1
|
Liu H, Luo J, Hou W, Pan X, Cai Y, Li J. An Effective Microsatellite Marker Panel for Noninvasive Samples in Tibetan Macaques (Macaca thibetana). INT J PRIMATOL 2022. [DOI: 10.1007/s10764-022-00348-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
2
|
Müller B, Mercker M, Brün J. Population size estimates based on the frequency of genetically assigned parent-offspring pairs within a subsample. Ecol Evol 2020; 10:6356-6363. [PMID: 32724517 PMCID: PMC7381586 DOI: 10.1002/ece3.6365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 03/09/2020] [Accepted: 04/17/2020] [Indexed: 01/28/2023] Open
Abstract
Estimating population density as precise as possible is a key premise for managing wild animal species. This can be a challenging task if the species in question is elusive or, due to high quantities, hard to count. We present a new, mathematically derived estimator for population size, where the estimation is based solely on the frequency of genetically assigned parent-offspring pairs within a subsample of an ungulate population. By use of molecular markers like microsatellites, the number of these parent-offspring pairs can be determined. The study's aim was to clarify whether a classical capture-mark-recapture (CMR) method can be adapted or extended by this genetic element to a genetic-based capture-mark-recapture (g-CMR). We numerically validate the presented estimator (and corresponding variance estimates) and provide the R-code for the computation of estimates of population size including confidence intervals. The presented method provides a new framework to precisely estimate population size based on the genetic analysis of a one-time subsample. This is especially of value where traditional CMR methods or other DNA-based (fecal or hair) capture-recapture methods fail or are too difficult to apply. The DNA source used is basically irrelevant, but in the present case the sampling of an annual hunting bag is to serve as data basis. In addition to the high quality of muscle tissue samples, hunting bags provide additional and essential information for wildlife management practices, such as age, weight, or sex. In cases where a g-CMR method is ecologically and hunting-wise appropriate, it enables a wide applicability, also through its species-independent use.
Collapse
Affiliation(s)
- Björn Müller
- Institute for Evolutionary Biology and EcologyUniversity of BonnBonnGermany
| | - Moritz Mercker
- Bionum‐Consultants in Biological, Ecological and Biomedical StatisticsHamburgGermany
| | - Jörg Brün
- Institute for Evolutionary Biology and EcologyUniversity of BonnBonnGermany
| |
Collapse
|
3
|
Purohit D, Ram MS, Pandey VK, Pravalika S, Deka PJ, Narayan G, Umapathy G. Cross-specific markers reveal retention of genetic diversity in captive-bred pygmy hog, a critically endangered suid. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01091-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
4
|
Beugin MP, Baubet E, Dufaure De Citres C, Kaerle C, Muselet L, Klein F, Queney G. A set of 20 multiplexed single nucleotide polymorphism (SNP) markers specifically selected for the identification of the wild boar (Sus scrofa scrofa) and the domestic pig (Sus scrofa domesticus). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0738-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
5
|
|
6
|
Kierepka EM, Unger SD, Keiter DA, Beasley JC, Rhodes OE, Cunningham FL, Piaggio AJ. Identification of robust microsatellite markers for wild pig fecal DNA. J Wildl Manage 2016. [DOI: 10.1002/jwmg.21102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Shem D. Unger
- University of GeorgiaSavannah River Ecology LaboratoryAikenSC29802USA
| | - David A. Keiter
- University of Georgia, Savannah River Ecology LaboratoryWarnell School of Forestry and Natural ResourcesAikenSC29802USA
| | - James C. Beasley
- University of Georgia, Savannah River Ecology LaboratoryWarnell School of Forestry and Natural ResourcesAikenSC29802USA
| | - Olin E. Rhodes
- University of GeorgiaSavannah River Ecology LaboratoryAikenSC29802USA
| | - Fred L. Cunningham
- U.S. Department of Agriculture, Mississippi Field Station, National Wildlife Research CenterWildlife ServicesPO Box 6099Mississippi StateMS39762USA
| | - Antoinette J. Piaggio
- U.S. Department of Agriculture, National Wildlife Research CenterWildlife Services4101 LaPorte AvenueFort CollinsCO80521USA
| |
Collapse
|
7
|
Huang J, Li YZ, Du LM, Yang B, Shen FJ, Zhang HM, Zhang ZH, Zhang XY, Yue BS. Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system. BMC Genomics 2015; 16:61. [PMID: 25888121 PMCID: PMC4335702 DOI: 10.1186/s12864-015-1268-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 01/22/2015] [Indexed: 12/02/2022] Open
Abstract
Background The giant panda (Ailuropoda melanoleuca) is a critically endangered species endemic to China. Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating population size, paternity test, genetic diversity for the critically endangered species. The availability of the giant panda complete genome sequences provided the opportunity to carry out genome-wide scans for all types of microsatellites markers, which now opens the way for the analysis and development of microsatellites in giant panda. Results By screening the whole genome sequence of giant panda in silico mining, we identified microsatellites in the genome of giant panda and analyzed their frequency and distribution in different genomic regions. Based on our search criteria, a repertoire of 855,058 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. A total of 160 primer pairs were designed to screen for polymorphic microsatellites using the selected tetranucleotide microsatellite sequences. The 51 novel polymorphic tetranucleotide microsatellite loci were discovered based on genotyping blood DNA from 22 captive giant pandas in this study. Finally, a total of 15 markers, which showed good polymorphism, stability, and repetition in faecal samples, were used to establish the novel microsatellite marker system for giant panda. Meanwhile, a genotyping database for Chengdu captive giant pandas (n = 57) were set up using this standardized system. What’s more, a universal individual identification method was established and the genetic diversity were analysed in this study as the applications of this marker system. Conclusion The microsatellite abundance and diversity were characterized in giant panda genomes. A total of 154,677 tetranucleotide microsatellites were identified and 15 of them were discovered as the polymorphic and stable loci. The individual identification method and the genetic diversity analysis method in this study provided adequate material for the future study of giant panda. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1268-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jie Huang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, P R China.
| | - Yu-Zhi Li
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, Sichuan, China.
| | - Lian-Ming Du
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, P R China.
| | - Bo Yang
- China Research and Conservation Centre for the Giant Panda, Wenchuan, 623006, China.
| | - Fu-Jun Shen
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.
| | - He-Min Zhang
- China Research and Conservation Centre for the Giant Panda, Wenchuan, 623006, China.
| | - Zhi-He Zhang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.
| | - Xiu-Yue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, P R China.
| | - Bi-Song Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, P R China.
| |
Collapse
|
8
|
Ringler E, Mangione R, Ringler M. Where have all the tadpoles gone? Individual genetic tracking of amphibian larvae until adulthood. Mol Ecol Resour 2014; 15:737-46. [PMID: 25388775 PMCID: PMC4402230 DOI: 10.1111/1755-0998.12345] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 11/29/2022]
Abstract
Reliably marking larvae and reidentifying them after metamorphosis is a challenge that has hampered studies on recruitment, dispersal, migration and survivorship of amphibians for a long time, as conventional tags are not reliably retained through metamorphosis. Molecular methods allow unique genetic fingerprints to be established for individuals. Although microsatellite markers have successfully been applied in mark–recapture studies on several animal species, they have never been previously used in amphibians to follow individuals across different life cycle stages. Here, we evaluate microsatellites for genetic across-stages mark–recapture studies in amphibians and test the suitability of available software packages for genotype matching. We sampled tadpoles of the dendrobatid frog Allobates femoralis, which we introduced on a river island in the Nature Reserve ‘Les Nouragues’ in French Guiana. In two subsequent recapture sessions, we searched for surviving juveniles and adults, respectively. All individuals were genotyped at 14 highly variable microsatellite loci, which yielded unique genetic fingerprints for all individuals. We found large differences in the identification success of the programs tested. The pairwise-relatedness-based approach, conducted with the programs kingroup or ML-Relate, performed best with our data set. Matching ventral patterns of juveniles and adult individuals acted as a control for the reliability of the genetic identification. Our results demonstrate that microsatellite markers are a highly powerful tool for studying amphibian populations on an individual basis. The ability to individually track amphibian tadpoles throughout metamorphosis until adulthood will be of substantial value for future studies on amphibian population ecology and evolution.
Collapse
Affiliation(s)
- Eva Ringler
- Department of Integrative Zoology, University of Vienna, Althanstrasse 14, Vienna, A-1090, Austria.,Department of Cognitive Biology, University of Vienna, Althanstrasse 14, Vienna, A-1090, Austria
| | - Rosanna Mangione
- Department of Integrative Zoology, University of Vienna, Althanstrasse 14, Vienna, A-1090, Austria.,Haus des Meeres-Aqua Terra Zoo, Fritz-Grünbaum-Platz 1, Vienna, A-1060, Austria
| | - Max Ringler
- Department of Integrative Zoology, University of Vienna, Althanstrasse 14, Vienna, A-1090, Austria
| |
Collapse
|
9
|
Nagai T, Murakami T, Masuda R. Effectiveness of Noninvasive DNA Analysis to Reveal Isolated-Forest Use by the Sable Martes zibellina on Eastern Hokkaido, Japan. MAMMAL STUDY 2014. [DOI: 10.3106/041.039.0205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Tomoko Nagai
- Department of Biology, School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | | | - Ryuichi Masuda
- Department of Biology, School of Science, Hokkaido University, Sapporo 060-0810, Japan
| |
Collapse
|
10
|
Engeman RM, Massei G, Sage M, Gentle MN. Monitoring wild pig populations: a review of methods. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:8077-8091. [PMID: 23881593 DOI: 10.1007/s11356-013-2002-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/10/2013] [Indexed: 06/02/2023]
Abstract
Wild pigs (Sus scrofa) are widespread across many landscapes throughout the world and are considered to be an invasive pest to agriculture and the environment, or conversely a native or desired game species and resource for hunting. Wild pig population monitoring is often required for a variety of management or research objectives, and many methods and analyses for monitoring abundance are available. Here, we describe monitoring methods that have proven or potential applications to wild pig management. We describe the advantages and disadvantages of methods so that potential users can efficiently consider and identify the option(s) best suited to their combination of objectives, circumstances, and resources. This paper offers guidance to wildlife managers, researchers, and stakeholders considering population monitoring of wild pigs and will help ensure that they can fulfill their monitoring objectives while optimizing their use of resources.
Collapse
Affiliation(s)
- R M Engeman
- National Wildlife Research Center, 4101 LaPorte Ave, Fort Collins, CO, 80521-2154, USA,
| | | | | | | |
Collapse
|
11
|
|
12
|
Kolodziej K, Nikolov I, Schulz HK, Theissinger K, Schulz R. Evaluation of fecal storage and DNA extraction methods in wild boar (Sus scrofa). Biochem Genet 2013; 51:406-12. [PMID: 23381667 DOI: 10.1007/s10528-013-9573-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 09/06/2012] [Indexed: 10/27/2022]
Affiliation(s)
- Karolina Kolodziej
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, D-76829 Landau, Germany.
| | | | | | | | | |
Collapse
|
13
|
Comparison of established methods for quantifying genotyping error rates in wildlife forensics. CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9729-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|