Panel of polymorphic heterologous microsatellite loci to genotype critically endangered Bengal tiger: a pilot study

SpringerPlus

Volumn 3, Issue 1, 2014, Pages

  Mishra, Sudhanshu ^a,b   Singh, Sujeet Kumar ^a   Munjal, Ashok Kumar ^b,c   Aspi, Jouni ^d   Goyal, Surendra Prakash ^a  

^a Wildlife Institute of India   (India)

^b BANASTHALI UNIVERSITY   (India)

^c INDIRA GANDHI NATIONAL TRIBAL UNIVERSITY   (India)

^d UNIVERSITY OF OULU   (Finland)

Author keywords

Bengal tiger; Genotyping panel; Heterologous microsatellite loci; Panthera tigris tigris

Indexed keywords

EID: 84928727024     PISSN: None     EISSN: 21931801     Source Type: Journal    
DOI: 10.1186/2193-1801-3-4     Document Type: Article

References (74)

1. Alasaad S, Soriguer RC, Chelomina G, Sushitsky YP, Fickel J: Siberian tiger’s recent population bottleneck in the Russian Far East revealed by microsatellite markers.Mamm Biol 2011, 76:722–726.
2. Anderson CR Jr, Lindzey FG, McDonald DB: Genetic structure of cougar populations across the wyoming basin: metapopulation or megapopulation.J Mammal 2004,85(6):1207–1214.
3. Arandjelovic M, Guschanski K, Schubert G, Harris TR, Thalmann O, Siedel H, Vigilant L: Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples.Mol Ecol 2009, 9:28–36.
4. Bellemain E, Taberlet P: Improved non-invasive genotyping method: application to brown bear (Ursus arctos) feces.Mol Ecol Notes 2004, 4:519–522.
5. Bellemain E, Swenson JE, Tallmon O, Brunberg S, Taberlet P: Estimating population size of elusive animals with DNA from hunter-collected feces: four methods for brown bears.Conserv Biol 2005, 19:150–161.
6. Bhagavatula J, Singh L: Genotyping fecal samples of Bengal tiger (Panthera tigris tigris) for population estimation: a pilot study.BMC Genet 2006,7(48):1471–2156.
7. Blouin MS: DNA-based methods for pedigree reconstruction and kinship analysis in natural populations.Trends Ecol Evol 2003,18(10):503–511.
8. Botstein D, White RL, Skolnick M, Davis RW: Construction of a genetic linkage map in man using restriction fragment length polymorphisms.Am J Hum Genet 1980, 32:314–331.
9. Castilho CS, Marins-Sá LG, Benedet RC, Freitas TRO: Genetic structure and conservation of Mountain Lions in the South-Brazilian Atlantic Rain Forest.Genet Mol Biol 2012,35(1):65–73.
10. Chang ZF, Liu ZJ, Yang JY, Li M, Vigilant L: Noninvasive genetic assessment of the population trend and sex ratio of the Shennongjia population of Sichuan snub-nosed monkeys (Rhinopithecus roxellana).Chin Sci Bull 2012, 57:1135–1141.
11. Charruau P, Fernandes C, Orozco-Terwengel P, Peters J, Hunter L, Ziaie H, Jourabchian A, Jowkar H, Schaller G, Ostrowski S, Vercammen P, Grange T, Schlotterer C, Kotze A, Geigl EM, Walzer C, Burger PA: Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates.Mol Ecol 2011, 20:706–724.
12. Cornuet JM, Luikart G: Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data.Genetics 1996, 144:2001–2014.
13. Creel S, Spong G, Sands JL, et al.: Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes.Mol Ecol 2003, 12:2003–2009.
14. Cullingham C, Curteanu M, Ball MC, Manseau M: Feasibility and recommendations for swift fox fecal DNA profiling.J Wildl Manag 2010,74(4):849–859.
15. Dinerstein E, Loucks C, Wikramanayake E, Ginsberg J, Sanderson E, Seidensticker J, Forrest J, Bryja G, Heydlauff A, Klenaendorf S, Leimgruber P, Mills J, O’Brien TG, Shrestha M, Simons R, Songer M: The fate of wild tigers.Bioscience 2007, 57:508–514.
16. Dutta T, Sharma S, Maldonado JE, Wood TC, Seidensticker J: A reliable method for individual identification and gender determination of wild leopards (Panthera pardus fusca) using non-invasive samples.Conserv Genet Resour 2012,4(3):665–667.
17. Dutta T, Sharma S, Maldonado JE, Wood TC, Panwar HS, Seidensticker J: Gene flow and demographic history of leopards (Panthera pardus) in the central Indian highlands.Evol Appl 2013. doi: 10.1111/eva.12078
18. Eiken HG, Andreassen RJ, Kopatz A, Bjervamoen SG, Wartiainen I, Tobiassen C, Knappskog PM, Aspholm PE, Smith ME, Aspi J: Population data for 12 STR loci in Northern European brown bear (Ursus arctos) and application of DNA profiles for forensic casework.Forensic Sci Int Genet Suppl 2009, 2:273–274.
19. FitzSimmons NN, Moritz C, Moore SS: Conservation and dynamics of microsatelite loci over 300 million years of marine turtle evolution.Mol Biol Evol 1995, 12:432–440.
20. Garner A, Rachlow JL, Hicks JF: Patterns of genetic diversity and its loss in mammalian populations.Conserv Biol 2005,19(4):1215–1221.
21. Garza JC, Williamson EG: Detection of reduction in population size using data from microsatellite loci.Mol Ecol 2001, 10:305–318.
22. Gill P, Brenner CH, Buckleton JS, Carracedo A, Krawczak M, Mayr WR, Morling N, Prinz M, Schneider PM, Weir BS: DNA Commission of the International Society of Forensic Genetics: recommendations on the interpretation of mixtures.Forensic Sci Int 2006, 160:90–101.
23. Gill P, Gusmao L, Haned H, Mayr WR, Morling N, Parson W, Prieto L, Prinz M, Schneider H, Schneider PM, Weir BS: DNA commission of the International Society of Forensic Genetics: Recommendations on the evaluation of STR typing results that may include drop-out and/or drop-in using probabilistic methods.Forensic Sci Int 2012, 6:679–688.
24. Goodrich JM, Kerley LL, Smirnov EN, Miquelle DG, McDonald L, Quigley HB, Hornocker MG, McDonald T: Survival rates and causes of mortality of Amur tigers on and near the Sikhote-Alin Biosphere Zapovednik.J Zool 2008, 276:323–329.
25. Goossens B, Waits LP, Taberlet P: Plucked hair samples as a source of DNA: reliability of dinucleotide microsatellite genotyping.Mol Ecol 1998, 7:1237–1241.
26. Gopal R, Sinha PR, Mathur VB, Jhala YV, Qureshi Q: Guidelines for preparation of Tiger Conservation Plan. National Tiger Conservation Authority, Ministry of Environment and Forests, Government of India. New Delhi, India: National Tiger Conservation Authority; 2007. Technical Report. NTCA/01/07
27. Guo SW, Thompson EA: Performing the exact test of Hardy–Weinberg proportion for multiple alleles.Biometrics 1992, 48:361–372.
28. Hansen H, Ben-David M, McDonald DB: Effects of genotyping protocols on success and errors in identifying individual river otters (Lontra canadensis) from their faeces.Mol Ecol Resour 2008, 8:282–289.
29. Holbrook JD, Caso A, DeYoung RW, Tewes ME: Population genetics of jaguarundis in Mexico: implications for future research and conservation.Wildlife Soc B 2013,37(2):336–341.
30. Janecka JE, Jackson R, Yuquang Z, Diqiang L, Munkhtsog B, Buckley-Beason V, Murphy WJ: Population monitoring of snow leopards using noninvasive collection of scat samples: a pilot study.Anim Conserv 2008, 11:401–411.
31. Jhala YV, Gopal R, Qureshi Q: Status of the Tigers, Co-predators and Prey in India. Dehradun, India: Wildlife Institute of India; 2008:164. [National Tiger Conservation Authority, Ministry of Environment and Forest, Govt. of India, New Delhi] Technical Report, 2008/001
32. Jhala YV, Qureshi Q, Gopal R, Sinha PR: Status of the Tigers, Co-predators and Prey in India, 2010. Dehradun, India: Wildlife Institute of India; 2011:302. [National Tiger Conservation Authority, Govt. of India, New Delhi] Technical Report, 2011/003
33. Kalinowski ST, Taper ML, Marshall TC: Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment.Mol Ecol 2007, 16:1099–1106.
34. Karanth KU, Nichols JD, Seidensticker J, Dinerstein E, Smith JLD, McDougal C, Johnsingh AJT, Chundawat RS, Thapar V: Science deficiency in conservation practice: the monitoring of tiger populations in India.Anim Conserv 2003, 6:141–146.
35. Karanth KU, Goodrich JM, Vaidyanathan S, Reddy GV: Landscape scale, ecology-based management of wild tiger populations. Washington, DC: Global Tiger Initiative, World Bank, and Wildlife Conservation Society; 2010.
36. Langergraber KE, Vigilant L: Genetic differences cannot be excluded from generating behavioural differences among chimpanzee groups (letter).Proc R Soc B 2011, 278:2094–2095.
37. Langergraber KE, Mitani JC, Watts DP, Vigilant L: Male–female socio-spatial relationships and reproduction in wild chimpanzees.Behav Ecol Sociobiol 2013, 67:861–873.
38. Linkie M, Chapron G, Martyr D, Holden J, Leader-Williams N: Assessing the viability of tiger subpopulations in a fragmented landscape.J Appl Ecol 2006, 43:576–586.
39. Lorenzini R, Cabras P, Fanelli R, Carboni GL: Wildlife molecular forensics: identification of the Sardinian mouflon using STR profiling and the Bayesian assignment test.Forensic Sci Int-Gen 2011, 5:345–349.
40. Luo SJ, Kim JH, Johnson WE, van der Walt J, Martenson J, Yuhki N, Miquelle DG, et al.: Phylogeography and genetic ancestry of tigers (Panthera tigris).PLoS Biol 2004, 2:2275–2293.
41. Lyke MM, Dubach J, Briggs MB: A molecular analysis of African lion (Panthera leo) mating structure and extra-group paternity in Etosha National Park.Mol Ecol 2013. doi: 10.1111/mec.12279
42. Mantellatto AMB, Carnelossi EAG, Duarte JMB: Transferability of microsatellite loci from exotic Cervidae to Brazilian brocket deer (Mazamaspp., Mammalia: Cervidae).Genet Mol Res 2010,9(1):277–282.
43. Matsumoto T, Yukawa W, Nozaki Y, Nakashige R, Shinya M, Makino S, Yagura M, Ikuta T, Imanishi T, Inoko H, Tamiya G, Gojobori T: Novel algorithm for automated genotyping of microsatellites.Nucleic Acids Res 2004,32(20):6069–6077.
44. Menotti-Raymond M, David VA, Lyons LA, Schaffer AA, Tomlin JF, Hutton MK, O’Brien SJ: A genetic linkage map of microsatellites in the domestic cat (Felis catus).Genomics 1999, 57:9–23.
45. Menotti-Raymond M, David VA, Wachter LL, Butler JM, O’Brien SJ: An STR forensic typing system for genetic individualization of domestic cat (Felis catus) samples.J Forensic Sci 2005, 50:1061–1070.
46. Mills L, Citta J, Lair K, Schwartz M, Tallmon D: Estimating animal abundance using non-invasive DNA sampling: promise and pitfalls.Ecol Appl 2000, 10:283–294.
47. Miotto RA, Rodrigues FP, Ciocheti G, Galetti PM: Determination of the minimum population size of pumas (Puma concolor) through fecal DNA analysis in two protected Cerrado areas in the Brazilian southeast.Biotropica 2007, 39:647–654.
48. Miotto RA, Cervini M, Begotti RA, Galetti PM: Monitoring a puma (Puma concolor) population in a fragmented landscape in southeast Brazil.Biotropica 2011,44(1):98–104.
49. Mishra S, Singh SK, Goyal SP: Panthera tigris genome: implication in wildlife forensics. Final project report. Dehradun: Wildlife Institute of India; 2012.
50. Mondol S, Karanth KU, Kumar NS, Gopalaswamy AM, Andheria A, Ramakrishnan U: Evaluation of non-invasive genetic sampling methods for estimating tiger population size.Biol Conserv 2009, 142:2350–2360.
51. Mondol S, Navya R, Athreya V, Sunagar K, Selvaraj VL, Ramakrishnan U: A panel of microsatellites to individually identify leopards and its application to leopard monitoring in human dominated landscapes.BMC Genet 2009, 10:79.
52. Moore SS, Sargeant LL, King TJ, Mattick JS, Georges M, Hetzel DJS: The conservation of dinucleotide microsatellites among mammalian genomes allows the use of heterologous PCR primer pairs in closely related species.Genomics 1991, 10:654–660.
53. Murphy MA, Kendall KC, Robinson A, Waits LP: The impact of time and field conditions on brown bear (Ursus arctos) fecal DNA amplification.Conserv Genet 2007, 8:1219–1224.
54. Navidi W, Arnheim N, Waterman MS: A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR: statistical considerations.Am J Hum Genet 1992, 50:347–359.
55. Peakall R, Smouse PE: GENALEX 6: genetic analysis in excel. Population genetic software for teaching and research.Mol Ecol Notes 2006, 6:288–295.
56. Queller DC, Goodnight KF: Estimating relatedness using genetic markers.Evolution 1989, 43:258–275.
57. Reddy PA, Gour DS, Bhavanishankar M, Jaggi K, Hussain SM, Harika K, Shivaji S: Genetic evidence of tiger population structure and migration within an isolated and fragmented landscape in northwest India.PLoS One 2012,7(1):e29827.
58. Rousset F: GENEPOP’007: a complete re-implementation of theGENEPOPsoftware for Windows and Linux.Mol Ecol Resour 2008, 8:103–106.
59. Ruiz-Garcia M, Payán E, Murillo A, Alvarez D: DNA microsatellite characterization of the jaguar (Panthera onca) in Colombia.Genes Genet Syst 2006, 81:115–127.
60. Sanderson E, Forrest J, Loucks C, Ginsberg J, Dinerstein E, et al.: Setting Priorities for the Conservation and Recovery of Wild Tigers: 2005–2015, the Technical Assessment. 2006. http://www.worldwildlife.org/species/finder/tigers/publications.html
61. Sharma S, Dutta T, Maldonado JE, Wood TC, Panwar HS, Seidensticker J: Forest corridors maintain historical gene flow in a tiger metapopulation in the highlands of central India.Proc R Soc Lond B Biol Sci 2013., 280: doi: 10.1098/rspb.2013.1506
62. Shepherd M, Cross M, Maguire TL, Dieters MJ, Williams GG, Henry RJ: Transpecific microsatellites for hard pines.Theor Appl Genet 2002, 104:819–827.
63. Singh A, Shailaja K, Gaur A, Singh L: Development and characterization of novel microsatellite markers in the Asiatic lion (Panthera leo persica).Mol Ecol Notes 2002, 2:542–543.
64. Smith DA, Ralls K, Hurt A, Adams B, Parker M, Maldonado JE: Assessing reliability of microsatellite genotypes from kit fox fecal samples using genetic and GIS analyses.Mol Ecol 2006, 15:387–406.
65. Sunquist M, Karanth KU, Sunquist F: Ecology, behaviour and resilience of the tiger and its conservation needs. In Riding the Tiger: Tiger Conservation in Human Dominated Landscapes. Edited by: Seidensticker J, Christie S, Jackson P. Cambridge: Cambridge University Press; 1999:5–18.
66. Valiere N: GIMLET: a computer program for analysing genetic individual identification data.Mol Ecol Notes 2002, 2:377–399.
67. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P: MICROCHECKER: software for identifying and correcting genotyping errors in microsatellite data.Mol Ecol Notes 2004, 4:535–538.
68. Waits LP, Luikart G, Taberlet P: Estimating probability of identity among genotypes in natural populations: cautions and guidelines.Mol Ecol 2001, 10:249–256.
69. Waits LP, Buckley-Beason VA, Johnson WE, Onoratos D, McCarthy T: A select panel of polymorphic microsatellite loci for individual identification of snow leopards (Panthera uncia).Mol Ecol Notes 2007, 7:311–314.
70. Walston J, Robinson JG, Bennett EL, Breitenmoser U, da Fonseca GAB, et al.: Bringing the tiger back from the brink: the six percent solution.PLoS Biol 2010,8(9):e1000485. doi: 10.1371/journal.pbio.1000485
71. Wasser SK, Shedlock AM, Comstock K, Ostrander EA, Mutayoba B, Stephens M: Assigning African elephant DNA to geographic region of origin: applications to the ivory trade.Proc Natl Acad Sci U S A 2004,101(41):14847–14852.
72. Weir BS, Cockerham CC: Estimating F statistics for the analysis of population structure.Evolution 1984, 38:1358–1370.
73. Williamson JE, Huebinger RM, Sommer JA, Louis EE, Barber RC: Development and cross amplification of 18 microsatellite markers in the Sumatran tiger (Panthera tigris sumatrae).Mol Ecol Notes 2002, 2:110–112.
74. Wilting A, Buckley-Beason VA, Feldhaar H, Gadau J, O’Brien SJ, Linsenmair KE: Clouded leopard phylogeny revisited: support for species recognition and population division between Borneo and Sumatra.Front Zool 2007, 4:15. doi:10.1186/1742–9994–4-15