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Cited by 41Genetic diversity and population structureGenetic and phenotypic traits in livestockWildlife Ecology and Conservation

High frequency of an otherwise rare phenotype in a small and isolated tiger population

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Sagar, Vinay, Kaelin, Christopher B., Natesh, Meghana, Reddy, P. Anuradha, Mohapatra, Rajesh K., Chhattani, Himanshu, Thatte, Prachi, Vaidyanathan, Srinivas +10 more·2021·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.2025273118PMC PMC8488692
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Abstract

Significance: Small and isolated populations have low genetic variation due to founding bottlenecks and genetic drift. Few empirical studies demonstrate visible phenotypic change associated with drift using genetic data in endangered species. We used genomic analyses of a captive tiger pedigree to identify the genetic basis for a rare trait, pseudomelanism, in tigers. Genome sequencing and extensive genotyping of noninvasive samples across tiger range revealed unique spatial presence of this allele in the Similipal Tiger Reserve, India. Population genetic analyses confirmed that Similipal is a small and isolated population. Simulations suggest that intense founding bottlenecks could result in the observed patterns, implicating drift. Our study highlights ongoing phenotypic evolution, potentially from human-induced fragmentation, in endangered large carnivore populations.

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  • All white pseudo-melanistic and pseudo-melanistic tigers trace their ancestry to tigers from the Similipal Tiger Reserve.

    “All white pseudo-melanistic and pseudo-melanistic trace their ancestry to tigers from the Similipal Tiger Reserve [34].”

    From Tiger colour morphs in zoos raise conservation and welfare concerns (2026) · cites this paper as [34]

    The Discussion section “A Novel Mutation for Pseudomelanism in Tigers” says all captive pseudomelanistic tigers have ancestral links to one individual from Similipal. It does not establish this for all pseudomelanistic tigers or specifically for white pseudomelanistic tigers; the “Drift and Isolation” section also notes historic sightings elsewhere and says the associated allele did not originate in Similipal. Page numbers are unavailable in our copy. (LLM, conf=0.86)

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  • There are currently pseudo-melanistic tigers in three captive populations in India.

    “There are currently pseudo-melanistic tigers in three captive populations in India [34].”

    From Tiger colour morphs in zoos raise conservation and welfare concerns (2026) · cites this paper as [34]

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Research works printed but not linked: 73

  1. [5]Khan A Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers bioRxiv 2021 Accessed 15 June 2021 [Preprint], https://doi.org/10.2021.05.18.444660 10.1073/pnas.2023018118 34848534 PMC8670471 · DOI
  2. [7]Lynch M Conery J Bürger R Mutational meltdowns in sexual populations Evolution 1995 49 1067 1080 28568521
  3. [11]Kimura M Solution of a process of random genetic drift with a continuous model Proc Natl Acad Sci USA 1955 41 144 150 10.1073/pnas.41.3.144 16589632 PMC528040 · DOI
  4. [12]Oxford GS Genetic drift within a protected polymorphism: Enigmatic variation in color-morph frequencies in the candy-stripe spider, Enoplognatha ovata Evolution 2005 59 2170 2184 16405161
  5. [13]O’Hara RB Comparing the effects of genetic drift and fluctuating selection on genotype frequency changes in the scarlet tiger moth Proc Biol Sci 2005 272 211 217 10.1098/rspb.2004.2929 15695213 PMC1634953 · DOI
  6. [14]Hoffman EA Schueler FW Jones AG Blouin MS An analysis of selection on a colour polymorphism in the northern leopard frog Mol Ecol 2006 15 2627 2641 16842432
  7. [15]Gray SM McKinnon JS Linking color polymorphism maintenance and speciation Trends Ecol Evol 2007 22 71 79 17055107
  8. [16]Gershony LC Who’s behind that mask and cape? The Asian leopard cat’s Agouti (ASIP) allele likely affects coat colour phenotype in the Bengal cat breed Anim Genet 2014 45 893 897 10.1111/age.12206 25143047 PMC4211939 · DOI
  9. [17]Ishida Y A homozygous single-base deletion in MLPH causes the dilute coat phenotype in the domestic cat Genomics 2006 88 698 705 16860533
  10. [18]Hubbard JK Uy JAC Hauber ME Hoekstra HE Safran RJ Vertebrate pigmentation: From underlying genes to adaptive function Trends Genet 2010 26 231 239 20381892
  11. [19]Takeuchi S Suzuki H Yabuuchi M Takahashi S A possible involvement of mela-nocortin 1-receptor in regulating feather color pigmentation in the chicken Bio-chim Biophys Acta 1996 1308 164 168 8764834
  12. [20]Bellone RR Differential gene expression of TRPM1, the potential cause of congenital stationary night blindness and coat spotting patterns (LP) in the Appaloosa horse (Equus caballus) Genetics 2008 179 1861 1870 10.1534/genetics.108.088807 18660533 PMC2516064 · DOI
  13. [21]Millar SE Miller MW Stevens ME Barsh GS Expression and transgenic studies of the mouse agouti gene provide insight into the mechanisms by which mammalian coat color patterns are generated Development 1995 121 3223 3232 7588057
  14. [22]Bennett DC Lamoreux ML The color loci of mice−A genetic century Pigment Cell Res 2003 16 333 344 12859616
  15. [23]Roulin A The evolution, maintenance and adaptive function of genetic colour polymorphism in birds Biol Rev Camb Philos Soc 2004 79 815 848 15682872
  16. [24]Protas ME Patel NH Evolution of coloration patterns Annu Rev Cell Dev Biol 2008 24 425 446 18593352
  17. [25]Tully G Genotype versus phenotype: Human pigmentation Forensic Sci Int Genet 2007 1 105 110 19083738
  18. [28]Hedrick PW Ritland K Population genetics of the white-phased “spirit” black bear of British Columbia Evolution 2012 66 305 313 22276530
  19. [29]Peters L Born blonde: A recessive loss-of-function mutation in the melanocortin 1 receptor is associated with cream coat coloration in Antarctic fur seals Ecol Evol 2016 6 5705 5717 10.1002/ece3.2290 27547348 PMC4983585 · DOI
  20. [30]Hauser-Davis RA Lemos LS Moreira SC Siciliano S A scientometric review on Leucism in wild dolphins Bol do Lab Hidrobiol 2020 30 1 9
  21. [31]Burnett KG Durica DS Mykles DL Stillman JH Schmidt C Recommendations for advancing genome to phenome research in non-model organisms Integr Comp Biol 2020 60 397 401 32497207
  22. [33]Xu X The genetics of tiger pelage color variations Cell Res 2017 27 954 957 10.1038/cr.2017.32 28281538 PMC5518981 · DOI · Paper page
  23. [37]Eizirik E Trindade FJ Genetics and evolution of mammalian coat pigmentation Annu Rev Anim Biosci 2021 9 125 148 33207915
  24. [38]Kaelin CB Specifying and sustaining pigmentation patterns in domestic and wild cats Science 2012 337 1536 1541 10.1126/science.1220893 22997338 PMC3709578 · DOI
  25. [39]Luo SJ Liu YC Xu X Tigers of the world: Genomics and conservation Annu Rev Anim Biosci 2019 7 521 548 30762441
  26. [40]Armstrong EE Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection Mol Biol Evol 2021 38 2366 2379 10.1093/molbev/msab032 33592092 PMC8136513 · DOI
  27. [41]Khan A Are shed hair genomes the most effective noninvasive resource for estimating relationships in the wild? Ecol Evol 2020 10 4583 4594 10.1002/ece3.6157 32551045 PMC7297754 · DOI
  28. [45]Natesh M Empowering conservation practice with efficient and economical genotyping from poor quality samples Methods Ecol Evol 2019 10 853 859 10.1111/2041-210X.13173 31511786 PMC6738957 · DOI
  29. [46]Purcell S PLINK: A tool set for whole-genome association and population-based linkage analyses Am J Hum Genet 2007 81 559 575 10.1086/519795 17701901 PMC1950838 · DOI · Paper page
  30. [47]Natesh M Conservation priorities for endangered Indian tigers through a genomic lens Sci Rep 2017 7 9614 10.1038/s41598-017-09748-3 28851952 PMC5575265 · DOI
  31. [48]Pritchard JK Stephens M Donnelly P Inference of population structure using multilocus genotype data Genetics 2000 155 945 959 10.1093/genetics/155.2.945 10835412 PMC1461096 · DOI
  32. [51]Karanth KU Nichols JD Kumar NS Hines JE Assessing tiger population dynamics using photographic capture-recapture sampling Ecology 2006 87 2925 2937 17168036
  33. [53]Laustsen PG Vang S Kristensen T Mutational analysis of the active site of human insulin-regulated aminopeptidase Eur J Biochem 2001 268 98 104 11121108
  34. [54]Vazeux G Wang J Corvol P Llorens-Cortès C Identification of glutamate residues essential for catalytic activity and zinc coordination in aminopeptidase A J Biol Chem 1996 271 9069 9074 8621556
  35. [55]Maruyama M Laeverin/aminopeptidase Q, a novel bestatin-sensitive leucine aminopeptidase belonging to the M1 family of aminopeptidases J Biol Chem 2007 282 20088 20096 17525158
  36. [56]Peer WA The role of multifunctional M1 metallopeptidases in cell cycle progression Ann Bot 2011 107 1171 1181 10.1093/aob/mcq265 21258033 PMC3091800 · DOI
  37. [57]Thompson MW Govindaswami M Hersh LB Mutation of active site residues of the puromycin-sensitive aminopeptidase: Conversion of the enzyme into a catalytically inactive binding protein Arch Biochem Biophys 2003 413 236 242 12729622
  38. [58]Fukasawa KM Aminopeptidase B is structurally related to leukotriene-A4 hydrolase but is not a bifunctional enzyme with epoxide hydrolase activity Biochem J 1999 339 497 502 10215585 PMC1220182
  39. [59]Swartz MD Small sample properties of rare variant analysis methods BMC Proc 2014 8 suppl. 1 S13 10.1186/1753-6561-8-S1-S13 25519366 PMC4143716 · DOI
  40. [60]Cooper GM NISC Comparative Sequencing Program, Distribution and intensity of constraint in mammalian genomic sequence Genome Res 2005 15 901 913 10.1101/gr.3577405 15965027 PMC1172034 · DOI · Paper page
  41. [61]Rentzsch P Witten D Cooper GM Shendure J Kircher M CADD: predicting the deleteriousness of variants throughout the human genome Nucleic Acids Res 2019 47 D1 D886 D894 10.1093/nar/gky1016 30371827 PMC6323892 · DOI · Paper page
  42. [62]Huber CD Kim BY Lohmueller KE Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution PLoS Genet 2020 16 e1008827 10.1371/journal.pgen.1008827 32469868 PMC7286533 · DOI
  43. [63]Fung T Keenan K Confidence intervals for population allele frequencies: the general case of sampling from a finite diploid population of any size PLoS One 2014 9 e85925 10.1371/journal.pone.0085925 24465792 PMC3897575 · DOI
  44. [65]Harihar A Population density modelling of mixed polymorphic phenotypes: An application of spatial mark-resight models Anim Conserv 2021 10.1111/acv.12677 · DOI
  45. [70]Naha D Ranging, activity and habitat use by tigers in the Mangrove Forests of the Sundarban PLoS One 2016 11 e0152119 10.1371/journal.pone.0152119 27049644 PMC4822765 · DOI
  46. [73]Joshi A Vaidyanathan S Mondol S Edgaonkar A Ramakrishnan U Connectivity of tiger (Panthera tigris) populations in the human-influenced forest mosaic of Central India PLoS One 2013 8 e77980 10.1371/journal.pone.0077980 24223132 PMC3819329 · DOI
  47. [75]Venables SK It’s not all black and white: Investigating colour polymorphism in manta rays across Indo-Pacific populations Proc Biol Sci 2019 286 20191879 10.1098/rspb.2019.1879 31594509 PMC6790782 · DOI
  48. [76]Velo-Antón G Becker CG Cordero-Rivera A Turtle carapace anomalies: The roles of genetic diversity and environment PLoS One 2011 6 e18714 10.1371/journal.pone.0018714 21533278 PMC3075271 · DOI
  49. [78]Robinson JA Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction Sci Adv 2019 5 eaau0757 10.1126/sciadv.aau0757 31149628 PMC6541468 · DOI · Paper page
  50. [80]Johnson WE Genetic restoration of the Florida panther Science 2010 329 1641 1645 10.1126/science.1192891 20929847 PMC6993177 · DOI · Paper page
  51. [81]Nielsen JF Inbreeding and inbreeding depression of early life traits in a cooperative mammal Mol Ecol 2012 21 2788 2804 22497583
  52. [82]Norén K Godoy E Dalén L Meijer T Angerbjörn A Inbreeding depression in a critically endangered carnivore Mol Ecol 2016 25 3309 3318 27135988
  53. [84]da Silva LG Mapping black panthers: Macroecological modeling of melanism in leopards (Panthera pardus) PLoS One 2017 12 e0170378 10.1371/journal.pone.0170378 28379961 PMC5381760 · DOI
  54. [86]Endler JA Natural selection on color patterns in Poecilia reticulata Evolution 1980 34 76 91 28563214
  55. [87]Narum SR Hess JE Comparison of F(ST) outlier tests for SNP loci under selection Mol Ecol Resour 2011 11 184 194 21429174
  56. [88]Lotterhos KE Whitlock MC Evaluation of demographic history and neutral parameterization on the performance of FST outlier tests Mol Ecol 2014 23 2178 2192 10.1111/mec.12725 24655127 PMC4228763 · DOI
  57. [89]Flanagan SP Jones AG Genome-wide selection components analysis in a fish with male pregnancy Evolution 2017 71 1096 1105 28067418
  58. [90]Aguirre-Liguori JA Luna-Sánchez JA Gasca-Pineda J Eguiarte LE Evaluation of the minimum sampling design for population genomic and microsatellite studies: An analysis based on wild maize Front Genet 2020 11 870 10.3389/fgene.2020.00870 33193568 PMC7531271 · DOI
  59. [92]Chen H Hey J Slatkin M A hidden Markov model for investigating recent positive selection through haplotype structure Theor Popul Biol 2015 99 18 30 10.1016/j.tpb.2014.11.001 25446961 PMC4277924 · DOI
  60. [93]Whiteley AR Fitzpatrick SW Funk WC Tallmon DA Genetic rescue to the rescue Trends Ecol Evol 2015 30 42 49 25435267
  61. [94]Hoffmann AA Miller AD Weeks AR Genetic mixing for population management: From genetic rescue to provenancing Evol Appl 2020 14 634 652 10.1111/eva.13154 33767740 PMC7980264 · DOI
  62. [96]Alexander DH Novembre J Lange K Fast model-based estimation of ancestry in unrelated individuals Genome Res 2009 19 1655 1664 10.1101/gr.094052.109 19648217 PMC2752134 · DOI · Paper page
  63. [98]Li H Durbin R Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 2009 25 1754 1760 10.1093/bioinformatics/btp324 19451168 PMC2705234 · DOI · Paper page
  64. [99]Li H A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data Bioinformatics 2011 27 2987 2993 10.1093/bioinformatics/btr509 21903627 PMC3198575 · DOI
  65. [102]Abecasis GR Cherny SS Cookson WO Cardon LR Merlin—rapid analysis of dense genetic maps using sparse gene flow trees Nat Genet 2002 30 97 101 11731797
  66. [104]McKenna A The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data Genome Res 2010 20 1297 1303 10.1101/gr.107524.110 20644199 PMC2928508 · DOI · Paper page
  67. [105]Danecek P 1000 Genomes Project Analysis Group The variant call format and VCFtools Bioinformatics 2011 27 2156 2158 10.1093/bioinformatics/btr330 21653522 PMC3137218 · DOI
  68. [106]Peakall ROD Smouse PE genalex 6: Genetic analysis in Excel. Population genetic software for teaching and research Mol Ecol Notes 2006 6 288 295 10.1093/bioinformatics/bts460 22820204 PMC3463245 · DOI
  69. [107]Peakall R Smouse PE GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research—An update Bioinformatics 2012 28 2537 2539 22820204 PMC3463245
  70. [108]Ugozzoli L Wallace RB Allele-specific polymerase chain reaction Methods 1991 2 42 48 1572640
  71. [109]Jombart T adegenet: A R package for the multivariate analysis of genetic markers Bioinformatics 2008 24 1403 1405 18397895
  72. [110]Paradis E pegas: An R package for population genetics with an integrated-modular approach Bioinformatics 2010 26 419 420 20080509
  73. [111]Kopelman NM Mayzel J Jakobsson M Rosenberg NA Mayrose I Clumpak: a program for identifying clustering modes and packaging population structure inferences across K Mol Ecol Resour 2015 15 1179 1191 10.1111/1755-0998.12387 25684545 PMC4534335 · DOI

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Authors
Sagar, V., Kaelin, C. B., Natesh, M., Reddy, P. A., Mohapatra, R. K., Chhattani, H., Thatte, P., Vaidyanathan, S., Biswas, S., Bhatt, S., Paul, S., Jhala, Y. V., Verma, M. M., Pandav, B., Mondol, S., Barsh, G. S., Swain, D., & Ramakrishnan, U.
Affiliations
  • Tata Institute of Fundamental Research (IN)
  • HudsonAlpha Institute for Biotechnology (US)
  • Centre for Cellular and Molecular Biology (IN)
  • Nandankanan Biological Park, Bhubaneswar 754005, India;
  • WWF-India (IN)
  • Foundation for Ecological Research, Advocacy and Learning, Auroville Post, Tamil Nadu 605101 India;
  • Wildlife Institute of India (IN)
  • Odisha Forest Department, Bhubaneswar 751023, India;
  • Wildlife Institute of India, Dehradun 248001, India;
  • State Forest Research Institute (IN)
  • Former Member Secretary, National Tiger Conservation Authority, New Delhi 110003, India;
Corresponding author
  • Sagar, Vinay
  • Ramakrishnan, Uma
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2021-09-13
Volume
118
Issue
39
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.2025273118
PMC
PMC8488692
OpenAlex
W3201045580
Cited by
41
References
4
Citations by year
2026: 8 · 2025: 10 · 2024: 9 · 2023: 3 · 2022: 7 · 2021: 4
FWCI
3.25
Type
journal article
Language
en
Open access
Licence
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Wellcome Trust
  • Tata Institute of Fundamental Research (RTI4006)
  • Department of Biotechnology, Ministry of Science and Technology, India (RTI 4006)
  • Department of Atomic Energy, Government of India (RTI 4006, D-TFR-5.04-0900)
  • The Wellcome Trust DBT India Alliance (IA/S/16/2/502714)
  • Directorate for Biological Sciences
  • National Centre for Biological Sciences (RTI 4006)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
  • Physical Sciences › Environmental Science › Ecology › Wildlife Ecology and Conservation
Keywords
tiger, genetic drift, founder effect, small isolated populations, phenotypic evolution, non-invasive genetic sampling
MeSH terms
Amino Acid Sequence, Animals, Conservation of Natural Resources, Biological Evolution, Genetics, Population, Genotype, India, Melanosis, Phenotype, Genetic Variation, Genome, Sequence Homology, Microsatellite Repeats, Genetic Drift, Tigers, Endangered Species

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