1932

Abstract

Until now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-animal-061220-023138
2021-02-15
2024-12-07
Loading full text...

Full text loading...

/deliver/fulltext/animal/9/1/annurev-animal-061220-023138.html?itemId=/content/journals/10.1146/annurev-animal-061220-023138&mimeType=html&fmt=ahah

Literature Cited

  1. 1. 
    Mikkelsen T, Hillier L, Eichler E, Zody M, Jaffe D et al. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:705569–87
    [Google Scholar]
  2. 2. 
    Varki A, Altheide TK. 2005. Comparing the human and chimpanzee genomes: searching for needles in a haystack. Genome Res 15:121746–58
    [Google Scholar]
  3. 3. 
    Kitzmiller v. Dover Area School District 400 F. Supp. 2d 707 (M.D. Pa 2005)
  4. 4. 
    Marques-Bonet T, Ryder OA, Eichler EE 2009. Sequencing primate genomes: What have we learned. Annu. Rev. Genom. Hum. Genet. 10:355–86
    [Google Scholar]
  5. 5. 
    Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV et al. 2011. Comparative and demographic analysis of orang-utan genomes. Nature 469:7331529–33
    [Google Scholar]
  6. 6. 
    Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483:7388169–75
    [Google Scholar]
  7. 7. 
    Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR et al. 2012. The bonobo genome compared with the chimpanzee and human genomes. Nature 486:7404527–31
    [Google Scholar]
  8. 8. 
    Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B et al. 2014. Gibbon genome and the fast karyotype evolution of small apes. Nature 513:7517195–201
    [Google Scholar]
  9. 9. 
    Dennis MY, Harshman L, Nelson BJ, Penn O, Cantsilieris S et al. 2017. The evolution and population diversity of human-specific segmental duplications. Nat. Ecol. Evol. 1:0069
    [Google Scholar]
  10. 10. 
    Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z et al. 2009. A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457:7231877–81
    [Google Scholar]
  11. 11. 
    Sudmant PH, Huddleston J, Catacchio CR, Malig M, Hillier LW et al. 2013. Evolution and diversity of copy number variation in the great ape lineage. Genome Res 23:91373–82
    [Google Scholar]
  12. 12. 
    Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L et al. 2015. Comprehensive identification and analysis of human accelerated regulatory DNA. Genome Res 25:91245–55
    [Google Scholar]
  13. 13. 
    Doan RN, Bae B-I, Cubelos B, Chang C, Hossain AA et al. 2016. Mutations in human accelerated regions disrupt cognition and social behavior. Cell 167:2341–54.e12
    [Google Scholar]
  14. 14. 
    Kamm GB, Pisciottano F, Kliger R, Franchini LF 2013. The developmental brain gene NPAS3 contains the largest number of accelerated regulatory sequences in the human genome. Mol. Biol. Evol. 30:51088–102
    [Google Scholar]
  15. 15. 
    Charrier C, Joshi K, Coutinho-Budd J, Kim J-E, Lambert N et al. 2012. Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation. Cell 149:4923–35
    [Google Scholar]
  16. 16. 
    Dennis MY, Nuttle X, Sudmant PH, Antonacci F, Graves TA et al. 2012. Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell 149:4912–22
    [Google Scholar]
  17. 17. 
    Florio M, Albert M, Taverna E, Namba T, Brandl H et al. 2015. Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion. Science 347:62291465–70
    [Google Scholar]
  18. 18. 
    Ju X-C, Hou Q-Q, Sheng A-L, Wu K-Y, Zhou Y et al. 2016. The hominoid-specific gene TBC1D3 promotes generation of basal neural progenitors and induces cortical folding in mice. eLife 5:e18197
    [Google Scholar]
  19. 19. 
    McLean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD et al. 2011. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471:7337216–19
    [Google Scholar]
  20. 20. 
    Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S et al. 2018. High-resolution comparative analysis of great ape genomes. Science 360:6393eaar6343
    [Google Scholar]
  21. 21. 
    Indjeian VB, Kingman GA, Jones FC, Guenther CA, Grimwood J et al. 2016. Evolving new skeletal traits by cis-regulatory changes in bone morphogenetic proteins. Cell 164:1–245–56
    [Google Scholar]
  22. 22. 
    Harding JD. 2017. Genomic tools for the use of nonhuman primates in translational research. ILAR J 58:159–68
    [Google Scholar]
  23. 23. 
    Landsteiner K, Wiener AS. 1940. An agglutinable factor in human blood recognized by immune sera for rhesus blood. Proc. Soc. Exp. Biol. Med. 43:1223
    [Google Scholar]
  24. 24. 
    Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM et al. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:5822222–34
    [Google Scholar]
  25. 25. 
    Yan G, Zhang G, Fang X, Zhang Y, Li C et al. 2011. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat. Biotechnol. 29:111019–23
    [Google Scholar]
  26. 26. 
    Rogers J, Raveendran M, Harris RA, Mailund T, Leppälä K et al. 2019. The comparative genomics and complex population history of Papio baboons. Sci. Adv 5:1eaau6947
    [Google Scholar]
  27. 27. 
    Warren WC, Jasinska AJ, García-Pérez R, Svardal H, Tomlinson C et al. 2015. The genome of the vervet (Chlorocebus aethiops sabaeus). Genome Res 25:121921–33
    [Google Scholar]
  28. 28. 
    Marmoset Genome Seq. Anal. Consort. 2014. The common marmoset genome provides insight into primate biology and evolution. Nat. Genet 46:8850–57
    [Google Scholar]
  29. 29. 
    Trichel AM, Rajakumar PA, Murphey‐Corb M 2002. Species-specific variation in SIV disease progression between Chinese and Indian subspecies of rhesus macaque. J. Med. Primatol. 31:4–5171–78
    [Google Scholar]
  30. 30. 
    Kang Y, Chu C, Wang F, Niu Y 2019. CRISPR/Cas9-mediated genome editing in nonhuman primates. Dis. Models Mech. 12:10dmm039982
    [Google Scholar]
  31. 31. 
    Estrada A, Garber PA, Rylands AB, Roos C, Fernandez-Duque E et al. 2017. Impending extinction crisis of the world's primates: why primates matter. Sci. Adv 3:1e1600946
    [Google Scholar]
  32. 32. 
    Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL et al. 2013. Great ape genetic diversity and population history. Nature 499:7459471–75
    [Google Scholar]
  33. 33. 
    Zhou X, Wang B, Pan Q, Zhang J, Kumar S et al. 2014. Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history. Nat. Genet. 46:121303–10
    [Google Scholar]
  34. 34. 
    Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q et al. 2015. Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding. Science 348:6231242–45
    [Google Scholar]
  35. 35. 
    Nater A, Mattle-Greminger MP, Nurcahyo A, Nowak MG, de Manuel M et al. 2017. Morphometric, behavioral, and genomic evidence for a new orangutan species. Curr. Biol. 27:223487–98.e10
    [Google Scholar]
  36. 36. 
    van der Valk T, Díez-del-Molino D, Marques-Bonet T, Guschanski K, Dalén L 2019. Historical genomes reveal the genomic consequences of recent population decline in eastern gorillas. Curr. Biol. 29:1165–70.e6
    [Google Scholar]
  37. 37. 
    de Manuel M, Kuhlwilm M, Frandsen P, Sousa VC, Desai T et al. 2016. Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 354:6311477–81
    [Google Scholar]
  38. 38. 
    Robinson JA, Räikkönen J, Vucetich LM, Vucetich JA, Peterson RO et al. 2019. Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction. Sci. Adv. 5:5eaau0757
    [Google Scholar]
  39. 39. 
    Lawler RR. 2018. Emerging and enduring issues in primate conservation genetics. Annu. Rev. Anthropol. 47:395–415
    [Google Scholar]
  40. 40. 
    Mason VC, Li G, Minx P, Schmitz J, Churakov G et al. 2016. Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates. Sci. Adv. 2:8e1600633
    [Google Scholar]
  41. 41. 
    Janecka JE, Miller W, Pringle TH, Wiens F, Zitzmann A et al. 2007. Molecular and genomic data identify the closest living relative of primates. Science 318:5851792–94
    [Google Scholar]
  42. 42. 
    Smith GE. 1912. The evolution of man Annu. Rep., Smithson. Inst Washington, DC:
    [Google Scholar]
  43. 43. 
    Jones FW. 1916. Arboreal Man London: E. Arnold
    [Google Scholar]
  44. 44. 
    Sussman RW, Raven PH. 1978. Pollination by lemurs and marsupials: an archaic coevolutionary system. Science 200:4343731–36
    [Google Scholar]
  45. 45. 
    Cartmill M. 1974. Rethinking primate origins. Science 184:4135436–43
    [Google Scholar]
  46. 46. 
    Orkin JD, Pontzer H. 2011. The Narrow Niche hypothesis: Gray squirrels shed new light on primate origins. Am. J. Phys. Anthropol. 144:4617–24
    [Google Scholar]
  47. 47. 
    Rasmussen DT. 1990. Primate origins: lessons from a neotropical marsupial. Am. J. Primatol. 22:4263–77
    [Google Scholar]
  48. 48. 
    Szalay FS, Dagosto M. 1980. Locomotor adaptations as reflected on the humerus of paleogene primates. Folia Primatol 34:1–21–45
    [Google Scholar]
  49. 49. 
    Lehman SM, Fleagle JG. 2006. Biogeography and primates: a review. Primate Biogeography: Progress and Prospects SM Lehman, JG Fleagle 1–58 Boston: Springer US
    [Google Scholar]
  50. 50. 
    Gouveia SF, Villalobos F, Dobrovolski R, Beltrão-Mendes R, Ferrari SF 2014. Forest structure drives global diversity of primates. J. Anim. Ecol. 83:61523–30
    [Google Scholar]
  51. 51. 
    Seiffert ER, Tejedor MF, Fleagle JG, Novo NM, Cornejo FM et al. 2020. A parapithecid stem anthropoid of African origin in the Paleogene of South America. Science 368:6487194–97
    [Google Scholar]
  52. 52. 
    Houle A. 1998. Floating islands: a mode of long-distance dispersal for small and medium-sized terrestrial vertebrates. Divers. Distrib. 4:5/6201–16
    [Google Scholar]
  53. 53. 
    Bond M, Tejedor MF, Campbell KE Jr, Chornogubsky L, Novo N, Goin F 2015. Eocene primates of South America and the African origins of New World monkeys. Nature 520:7548538–41
    [Google Scholar]
  54. 54. 
    Gunnell GF, Boyer DM, Friscia AR, Heritage S, Manthi FK et al. 2018. Fossil lemurs from Egypt and Kenya suggest an African origin for Madagascar's aye-aye. Nat. Commun. 9:3193
    [Google Scholar]
  55. 55. 
    Kappeler PM. 2000. Lemur origins: Rafting by groups of hibernators. Folia Primatol 71:6422–25
    [Google Scholar]
  56. 56. 
    Fleagle JG. 2013. Primate Adaptation and Evolution San Diego, CA: Academic
    [Google Scholar]
  57. 57. 
    Seiffert ER, Perry JMG, Simons EL, Boyer DM 2009. Convergent evolution of anthropoid-like adaptations in Eocene adapiform primates. Nature 461:72671118–21
    [Google Scholar]
  58. 58. 
    Yoder AD, Yang Z. 2004. Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Mol. Ecol. 13:4757–73
    [Google Scholar]
  59. 59. 
    Martin RD. 2000. Origins, diversity and relationships of lemurs. Int. J. Primatol. 21:1021–49
    [Google Scholar]
  60. 60. 
    Kappeler PM, Fichtel C. 2015. Eco-evo-devo of the lemur syndrome: Did adaptive behavioral plasticity get canalized in a large primate radiation. Front. Zool. 12:Suppl. 1S15
    [Google Scholar]
  61. 61. 
    Burney DA, Burney LP, Godfrey LR, Jungers WL, Goodman SM et al. 2004. A chronology for late prehistoric Madagascar. J. Hum. Evol. 47:1–225–63
    [Google Scholar]
  62. 62. 
    Walker A. 1969. The locomotion of the lorises, with special reference to the potto. Afr. J. Ecol. 7:11–5
    [Google Scholar]
  63. 63. 
    Rasmussen DT, Izard MK. 1988. Scaling of growth and life history traits relative to body size, brain size, and metabolic rate in lorises and galagos (Lorisidae, primates). Am. J. Phys. Anthropol. 75:3357–67
    [Google Scholar]
  64. 64. 
    Groves C, Shekelle M. 2010. The genera and species of Tarsiidae. Int. J. Primatol. 31:61071–82
    [Google Scholar]
  65. 65. 
    Rosenberger AL. 2010. The skull of Tarsius: functional morphology, eyeballs, and the nonpursuit predatory lifestyle. Int. J. Primatol. 31:61032–54
    [Google Scholar]
  66. 66. 
    Schmitz J, Noll A, Raabe CA, Churakov G, Voss R et al. 2016. Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. Nat. Commun. 7:12997
    [Google Scholar]
  67. 67. 
    Lynch Alfaro J. 2017. The monkeying of the Americas: primate biogeography in the Neotropics. Annu. Rev. Anthropol. 46:317–36
    [Google Scholar]
  68. 68. 
    Bezanson M. 2012. The ontogeny of prehensile-tail use in Cebus capucinus and Alouatta palliata.Am. J. Primatol 74:8770–82
    [Google Scholar]
  69. 69. 
    Hamrick MW. 1998. Functional and adaptive significance of primate pads and claws: evidence from New World anthropoids. Am. J. Phys. Anthropol. 106:2113–27
    [Google Scholar]
  70. 70. 
    Ankel-Simons F, Rasmussen DT. 2008. Diurnality, nocturnality, and the evolution of primate visual systems. Am. J. Phys. Anthropol. 137:Suppl. 47100–17
    [Google Scholar]
  71. 71. 
    Melin AD, Khetpal V, Matsushita Y, Zhou K, Campos FA et al. 2017. Howler monkey foraging ecology suggests convergent evolution of routine trichromacy as an adaptation for folivory. Ecol. Evol. 7:51421–34
    [Google Scholar]
  72. 72. 
    Proffitt T, Luncz LV, Falótico T, Ottoni EB, de la Torre I, Haslam M 2016. Wild monkeys flake stone tools. Nature 539:762785–88
    [Google Scholar]
  73. 73. 
    Woods R, Turvey ST, Brace S, MacPhee RDE, Barnes I 2018. Ancient DNA of the extinct Jamaican monkey Xenothrix reveals extreme insular change within a morphologically conservative radiation. PNAS 115:5012769–74
    [Google Scholar]
  74. 74. 
    Mitani JC, Call J, Kappeler PM, Palombit RA, Silk JB 2012. The Evolution of Primate Societies Chicago: Univ. Chicago Press
    [Google Scholar]
  75. 75. 
    Fuentes A. 2012. Ethnoprimatology and the anthropology of the human-primate interface. Annu. Rev. Anthropol. 41:101–17
    [Google Scholar]
  76. 76. 
    Yu L, Wang G-D, Ruan J, Chen Y-B, Yang C-P et al. 2016. Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation. Nat. Genet. 48:8947–52
    [Google Scholar]
  77. 77. 
    Quan R-C, Ren G, Behm JE, Wang L, Huang Y et al. 2011. Why does Rhinopithecus bieti prefer the highest elevation range in winter? A test of the sunshine hypothesis. PLOS ONE 6:9e24449
    [Google Scholar]
  78. 78. 
    Cords M. 2012. The behavior, ecology, and social evolution of cercopithecine monkeys. The Evolution of Primate Societies J Mitani, J Call, PM Kappeler, RA Palombit, JB Silk 91–112 Chicago: Univ. Chicago Press
    [Google Scholar]
  79. 79. 
    Winters S, Allen WL, Higham JP 2020. The structure of species discrimination signals across a primate radiation. eLife 9:e47428
    [Google Scholar]
  80. 80. 
    Begun DR. 2010. Miocene hominids and the origins of the African apes and humans. Annu. Rev. Anthropol. 39:67–84
    [Google Scholar]
  81. 81. 
    DeCasien AR, Williams SA, Higham JP 2017. Primate brain size is predicted by diet but not sociality. Nat. Ecol. Evol. 1:0112
    [Google Scholar]
  82. 82. 
    Moyà-Solà S, Köhler M. 1996. A Dryopithecus skeleton and the origins of great-ape locomotion. Nature 379:6561156–59
    [Google Scholar]
  83. 83. 
    Street SE, Navarrete AF, Reader SM, Laland KN 2017. Coevolution of cultural intelligence, extended life history, sociality, and brain size in primates. PNAS 114:307908–14
    [Google Scholar]
  84. 84. 
    Michilsens F, Vereecke EE, D'Août K, Aerts P 2009. Functional anatomy of the gibbon forelimb: adaptations to a brachiating lifestyle. J. Anat. 215:3335–54
    [Google Scholar]
  85. 85. 
    Fuentes A. 2000. Hylobatid communities: changing views on pair bonding and social organization in hominoids. Am. J. Phys. Anthropol. 113:Suppl. 3133–60
    [Google Scholar]
  86. 86. 
    Smith RJ, Jungers WL. 1997. Body mass in comparative primatology. J. Hum. Evol. 32:6523–59
    [Google Scholar]
  87. 87. 
    Musgrave S, Morgan D, Lonsdorf E, Mundry R, Sanz C 2016. Tool transfers are a form of teaching among chimpanzees. Sci. Rep. 6:34783
    [Google Scholar]
  88. 88. 
    Kaplan H, Hill K, Lancaster J, Magdalena Hurtado A 2000. A theory of human life history evolution: diet, intelligence, and longevity. Evol. Anthropol. 9:4156–85
    [Google Scholar]
  89. 89. 
    Schwitzer C, Mittermeier R, Rylands A, Chiozza F, Williamson L et al. 2019. Primates in Peril: The World's Most Endangered Primates 20182020 Washington, DC: Glob. Wildl. Conserv.
    [Google Scholar]
  90. 90. 
    Mace GM, Collar NJ, Gaston KJ, Hilton-Taylor C, Akçakaya HR et al. 2008. Quantification of extinction risk: IUCN's system for classifying threatened species. Conserv. Biol. 22:61424–42
    [Google Scholar]
  91. 91. 
    Leendertz SAJ, Wich SA, Ancrenaz M, Bergl RA, Gonder MK et al. 2017. Ebola in great apes—current knowledge, possibilities for vaccination, and implications for conservation and human health. Mamm. Rev. 47:298–111
    [Google Scholar]
  92. 92. 
    Laurance WF, Sayer J, Cassman KG 2014. Agricultural expansion and its impacts on tropical nature. Trends Ecol. Evol. 29:2107–16
    [Google Scholar]
  93. 93. 
    Cowlishaw G, Dunbar RIM. 2000. Primate Conservation Biology. Chicago: Univ. Chicago Press
    [Google Scholar]
  94. 94. 
    Purvis A, Gittleman JL, Cowlishaw G, Mace GM 2000. Predicting extinction risk in declining species. Proc. R. Soc. Lond. B Biol. Sci. 267:1947–52
    [Google Scholar]
  95. 95. 
    Brockington D, Igoe J, Schmidt-Soltau K 2006. Conservation, human rights, and poverty reduction. Conserv. Biol. 20:1250–52
    [Google Scholar]
  96. 96. 
    Garland E. 2008. The elephant in the room: confronting the colonial character of wildlife conservation in Africa. Afr. Stud. Rev. 51:351–74
    [Google Scholar]
  97. 97. 
    Fuentes A, Cortez AD, Peterson JV 2016. Ethnoprimatology and conservation: applying insights and developing practice. Ethnoprimatology: Primate Conservation in the 21st Century MT Waller 1–19 Cham, Switz: Springer Int. Publ.
    [Google Scholar]
  98. 98. 
    Shaffer CA, Milstein MS, Yukuma C, Marawanaru E, Suse P 2017. Sustainability and comanagement of subsistence hunting in an indigenous reserve in Guyana. Conserv. Biol. 31:51119–31
    [Google Scholar]
  99. 99. 
    De Queiroz K. 2007. Species concepts and species delimitation. Syst. Biol. 56:6879–86
    [Google Scholar]
  100. 100. 
    Ryder O. 1986. Species conservation and systematics: the dilemma of subspecies. Trends Ecol. Evol. 1:19–10
    [Google Scholar]
  101. 101. 
    Casacci LP, Barbero F, Balletto E 2014. The “evolutionarily significant unit” concept and its applicability in biological conservation. Ital. J. Zool. 81:2182–93
    [Google Scholar]
  102. 102. 
    Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475:7357493–96
    [Google Scholar]
  103. 103. 
    Terhorst J, Kamm JA, Song YS 2017. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat. Genet. 49:2303–9
    [Google Scholar]
  104. 104. 
    Schiffels S, Durbin R. 2014. Inferring human population size and separation history from multiple genome sequences. Nat. Genet. 46:8919–25
    [Google Scholar]
  105. 105. 
    Ceballos FC, Joshi PK, Clark DW, Ramsay M, Wilson JF 2018. Runs of homozygosity: windows into population history and trait architecture. Nat. Rev. Genet. 19:4220–34
    [Google Scholar]
  106. 106. 
    Kuhlwilm M, Han S, Sousa VC, Excoffier L, Marques-Bonet T 2019. Ancient admixture from an extinct ape lineage into bonobos. Nat. Ecol. Evol. 3:6957–65
    [Google Scholar]
  107. 107. 
    Int. Union Conserv. Nat. (IUCN). 2020. The IUCN Red List of Threatened Species. Version 20201 Gland, Switz: IUCN https://www.iucnredlist.org
    [Google Scholar]
  108. 108. 
    Bryant JV, Gottelli D, Zeng X, Hong X, Chan BPL et al. 2016. Assessing current genetic status of the Hainan gibbon using historical and demographic baselines: implications for conservation management of species of extreme rarity. Mol. Ecol. 25:153540–56
    [Google Scholar]
  109. 109. 
    Veeramah KR, Woerner AE, Johnstone L, Gut I, Gut M et al. 2015. Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate Bayesian computation approach. Genetics 200:1295–308
    [Google Scholar]
  110. 110. 
    Wall JD, Schlebusch SA, Alberts SC, Cox LA, Snyder-Mackler N et al. 2016. Genome-wide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons. Mol. Ecol. 25:143469–83
    [Google Scholar]
  111. 111. 
    Mathieson I, Abascal F, Vinner L, Skoglund P, Pomilla C et al. 2020. An ancient baboon genome demonstrates long-term population continuity in Southern Africa. Genome Biol. Evol. 12:4407–12
    [Google Scholar]
  112. 112. 
    Zhong X, Peng J, Shen QS, Chen J-Y, Gao H et al. 2016. RhesusBase PopGateway: genome-wide population genetics atlas in rhesus macaque. Mol. Biol. Evol. 33:51370–75
    [Google Scholar]
  113. 113. 
    Xue C, Raveendran M, Harris RA, Fawcett GL, Liu X et al. 2016. The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences. Genome Res 26:121651–62
    [Google Scholar]
  114. 114. 
    Liu Z, Tan X, Orozco-terWengel P, Zhou X, Zhang L et al. 2018. Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research. GigaScience 7:9giy106
    [Google Scholar]
  115. 115. 
    Southwick CH, Siddiqi MF. 2001. Status, conservation and management of primates in India. ENVIS Bull 1:181–91
    [Google Scholar]
  116. 116. 
    Murray GGR, Soares AER, Novak BJ, Schaefer NK, Cahill JA et al. 2017. Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science 358:6365951–54
    [Google Scholar]
  117. 117. 
    Svardal H, Jasinska AJ, Apetrei C, Coppola G, Huang Y et al. 2017. Ancient hybridization and strong adaptation to viruses across African vervet monkey populations. Nat. Genet. 49:121705–13
    [Google Scholar]
  118. 118. 
    van der Valk T, Gonda CM, Silegowa H, Almanza S, Sifuentes-Romero I et al. 2020. The genome of the endangered dryas monkey provides new insights into the evolutionary history of the vervets. Mol. Biol. Evol. 37:1183–94
    [Google Scholar]
  119. 119. 
    Liu Z, Zhang L, Yan Z, Ren Z, Han F et al. 2020. Genomic mechanisms of physiological and morphological adaptations of limestone langurs to karst habitats. Mol. Biol. Evol. 37:4952–68
    [Google Scholar]
  120. 120. 
    Kuderna LFK, Esteller-Cucala P, Marques-Bonet T 2020. Branching out: what omics can tell us about primate evolution 62:65–71
    [Google Scholar]
  121. 121. 
    Thomas GWC, Wang RJ, Puri A, Harris RA, Raveendran M et al. 2018. Reproductive longevity predicts mutation rates in primates. Curr. Biol. 28:193193–97.e5
    [Google Scholar]
  122. 122. 
    Orkin JD, Montague MJ, Tejada-Martinez D, de Manuel M, del Campo J et al. 2020. The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. PNAS In press
    [Google Scholar]
  123. 123. 
    Meyer WK, Venkat A, Kermany AR, van de Geijn B, Zhang S, Przeworski M 2015. Evolutionary history inferred from the de novo assembly of a nonmodel organism, the blue-eyed black lemur. Mol. Ecol. 24:174392–405
    [Google Scholar]
  124. 124. 
    Larsen PA, Harris RA, Liu Y, Murali SC, Campbell CR et al. 2017. Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). BMC Biol 15:110
    [Google Scholar]
  125. 125. 
    Perry GH, Louis EE, Ratan A, Bedoya-Reina OC, Burhans RC et al. 2013. Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar. PNAS 110:155823–28
    [Google Scholar]
  126. 126. 
    Perry GH, Reeves D, Melsted P, Ratan A, Miller W et al. 2012. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biol. Evol. 4:2126–35
    [Google Scholar]
  127. 127. 
    Williams RC, Blanco MB, Poelstra JW, Hunnicutt KE, Comeault AA, Yoder AD 2020. Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar's hibernating dwarf lemurs. Heredity 124:1236–51
    [Google Scholar]
  128. 128. 
    Hawkins MTR, Culligan RR, Frasier CL, Dikow RB, Hagenson R et al. 2018. Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation. BMC Genom 19:445
    [Google Scholar]
  129. 129. 
    Frandsen P, Fontsere C, Nielsen SV, Hanghøj K, Castejon-Fernandez N et al. 2020. Targeted conservation genetics of the endangered chimpanzee. Heredity 125:15–27
    [Google Scholar]
  130. 130. 
    Watsa M, Erkenswick G, Halloran D, Kane EE, Poirier A et al. 2015. A field protocol for the capture and release of callitrichids. Neotropical Primates 22:259–68
    [Google Scholar]
  131. 131. 
    Eaton MJ, Meyers GL, Kolokotronis S-O, Leslie MS, Martin AP, Amato G 2010. Barcoding bushmeat: molecular identification of Central African and South American harvested vertebrates. Conserv. Genet. 11:41389–404
    [Google Scholar]
  132. 132. 
    Ben-Nun IF, Montague SC, Houck ML, Tran HT, Garitaonandia I et al. 2011. Induced pluripotent stem cells from highly endangered species. Nat. Methods 8:10829–31
    [Google Scholar]
  133. 133. 
    Chiou KL, Bergey CM. 2018. Methylation-based enrichment facilitates low-cost, noninvasive genomic scale sequencing of populations from feces. Sci. Rep. 8:1975
    [Google Scholar]
  134. 134. 
    Hernandez-Rodriguez J, Arandjelovic M, Lester J, de Filippo C, Weihmann A et al. 2018. The impact of endogenous content, replicates and pooling on genome capture from faecal samples. Mol. Ecol. Resour. 18:2319–33
    [Google Scholar]
  135. 135. 
    White LC, Fontsere C, Lizano E, Hughes DA, Angedakin S et al. 2019. A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture. Mol. Ecol. Resour. 19:3609–22
    [Google Scholar]
  136. 136. 
    Améndola-Pimenta M, García-Feria L, Serio-Silva JC, Rico-Gray V 2009. Noninvasive collection of fresh hairs from free-ranging howler monkeys for DNA extraction. Am. J. Primatol. 71:4359–63
    [Google Scholar]
  137. 137. 
    Ozga AT, Webster TH, Gilby IC, Wilson MA, Nockerts RS et al. 2020. Urine as a high-quality source of host genomic DNA from wild populations. Mol. Ecol. Resour. 21170–82
    [Google Scholar]
  138. 138. 
    Orkin JD, Campos FA, Myers MS, Cheves Hernandez SE, Guadamuz A, Melin AD 2019. Seasonality of the gut microbiota of free-ranging white-faced capuchins in a tropical dry forest. ISME J 13:183–96
    [Google Scholar]
  139. 139. 
    Chiou KL, Bergey CM, Burrell AS, Disotell TR, Rogers J et al. 2019. Genome-wide ancestry and introgression in a Zambian baboon hybrid zone. bioRxiv. https://doi.org/10.1101/578781
    [Crossref]
  140. 140. 
    Murphy MA, Evans JS, Cushman SA, Storfer A 2008. Representing genetic variation as continuous surfaces: an approach for identifying spatial dependency in landscape genetic studies. Ecography 31:6685–97
    [Google Scholar]
  141. 141. 
    Hansen H, Ben-David M, McDonald DB 2008. Effects of genotyping protocols on success and errors in identifying individual river otters (Lontra canadensis) from their faeces. Mol. Ecol. Resour. 8:2282–89
    [Google Scholar]
  142. 142. 
    Carøe C, Gopalakrishnan S, Vinner L, Mak SST, Sinding MHS et al. 2018. Single‐tube library preparation for degraded DNA. Methods Ecol. Evol. 9:2410–19
    [Google Scholar]
  143. 143. 
    Troll CJ, Kapp J, Rao V, Harkins KM, Cole C et al. 2019. A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos. BMC Genom 20:1023
    [Google Scholar]
  144. 144. 
    Perry GH, Marioni JC, Melsted P, Gilad Y 2010. Genomic-scale capture and sequencing of endogenous DNA from feces. Mol. Ecol. 19:245332–44
    [Google Scholar]
  145. 145. 
    Snyder-Mackler N, Majoros WH, Yuan ML, Shaver AO, Gordon JB et al. 2016. Efficient genome-wide sequencing and low-coverage pedigree analysis from noninvasively collected samples. Genetics 203:2699–714
    [Google Scholar]
  146. 146. 
    Bergey CM, Pozzi L, Disotell TR, Burrell AS 2013. A new method for genome-wide marker development and genotyping holds great promise for molecular primatology. Int. J. Primatol. 34:2303–14
    [Google Scholar]
  147. 147. 
    Tiley GP, Blanco MB, Ralison JM, Rasoloarison RM, Stahlke AR et al. 2020. Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests. bioRxiv. http://doi.org/10.1101/2020.01.30.923300
    [Crossref]
  148. 148. 
    Payne A, Holmes N, Clarke T, Munro R, Debebe B, Loose M 2020. Nanopore adaptive sequencing for mixed samples, whole exome capture and targeted panels. bioRxiv. http://doi.org/10.1101/2020.02.03.926956
    [Crossref] [Google Scholar]
  149. 149. 
    Kovaka S, Fan Y, Ni B, Timp W, Schatz MC 2020. Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. bioRxiv. https://doi.org/10.1101/2020.02.03.931923
    [Crossref]
  150. 150. 
    Orkin JD, Yang Y, Yang C, Yu DW, Jiang X 2016. Cost-effective scat-detection dogs: unleashing a powerful new tool for international mammalian conservation biology. Sci. Rep. 6:34758
    [Google Scholar]
  151. 151. 
    Arandjelovic M, Bergl RA, Ikfuingei R, Jameson C, Parker M, Vigilant L 2015. Detection dog efficacy for collecting faecal samples from the critically endangered Cross River gorilla (Gorilla gorilla diehli) for genetic censusing. R. Soc. Open Sci. 2:2140423
    [Google Scholar]
  152. 152. 
    Sharma AK, Pafčo B, Vlčková K, Červená B, Kreisinger J et al. 2019. Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq. BMC Genom 20:493
    [Google Scholar]
  153. 153. 
    Aylward ML, Sullivan AP, Perry GH, Johnson SE, Louis EE Jr 2018. An environmental DNA sampling method for aye-ayes from their feeding traces. Ecol. Evol. 8:189229–40
    [Google Scholar]
  154. 154. 
    Melin AD, Janiak MC, Marrone F, Arora PS, Higham JP 2020. Comparative ACE2 variation and primate COVID-19 risk. Commun. Biol. 3:641
    [Google Scholar]
  155. 155. 
    Damas J, Hughes GM, Keough KC, Painter CA, Persky NS et al. 2020. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. PNAS 117:3622311–22
    [Google Scholar]
/content/journals/10.1146/annurev-animal-061220-023138
Loading
/content/journals/10.1146/annurev-animal-061220-023138
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error