Alcala N, Goldberg A, Ramakrishnan U, Rosenberg NA (2019) Coalescent theory of migration network motifs. Mol Biol Evol 36:2358–2374
Google Scholar
Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664
Google Scholar
Anjana S, Sammeta SP, Das R (2020) Developing ancestry informative marker panel for Nigeria-Cameroonian chimpanzees. J Genet 99:1–7
Armstrong E, Khan A, Taylor RW, Gouy A, Greenbaum G, Thiéry A et al. (2021) Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection. Mol Biol Evol 38:2366–2379
Google Scholar
Ballou JD (1992) Genetic and demographic considerations in endangered species captive breeding and reintroduction programs. In: Wildlife 2001: populations, Springer: Dordrecht, pp. 262–275
Balloux F, Lugon‐Moulin N (2002) The estimation of population differentiation with microsatellite markers. Mol Ecol 11:155–165
Google Scholar
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
Google Scholar
Brandies P, Peel E, Hogg CJ, Belov K (2019) The value of reference genomes in the conservation of threatened species. Genes (Basel) 10:846
Google Scholar
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140
Google Scholar
Chapman JR, Nakagawa S, Coltman DW, Slate J, Sheldon BC (2009) A quantitative review of heterozygosity–fitness correlations in animal populations. Mol Ecol 18:2746–2765
Google Scholar
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA et al. (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158
Google Scholar
Das R, Roy R, Venkatesh N (2019) Using ancestry informative markers (AIMs) to detect fine structure within gorilla populations. Front Genet 10:43
Google Scholar
Das R, Upadhyai P (2018) An ancestry informative marker set which recapitulates the known fine structure of populations in South Asia. Genome Biol Evol 10:2408–2416
Google Scholar
Das R, Upadhyai P (2019) Application of the geographic population genetic structure (GPS) algorithm for biogeographical analyses of wild and captive gorillas. BMC Bioinforma 20:35
Dudash MR, Fenster CB (2000) Inbreeding and outbreeding depression in fragmented populations. Conserv Biol Ser 35–54
Esposito U, Das R, Syed S, Pirooznia M, Elhaik E (2018) Ancient ancestry informative markers for identifying fine-scale ancient population genetic structure in Eurasians. Genes (Basel) 9:625
Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH et al. (2020) Dense sampling of bird diversity increases power of comparative genomics. Nature 587:252–257
Google Scholar
Frantz AC, Pourtois JT, Heuertz M, Schley L, Flamand MC, Krier A et al. (2006) Genetic structure and assignment tests demonstrate illegal translocation of red deer (Cervus elaphus) into a continuous population. Mol Ecol 15:3191–3203
Google Scholar
Friar EA, Boose DL, LaDoux T, Roalson EH, Robichaux RH (2001) Population genetic structure in the endangered Mauna Loa silversword, Argyroxiphium kauense (Asteraceae), and its bearing on reintroduction. Mol Ecol 10:1657–1663
Google Scholar
Fuentes‐Pardo AP, Ruzzante DE (2017) Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations. Mol Ecol 26:5369–5406
Google Scholar
Goodrich J, Lynam A, Miquelle D, Wibisono H, Kawanishi K, Pattanavibool A et al. (2015) Panthera tigris. In: The IUCN Red List of Threatened Species 2015, p. 15955 50659951
Ivy JA, Lacy RC (2010) Using molecular methods to improve the genetic management of captive breeding programs for threatened species. In: Molecular approaches in natural resource conservation and management, pp. 267–295
Jangtarwan K, Koomgun T, Prasongmaneerut T, Thongchum R, Singchat W, Tawichasri P et al. (2019) Take one step backward to move forward: Assessment of genetic diversity and population structure of captive Asian woolly-necked storks (Ciconia episcopus). PLoS One 14:e0223726
Google Scholar
Jiménez‐Mena B, Schad K, Hanna N, Lacy RC (2016) Pedigree analysis for the genetic management of group‐living species. Ecol Evol 6:3067–3078
Google Scholar
Kanthaswamy S, Johnson Z, Trask JS, Smith DG, Ramakrishnan R, Bahk J et al. (2014) Development and validation of a SNP‐based assay for inferring the genetic ancestry of rhesus macaques (Macaca mulatta). Am J Primatol 76:1105–1113
Google Scholar
Khan A, Patel K, Bhattacharjee S, Sharma S, Chugani AN, Sivaraman K et al. (2020) Are shed hair genomes the most effective noninvasive resource for estimating relationships in the wild? Ecol Evol 10:4583–4594
Google Scholar
Khan A, Patel K, Shukla H, Viswanathan A, van der Valk T, Borthakur U, et al. (2021). Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. bioRxiv
Khan A, Tyagi A (2021) Considerations for initiating a wildlife genomics research project in South and South-East Asia. J Indian Inst Sci 101:243–256. https://doi.org/10.1007/s41745-021-00243-3
Google Scholar
Kirk H, Freeland JR (2011) Applications and implications of neutral versus non-neutral markers in molecular ecology. Int J Mol Sci 12:3966–3988
Google Scholar
Kolipakam V, Singh S, Pant B, Qureshi Q, Jhala YV (2019) Genetic structure of tigers (Panthera tigris tigris) in India and its implications for conservation. Glob. Ecol Conserv 20:710
Kunde MN, Martins RF, Premier J, Fickel J, Förster DW (2020) Population and landscape genetic analysis of the Malayan sun bear Helarctos malayanus. Conserv Genet 21:123–135
Google Scholar
Laikre L, Palm S, Ryman N (2005) Genetic population genetic structure of fishes: implications for coastal zone management. AMBIO A J Hum Environ 34:111–119
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357
Google Scholar
Liang Z, Bu L, Qin Y, Peng Y, Yang R, Zhao Y (2019) Selection of optimal ancestry informative markersfor classification and ancestry proportion estimation in pigs. Front genet 10:183
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079
Google Scholar
Lott MJ, Wright BR, Kemp LF, Johnson RN, Hogg CJ (2020) Genetic Management of Captive and Reintroduced Bilby Populations. J Wildl Manag 84:20–32
Luo SJ, Johnson WE, Martenson J, Antunes A, Martelli P, Uphyrkina O et al. (2008) Subspecies genetic assignments of worldwide captive tigers increase conservation value of captive populations. Curr Biol 18:592–596
Google Scholar
Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J et al. (2011) Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil) Proc Natl Acad Sci 108:12348–12353
Google Scholar
Mondol S, Bruford MW, Ramakrishnan U (2013) Demographic loss, genetic structure and the conservation implications for Indian tigers. Proc R Soc B Biol Sci 280:20130496
Muñoz I, Henriques D, Johnston JS, Chávez-Galarza J, Kryger P, Pinto MA (2015) Reduced SNP Panels for Genetic Identification and Introgression Analysis in the Dark Honey Bee (Apis mellifera mellifera) PLOS One 10:e0124365
Google Scholar
Nassir R, Kosoy R, Tian C, White PA, Butler LM, Silva G et al. (2009) An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels. BMC Genet 10:39
Google Scholar
Natesh M, Atla G, Nigam P, Jhala YV, Zachariah A, Borthakur U et al. (2017) Conservation priorities for endangered Indian tigers through a genomic lens. Sci Rep. 7:1–11
Natesh M, Taylor RW, Truelove NK, Hadly EA, Palumbi SR, Petrov DA et al. (2019) Empowering conservation practice with efficient and economical genotyping from poor quality samples. Methods Ecol evolution 10:853–859
Patterson N, Price AL, Reich D (2006) Population genetic structure and eigenanalysis. PLoS Genet 2:190
Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904–909
Google Scholar
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population genetic structure using multilocus genotype data. Genetics 155:945–959
Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–575
Google Scholar
Putnam AS, Ivy JA (2014) Kinship-based management strategies for captive breeding programs when pedigrees are unknown or uncertain. J Hered 105:303–311
Google Scholar
Rosenberg NA, Li LM, Ward R, Pritchard JK (2003) Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73:1402–1422
Google Scholar
Sagar V, Kaelin CB, Natesh M, Reddy PA, Mohapatra RK, Chhattani H et al. (2021) High frequency of an otherwise rare phenotype in a small and isolatedtiger population. Proc Natl Acad Sci p. 118
Saunders CT, Wong WS, Swamy S, Becq J, Murray LJ, Cheetham RK (2012) Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs. Bioinformatics 28:1811–1817
Google Scholar
Schlaepfer DR, Braschler B, Rusterholz HP, Baur B (2018) Genetic effects of anthropogenic habitat fragmentation on remnant animal and plant populations: a meta‐analysis. Ecosphere 9:2488
Shriver MD, Parra EJ, Dios S, Bonilla C, Norton H, Jovel C et al. (2003) Skin pigmentation, biogeographical ancestry and admixture mapping. Hum Genet 112:387–399
Google Scholar
Somenzi E, Ajmone-Marsan P, Barbato M (2020) Identification of ancestry informative marker (AIM) panels to assess hybridisation between feral and domestic sheep. Animals 10:582
Google Scholar
Supple MA, Shapiro B (2018) Conservation of biodiversity in the genomics era. Genome Biol 19:1–12
Svardal H, Jasinska AJ, Apetrei C, Coppola G, Huang Y, Schmitt CA et al. (2017) Ancient hybridization and strong adaptation to viruses across African vervet monkey populations. Nat genet 49:1705–1713
Google Scholar
Vongpaisarnsin K, Listman JB, Malison RT, Gelernter J (2015) Ancestry informative markers for distinguishing between Thai populations based on genome-wide association datasets. Leg Med 17:245–250
Google Scholar
Wasser SK, Brown L, Mailand C, Mondol S, Clark W, Laurie C et al. (2015) Genetic assignment of large seizures of elephant ivory reveals Africa’s major poaching hotspots. Science (80-) 349:84–87
Google Scholar
Wilkinson S, Wiener P, Archibald AL, Law A, Schnabel RD, McKay SD et al. (2011) Evaluation of approaches for identifying population informative markers from high density SNP chips. BMC genetics 12:1–14
Wright S (1969) Evolution and the genetics of populations
Wultsch C, Caragiulo A, Dias-Freedman I, Quigley H, Rabinowitz S, Amato G (2016) Genetic diversity and population genetic structure of Mesoamerican jaguars (Panthera onca): implications for conservation and management. PLoS One 11:162377
Source: Ecology - nature.com