta T, Maldonado JE, Wood TC, Panwar HS, Seidensticker J. Spatial genetic analysis reveals high connectivity of tiger (Panthera tigris) populations in the Satpura-Maikal landscape of Central India. Ecol Evol 2012; 3:48-60. [PMID: 23403813 PMCID: PMC3568842 DOI: 10.1002/ece3.432] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 10/21/2012] [Accepted: 10/29/2012] [Indexed: 01/28/2023] Open
Abstract
We investigated the spatial genetic structure of the tiger meta-population in the Satpura–Maikal landscape of central India using population- and individual-based genetic clustering methods on multilocus genotypic data from 273 individuals. The Satpura–Maikal landscape is classified as a global-priority Tiger Conservation Landscape (TCL) due to its potential for providing sufficient habitat that will allow the long-term persistence of tigers. We found that the tiger meta-population in the Satpura–Maikal landscape has high genetic variation and very low genetic subdivision. Individual-based Bayesian clustering algorithms reveal two highly admixed genetic populations. We attribute this to forest connectivity and high gene flow in this landscape. However, deforestation, road widening, and mining may sever this connectivity, impede gene exchange, and further exacerbate the genetic division of tigers in central India.
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Affiliation(s)
- Sandeep Sharma
- Smithsonian Conservation Biology Institute, National Zoological Park Washington, District of Columbia, 20013-7012 ; Environmental Science & Policy Department, George Mason University Fairfax, Virginia, 22030-4444
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Borthakur U, Barman RD, Das C, Basumatary A, Talukdar A, Ahmed MF, Talukdar BK, Bharali R. Noninvasive genetic monitoring of tiger (Panthera tigris tigris) population of Orang National Park in the Brahmaputra floodplain, Assam, India. EUR J WILDLIFE RES 2010. [DOI: 10.1007/s10344-010-0471-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Dawnay N, Ogden R, Thorpe RS, Pope LC, Dawson DA, McEwing R. A forensic STR profiling system for the Eurasian badger: a framework for developing profiling systems for wildlife species. Forensic Sci Int Genet 2007; 2:47-53. [PMID: 19083789 DOI: 10.1016/j.fsigen.2007.08.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 07/19/2007] [Accepted: 08/13/2007] [Indexed: 10/22/2022]
Abstract
Developing short tandem repeat (STR) profiling systems for forensic identification is complicated in animal species. Obtaining a representative number of individuals from populations, limited access to family groups and a lack of developed STR markers can make adhering to human forensic guidelines difficult. Furthermore, a lack of animal specific guidelines may explain why many wildlife forensic STR profiling systems developed to date have not appropriately addressed areas such as marker validation or the publication and analysis of population data necessary for the application of these tools to forensic science. Here we present a methodology used to develop an STR profiling system for a legally protected wildlife species, the Eurasian badger Meles meles. Ten previously isolated STR loci were selected based on their level of polymorphism, adherence to Hardy-Weinberg expectations and their fragment size. Each locus was individually validated with respect to its reproducibility, inheritance, species specificity, DNA template concentration and thermocycling parameters. The effects of chemical, substrate and environmental exposure were also investigated. All ten STR loci provided reliable and reproducible results, and optimal amplification conditions were defined. Allele frequencies from 20 representative populations in England and Wales are presented and used to calculate the level of population substructure (theta) and inbreeding (f). Accounting for these estimates, the average probability of identity (PI(ave)) was 2.18 x 10(-7). This case study can act as a framework for others attempting to develop wildlife forensic profiling systems.
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Affiliation(s)
- Nick Dawnay
- School of Biological Sciences, University of Wales, Bangor LL57 2UW, United Kingdom.
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9
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Sustainability of the South China tiger: implications of inbreeding depression and introgression. CONSERV GENET 2007. [DOI: 10.1007/s10592-006-9276-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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