Tigers of Sundarbans in India: Is the population a separate conservation unit?

PLoS ONE

Volumn 10, Issue 4, 2015, Pages

  Singh, Sujeet Kumar ^a,b   Mishra, Sudhanshu ^b   Aspi, Jouni ^a   Kvist, Laura ^a   Nigam, Parag ^b   Pandey, Puneet ^b   Sharma, Reeta ^c   Goyal, Surendra Prakash ^b  

^a UNIVERSITY OF OULU   (Finland)

^b Wildlife Institute of India   (India)

^c INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS DNA; MITOCHONDRIAL DNA; MICROSATELLITE DNA;

ADAPTIVE BEHAVIOR; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CYTB GENE; FEMALE; GENE; GENE FLOW; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC IDENTIFICATION; GENETIC TRAIT; GENETIC VARIABILITY; HABITAT FRAGMENTATION; INDIA; MALE; MICROSATELLITE MARKER; ND2 GENE; ND5 GENE; ND6 GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION MIGRATION; POPULATION SIZE; POPULATION STRUCTURE; SPECIES DIFFERENCE; SPECIES HABITAT; TIGER; ADAPTATION; ANIMAL; CLASSIFICATION; ENVIRONMENTAL PROTECTION; GENETIC VARIATION; GENETICS; MOLECULAR EVOLUTION; PHYLOGEOGRAPHY; PHYSIOLOGY; POPULATION DYNAMICS;

PANTHERA TIGRIS TIGRIS;

ADAPTATION, BIOLOGICAL; ANIMALS; CONSERVATION OF NATURAL RESOURCES; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENE FLOW; GENETIC VARIATION; INDIA; MICROSATELLITE REPEATS; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION DYNAMICS; TIGERS;

EID: 84928737302     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0118846     Document Type: Article

References (94)

1. Nowell K, Jackson P (1996) Wild Cats: Status Survey and Conservation Action Plan. IUCN World Conservation Union, Gland, Switzerland. 406 p.
2. Luo SJ, Kim JH, Johnson WE, Van der Walt J, Martenson J, Yunki N et al (2004) Phylogeography and genetic ancestry of tigers (Panthera tigris). PLOS Biology 2: 2275-2293.
3. Sanderson E, Forrest J, Loucks C, Ginsberg J, Dinerstein E, Seidensticker J, et al (2006) Setting priorities for the conservation and recovery of wild tigers 2005-2015. A technical report. New York and Washington, D.C.: Wildlife Conservation Society, World Wildlife Fund, Smithsonian, and National Fish and Wildlife Foundation-Save the Tiger Fund. 206 p.
4. Jhala YV, Gopal R, Qureshi Q (2008) Status of the Tigers, Co-predators, and Prey in India. National Tiger Conservation Authority, Government of India, New Delhi, and Wildlife Institute of India, Dehradun. 151 p.
5. Jhala YV, Qureshi Q, Gopal R, Sinha PR (2011) Status of the Tigers, Co-predators, and Prey in India, 2010. National Tiger Conservation Authority, Govt. of India, New Delhi, and Wildlife Institute of India, Dehradun. 302 p.
6. Dinerstein E, Loucks C, Wikramnayake E, Ginsberg J, Sanderson E, Seidensticker J, et al (2007) The fate of wild tigers. BioScience 57:508-514.
7. Reza A, Feeroz MM, Islam MA (2001) Food habits of the Bengal tiger (Panthera tigris tigris) in the Sundarbans, Bangladesh. Jour of Zool 29:173-180.
8. Khan H, Monirul M (2008) Prey selection by tigers (Panthera tigris) (Linnaeus 1758) in the Sundarbans East Wildlife Sanctuary of Bangladesh. J Bombay Nat Hist Soc 105 (3).
9. Loucks C, Barber-Meyer S, Hossain MAA, Barlow A, Chowdhury RM (2010) Sea level rise and tigers: predicted impacts to Bangladesh's Sundarbans mangroves. Clim Chang 98:291-298.
10. Barlow ACD, Mazák J, Ahmad IU, Smith JLD (2010) A preliminary investigation of Sundarbans tiger morphology. Mammalia 74: 329-331.
11. Fraser DJ, Bernatchez L (2001) Adaptive evolutionary conservation: towards a unified concept for defining conservation units. Mol Ecol 10: 2741-2752. PMID: 11903888
12. Allendorf FW, Luikart G (2007) Conservation and the genetics of populations. Malden Massachusetts USA, Blackwell Publishing 642 p.
13. Ryder OA (1986) Conservation and systematic: The dilemma of subspecies. Trends Ecol Evol 1: 9-10.
14. Moritz C (1994) Application of mitochondrial DNA analysis in conservation: A critical review. Mol Ecol 3: 401-411.
15. Crandall KA, Olaf RP, Bininda-Emonds, Georgina MM, Wayne RK (2000) Considering evolutionary processes in conservation biology. Trends Ecol Evol 15:290-295. PMID: 10856956
16. Palsbøll PJ, Bérubé M, Allendorf FW (2007) Identification of management units using population genetic data. Trends Ecol Evo 22:11-16.
17. Fernando P, Vidya TNC, Payne J, Stuewe M, Davison G, Alfred RJ, et al (2003) DNA analysis indicates that Asian elephants are native to Borneo and are therefore a high priority for conservation. PLOS ONE 3:382-388.
18. Holycross AT, Douglas ME (2007) Geographic isolation, genetic divergence, and ecological non-exchangeability define ESUs in a threatened sky-island rattlesnake. Biol Conserv 134:142-154.
19. Zhu Y, Wan QH, Yu B, Ge YF, Fang SG (2013) Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda. BMC Evol Biol 13: 227. doi: 10.1186/1471-2148-13-227 PMID: 24144019
20. Kershaw F, Matthew SL, Collins T, Mansur RM, Smith BD, Minton G, et al (2013) Population Differentiation of two Forms of Bryde's Whales in the Indian and Pacific Oceans. doi: 10.1093/jhered/est057.
21. Sharma R, Stuckas H, Bhaskar R, Rajput S, Khan I, Goyal SP, et al (2009) mtDNA indicates profound population structure in India tiger (Panthera tigris tigris). Conserv Genet 10: 909-914.
22. Mondol S, Karanth KU, Ramakrishnan U (2009) Why the Indian subcontinent holds the key to global tiger recovery. PLOS Genetics 5(8): e1000585. doi: 10.1371/journal.pgen.1000585 PMID: 19680439
23. Sharma R, Stuckas H, Bhaskar R, Khan I, Goyal SP, Tiedemann R (2011) Genetically distinct population of Bengal tiger (Panthera tigris tigris) in Terai Arc Landscape (TAL) of India. Mammal Biol 76: 484-490.
24. Borthakur U, Barman RD, Das C, Basumatary A, Talukdar A, Ahmed MF, et al (2010) Noninvasive genetic monitoring of tiger, (Panthera tigris tigris) population of Orang National Park in the Brahmaputra floodplain, Assam, India doi: 10.1007/s10344-010-0471-0.
25. Reddy PA, Gour DS, Bhavanishankar M, Jaggi K, Hussain SM, Harika K, et al. (2012) Genetic evidence of tiger population structure and migration within an isolated and fragmented landscape in northwest India. PLOS ONE 7(1): e29827. doi: 10.1371/journal.pone.0029827 PMID: 22253791
26. Mondol S, Bruford MW, Ramakrishnan U (2013) Demographic loss, genetic structure and the conservation implications for Indian tigers. Proc R Soc B 280: 20130496. doi: 10.1098/rspb.2013.0496 PMID: 23677341
27. Sharma S, Dutta T, Maldonado JE, Wood TC, Panwar HS, Seidensticker J (2013) Forest corridors maintain historical gene flow in a tiger metapopulation in the highlands of central India. Proc R Soc B 280: 20131506. doi: 10.1098/rspb.2013.1506 PMID: 23902910
28. Joshi A, Vaidyanathan S, Mondol S, Edgaonkar A, Ramakrishnan U (2013) Connectivity of Tiger (Panthera tigris) Populations in the Human-Influenced Forest Mosaic of Central India. PLOS ONE 8(11): e77980. doi: 10.1371/journal.pone.0077980 PMID: 24223132
29. Smith LM, Burgoyne LA (2004) Collecting, archiving and processing DNA from wildlife samples using FTA data basing paper. BMC Ecol 4: 1-11. PMID: 15005805
30. Sharma R, Stuckas H, Khan I, Bhaskar R, Goyal SP, Tiedemann R (2008) Fourteen new di- and tetra nucleotide microsatellite loci for the critically endangered Indian tiger (Panthera tigris tigris). Mol Ecol Resour 8: 1480-1482. doi: 10.1111/j.1755-0998.2008.02292.x PMID: 21586082
31. Janečka JE, Jackson R, Yuquang Z, Diqiang L, Munkhtsog B, Buckley-Beason V, et al (2008) Population monitoring of snow leopards using noninvasive collection of scat samples: a pilot study. Anim Conserv 11:401-411.
32. Menotti-Raymond M, David VA, Lyons LA, Schaffer AA, Tomlin JF, Hutton MK, et al (1999) A genetic linkage map of microsatellites in the domestic cat (Felis catus). Genomics 57: 9-23. PMID: 10191079
33. Mishra S, Singh SK, Munjal A, Aspi J, Goyal SP (2014) A panel of polymorphic heterologous microsatellite loci for genotyping of critically endangered Bengal tiger (Panthera tigris tigris): A pilot study based on captive animals. Springer Plus 3:4. doi: 10.1186/2193-1801-3-4 PMID: 24455462
34. Mishra S, Sharma R, Singh SK, Munjal A, Goyal SP (2014) A comparative studies on the use of specific and heterologous, microsatellite primer for population genetics of Bengal tiger (Panthera tigris tigris). Afri J Biot doi: 10.5897/AJB12.2977.
35. Hall TA (1999) BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Aci Symp Serie 41: 95-98.
36. Librado P, Rozas J (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 145-452.
37. Bendelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37-48 PMID: 10331250
38. Crandall KA, Templeton AR (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134 (3):959-969. PMID: 8349118
39. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McInerney JO (2006) Assessment of methods for amino acids matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol 6:29 doi: 10.1186/1471-2148-6-29 PMID: 16563161
40. Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793-808. PMID: 15545256
41. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160-174. PMID: 3934395
42. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
43. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10: 564-567. doi: 10.1111/j.1755-0998.2010.02847.x PMID: 21565059
44. Johnson PCD, Haydon DT (2007) Maximum-likelihood estimation of allelic dropout and false allele error rates from microsatellite genotypes in the absence of reference data. Genetics 175:827-842. PMID: 17179070
45. Van Oosterhout C, Hutchinson B, Wills D, Shipley P (2004) Microchecker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535-538.
46. Goudet J (1995) FSTAT (Version 1.2): A computer program to calculate F-statistics. J Heredity 86: 485-486.
47. Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48: 361-372 PMID: 1637966
48. Raymond M, Rousset F (1995) GENEPOP Version 1.2: population genetics software for exact tests and ecumenicism. J Heredity 86: 248-249.
49. Hardy OJ, Vekemans X (2002). SPAGeDi: a versatile computer program to analyse spatial genetic structure the individual or population levels. Mol Ecol Notes 2(4): 618-620
50. Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457-462. PMID: 7705646
51. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959. PMID: 10835412
52. Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9: 1322-1332. doi: 10.1111/j.1755-0998.2009.02591.x PMID: 21564903
53. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Eco 14: 2611-2620.
54. Earl Dent A, vonHoldt BridgettM(2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evannomethod. Conserv Genet Resour. 4 (2) 359-361.
55. Rosenberg NA (2004) Distruct: a program for the graphical display of population structure. Mol. Ecol. Notes 4: 137-138.
56. Chen C, Durand E, Forbes F, François O (2007) Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Mol Ecol Notes 7:747-756.
57. Durand E, Jay F, Gaggiotti OE, François O (2009) Spatial inference of admixture proportions and secondary contact zones. Mol Biol Evol. 26:1963-1973. doi: 10.1093/molbev/msp106 PMID: 19461114
58. Waples RS, Do C (2008) LDNe: a program for estimating effective population size from data on linkage disequilibrium. Mol Ecol Resour 8:753-756. doi: 10.1111/j.1755-0998.2007.02061.x PMID: 21585883
59. England PE, Luikart G, Waples RS (2010) Early detection of population fragmentation using linkage disequilibrium estimation of effective population size. Conserv Genet 11:2425-2430.
60. Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin L, Estoup A (2004) GeneClass2: A Software for Genetic Assignment and First-Generation Migrant Detection. J Heredity 95:536-539. PMID: 15475402
61. Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci USA 94, 9197-9201. PMID: 9256459
62. Paetkau D, Slade R, Burden M, Estoup A (2004) Direct, real-time estimation of migration rate using assignment methods: a simulation-based exploration of accuracy and power. Mol Ecol 13:55-65. PMID: 14653788
63. Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163(3): 1177-1191. PMID: 12663554
64. Smith JLD, McDougal C (1991) The contribution of variance in lifetime reproduction to effective population size in tigers. Conserv Biol 5(4):484-490.
65. Hedrick PW, Allendorf FW, Baker SC (2013) Estimation of Male Gene Flow from Measures of Nuclear and Female Genetic Differentiation. J Heredity 104(5) 713-717. doi: 10.1093/jhered/est047 PMID: 23894193
66. Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences. Mol Biol Evol 22: 1185-1192. PMID: 15703244
67. Cornuet JM, Veyssier J, Pudlo P, Dehne-Garcia A, Gautier M, Leblois R, et al (2014) DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using Single Nucleotide Polymorphism, DNA sequence and microsatellite data. Bioinformatics 30: 1187-1189.
68. Chakrabarti K (1992) Man-eating Tigers. Darbari Print-Pro (P) Ltd., Calcutta
69. Karanth KU (2003) Tiger ecology and conservation in the Indian subcontinent. J Bombay Nat Hist Soc 100: 169-189.
70. Karanth KU, Nichols JD, Kumar NS, Link WA, Hanes JE (2004) Tiger and their prey: predicting carnivore densities from prey abundance. Proc Nat Acad Sci, USA 101:4854-4858. PMID: 15041746
71. Balow DCA (2009) The Sundarbans tiger adaptation, population status and conflict management. University of Minnesota PhD. Thesis. pp. 29-54.
72. Wright S (1931) Evolution in Mendelian populations. Genetics 16:97-159. PMID: 17246615
73. Waples RS, Gaggiotti OE (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol Ecol 15:1419-1439. PMID: 16629801
74. Faubet P. Waples RS, Gaggiotti OE (2007) Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates. Mol Ecol 16: 1149-1166. PMID: 17391403
75. Waples RS, Gaggiotti OE (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol Ecol 15:1419-1439. PMID: 16629801
76. Hemmer H, Kahlke RD, Vekua AK (2004) The Old World puma - Puma pardoides (Owen, 1846) (Carnivora: Felidae) - In the Lower Villafranchian (Upper Pliocene) of Kvabebi (East Georgia, Transcaucasia) and its evolutionary and biogeographical significance. Neues Jahrbuch fur Geologie und Palaontologie - Abhandlungen 233:97-231.
77. Iriarte JA, Franklin WL, Johnson WE, Redford KH (1990) Biogeographic variation of food habits and body size of the America puma. Oecologia 85:185-190.
78. Hoogesteijn RE, Mondolfi H (1996) Body mass and skull measurements in four Jaguar populations and observations on their prey base. The Florida Museum of Natural History Bulletin 39:195-219.
79. Owen-Smith N, Mills MGL (2008) Predator-prey size relationships in an African large-mammal food web. J Anim Ecol 77:173-183. doi: 10.1111/j.1365-2656.2007.01314.x PMID: 18177336
80. Allendorf FW, Luikart G, Atiken SN (2013) Conservation and the Genetics of Populations. 2nd edition Blackwell Publishing.
81. Hale ML, Burg TM, Steeves TE (2012) Sampling for Microsatellite-Based Population Genetic Studies: 25 to 30 Individuals per Population Is Enough to Accurately Estimate Allele Frequencies. PLOS ONE 7(9): e45170. doi: 10.1371/journal.pone.0045170 PMID: 22984627
82. Khan MMH (2004) Ecology and conservation of the Bengal tiger in the Sundarbans mangrove forest of Bangladesh. PhD Thesis, University of Cambridge.
83. Balloux F, Lugon-Moulin N, Hausser J (2000) Estimating interracial gene flow in hybrid zones: how reliable are microsatellites? Acta Theriol 45:93-101.
84. Eaton RM (1990). Human settlement and colonization in the Sundarbans, 1200-1750.Agriculture and Human Values 7:6-16.
85. Bera GK, Sahay VS (2010) In the lagoons of the Gangetic delta. Mittal Publications, New Delhi. 237p.
86. Nunn PD, Kumar R (2006) Coastal history in the Asia-Pacific region. In: Harvey N. (ed.). Global Change and Integrated Coastal Management: The Asia-Pacific Region. Berlin: Springer, pp. 93-116.
87. Najman Y, Bickle M, BouDagher-Fadel M, Carter A, Garzanti E, Paul M, et al (2008) The Paleogene record of Himalayan erosion: Bengal Basin, Bangledesh. Earth Planet Sci Lett 273: 1-14.
88. Qureshi Q, Gopal R, Kyatham S, Basu S, Mitra A, Jhala YV (2006) Evaluating tiger habitat at the tehsil level. Project Tiger Directorate, Govt. of India, New Delhi and the Wildlife Institute of India, Dehradun. 162 p.
89. Johnsingh AJT, Ramesh K, Qureshi Q, David A, Goyal SP, Rawat GS, et al (2004) Conservation status of tiger and associated species in the Terai Arc Landscape, India. Wildlife Institute of India, Dehradun. 110 p.
90. Mayr E (1942) Systematics and the Origin of Species from the Viewpoint of a Zoologist. Columbia University Press, New York. PMID: 15851666
91. Coyne JA, Orr HA (2004) Speciation. Sinauer & Associates, Sunderland, Massachusetts.
92. Prager EM, Wilson AC (1995) slow evolutionary loss of the potential for interspecific hybridization in birds: a manifestation of slow regulatory evolution. Proc Natl Acad Sci USA 72:200-204.
93. Benjamin M. Fitzpatrick (2004) Rates of evolution of hybrid inviability in birds and mammal. Evolution 58: 1865-1870. PMID: 15446440
94. Waples RS (1991) Pacific salmon, Oncorhynchhus spp. and the definition of the species under the Endangered Species Act. Marine Fisheries Review 53: 11-22.