Skip to main content

Advertisement

Log in

Considerations for Initiating a Wildlife Genomics Research Project in South and South-East Asia

  • Review Article
  • Published:
Journal of the Indian Institute of Science Aims and scope

Abstract

Next-generation sequencing (NGS) based genomic studies are revolutionizing the field of wildlife biology. These methods have yielded unprecedented insights for understanding ecology, evolution and conservation of wild populations. Despite the advantages, biodiversity rich regions in the tropics need more NGS-based studies to understand their native species. However, the field has progressed very slowly in these regions due to several challenges, including that most experts in the field are not based here. In this article, we highlight the factors that need to be considered before initiating a wildlife genomics research project with a focus on south and south-east Asia, though several factors apply to other regions as well. We highlight the challenges like policy issues for collecting samples and need for better sequencing and computational infrastructure. Finally, we discuss how global initiatives can help such regions setup NGS-based studies of wildlife.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Adams CI, Knapp M, Gemmell NJ, Jeunen GJ, Bunce M, Lamare MD, Taylor HR (2019) Beyond biodiversity: can environmental DNA (eDNA) cut it as a population genetics tool? Genes 10(3):192

    Article  CAS  Google Scholar 

  2. Ahmed J, Buragohain N, Mekola I, Kyarong S, Choudhury B, Ahmed N (2020) First extant record of Royal Bengal Tiger (Panthera tigris) in Dibang valley of Arunachal Pradesh, India with a note on translocation using Xylazine and ketamine anaesthetics. J Entomol Zool Stud 8(2):531–533

    Google Scholar 

  3. Allendorf FW, Hohenlohe PA, Luikart G (2010) Genomics and the future of conservation genetics. Nat Rev Genet 11(10):697–709

    Article  CAS  Google Scholar 

  4. Amarasinghe SL, Su S, Dong X, Zappia L, Ritchie ME, Gouil Q (2020) Opportunities and challenges in long-read sequencing data analysis. Genome Biol 21(1):1–16

    Article  Google Scholar 

  5. Andriyono S, Alam MJ, Kim HW (2019) Environmental DNA (eDNA) metabarcoding: diversity study around the Pondok Dadap fish landing station, Malang, Indonesia. Biodiversitas 20(12):3772–3781

  6. Angelier F, Tonra CM, Holberton RL, Marra PP (2010) How to capture wild passerine species to study baseline corticosterone levels. J Ornithol 151(2):415–422

    Article  Google Scholar 

  7. Ansil BR, Mendenhall IH, Ramakrishnan U (2021) High prevalence and diversity of Bartonella in small mammals from the biodiverse Western Ghats. PLoS Negl Trop Dis 15(3):e0009178

    Article  CAS  Google Scholar 

  8. Armstrong E, Khan A, Taylor RW, Gouy A, Greenbaum G, Thiéry A, Kang JT, Redondo SA, Prost S, Barsh G, Kaelin C (2019) Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection. Mol Biol Evol 38(6):2366–2379

    Article  Google Scholar 

  9. Arumugam R, Uli JE, Annavi G (2019) A review of the application of next generation sequencing (NGS) in wild terrestrial vertebrate research. Annu Res Rev Biol 31(5):1–9

    Google Scholar 

  10. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376. https://doi.org/10.1371/journal.pone.0003376

    Article  CAS  Google Scholar 

  11. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51(5):910–918

    Article  CAS  Google Scholar 

  12. Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM (2014) Environmental conditions influence eDNA persistence in aquatic systems. Environ Sci Technol 48(3):1819–1827

    Article  CAS  Google Scholar 

  13. Barroso GV, Puzović N, Dutheil JY (2019) Inference of recombination maps from a single pair of genomes and its application to ancient samples. PLoS Genet 15(11):e1008449

    Article  CAS  Google Scholar 

  14. Baveja P, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Yuda P, Lee JG, Rheindt FE (2021) Using historical genome-wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild. Evol Appl 14(3):698–709

    Article  CAS  Google Scholar 

  15. Beja-Pereira A, Oliveira R, Alves PC, Schwartz MK, Luikart G (2009) Advancing ecological understandings through technological transformations in noninvasive genetics. Mol Ecol Resour 9(5):1279–1301

    Article  Google Scholar 

  16. Benestan LM, Ferchaud AL, Hohenlohe PA, Garner BA, Naylor GJ, Baums IB, Schwartz MK, Kelley JL, Luikart G (2016) Conservation genomics of natural and managed populations: building a conceptual and practical framework. Mol Ecol 25(13):2967–2977

    Article  Google Scholar 

  17. Bohmann K, Evans A, Gilbert MTP, Carvalho GR, Creer S, Knapp M, Douglas WY, De Bruyn M (2014) Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol Evol 29(6):358–367

    Article  Google Scholar 

  18. Brown C (2007) Blood sample collection in lizards. Lab Anim 36(8):23–25

    Article  Google Scholar 

  19. Brüniche-Olsen A, Kellner KF, Anderson CJ, DeWoody JA (2018) Runs of homozygosity have utility in mammalian conservation and evolutionary studies. Conserv Genet 19(6):1295–1307

    Article  CAS  Google Scholar 

  20. Burkard M, Whitworth D, Schirmer K, Nash SB (2015) Establishment of the first humpback whale fibroblast cell lines and their application in chemical risk assessment. Aquat Toxicol 167:240–247

    Article  CAS  Google Scholar 

  21. Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J (2013) Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol 31(12):1119–1125

    Article  CAS  Google Scholar 

  22. Camacho-Sanchez M, Burraco P, Gomez-Mestre I, Leonard JA (2013) Preservation of RNA and DNA from mammal samples under field conditions. Mol Ecol Resour 13(4):663–673

    Article  CAS  Google Scholar 

  23. Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J (2018) Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 11(7):1094–1119

    Article  CAS  Google Scholar 

  24. Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124-f3140

    Article  Google Scholar 

  25. Chai V, Vassilakos A, Lee Y, Wright JA, Young AH (2005) Optimization of the PAXgeneTM blood RNA extraction system for gene expression analysis of clinical samples. J Clin Lab Anal 19(5):182–188

    Article  CAS  Google Scholar 

  26. Chiou KL, Bergey CM (2018) Methylation-based enrichment facilitates low-cost, noninvasive genomic scale sequencing of populations from feces. Sci Rep 8(1):1–10

    Article  Google Scholar 

  27. Cho YS, Hu L, Hou H, Lee H, Xu J, Kwon S, Oh S, Kim HM, Jho S, Kim S, Shin YA (2013) The tiger genome and comparative analysis with lion and snow leopard genomes. Nat Commun 4:2433

    Article  CAS  Google Scholar 

  28. Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen HC, Agarwala R, McLaren WM, Ritchie GR, Albracht D (2011) Modernizing reference genome assemblies. PLoS Biol 9(7):e1001091

    Article  CAS  Google Scholar 

  29. Dahal N, Kumar S, Noon BR, Nayak R, Lama RP, Ramakrishnan U (2020) The role of geography, environment, and genetic divergence on the distribution of pikas in the Himalaya. Ecol Evol 10(3):1539–1551

    Article  Google Scholar 

  30. Dennis C (2006) Conservation at a distance: a gentle way to age. Nature 442(7102):507–509

    Article  CAS  Google Scholar 

  31. Derkarabetian S, Benavides LR, Giribet G (2019) Sequence capture phylogenomics of historical ethanol-preserved museum specimens: Unlocking the rest of the vault. Mol Ecol Resour 19(6):1531–1544

    Article  CAS  Google Scholar 

  32. Elbers JP, Rogers MF, Perelman PL, Proskuryakova AA, Serdyukova NA, Johnson WE, Horin P, Corander J, Murphy D, Burger PA (2019) Improving illumina assemblies with Hi-C and long reads: an example with the North African dromedary. Mol Ecol Resour 19(4):1015–1026

    Article  CAS  Google Scholar 

  33. Field MA, Rosen BD, Dudchenko O, Chan EK, Minoche AE, Edwards RJ, Barton K, Lyons RJ, Tuipulotu DE, Hayes VM, Omer D, A. (2020) Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. GigaScience 9(4):giaa027

    Article  CAS  Google Scholar 

  34. Gaithuma A, Yamagishi J, Hayashida K, Kawai N, Namangala B, Sugimoto C (2020) Blood meal sources and bacterial microbiome diversity in wild-caught tsetse flies. Sci Rep 10(1):1–10

    Article  CAS  Google Scholar 

  35. Garner BA, Hand BK, Amish SJ, Bernatchez L, Foster JT, Miller KM, Morin PA, Narum SR, O’Brien SJ, Roffler G, Templin WD (2016) Genomics in conservation: case studies and bridging the gap between data and application. Trends Ecol Evol 31(2):81–83

    Article  Google Scholar 

  36. Gayral P, Weinert L, Chiari Y, Tsagkogeorga G, Ballenghien M, Galtier N (2011) Next-generation sequencing of transcriptomes: a guide to RNA isolation in nonmodel animals. Mol Ecol Resour 11(4):650–661

    Article  CAS  Google Scholar 

  37. Giani AM, Gallo GR, Gianfranceschi L, Formenti G (2020) Long walk to genomics: History and current approaches to genome sequencing and assembly. Comput Struct Biotechnol J 18:9–19

    Article  CAS  Google Scholar 

  38. Gopalakrishnan S, Sinding MHS, Ramos-Madrigal J, Niemann J, Castruita JAS, Vieira FG, Carøe C, de Manuel Montero M, Kuderna L, Serres A, González-Basallote VM (2018) Interspecific gene flow shaped the evolution of the genus Canis. Curr Biol 28(21):3441–3449

    Article  CAS  Google Scholar 

  39. Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A (2011) Bayesian inference of ancient human demography from individual genome sequences. Nat Genet 43(10):1031

    Article  CAS  Google Scholar 

  40. Grossen C, Guillaume F, Keller LF, Croll D (2020) Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex. Nat Commun 11(1):1–12

    Article  CAS  Google Scholar 

  41. Harrison JB, Sunday JM, Rogers SM (2019) Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proc R Soc B 286(1915):20191409

    Article  CAS  Google Scholar 

  42. Hedmark E, Flagstad Ø, Segerström P, Persson J, Landa A, Ellegren H (2004) DNA-based individual and sex identification from wolverine (Gulo gulo) faeces and urine. Conserv Genet 5(3):405–410

    Article  CAS  Google Scholar 

  43. Hirsch CD, Evans J, Buell CR, Hirsch CN (2014) Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes. Brief Funct Genomics 13:257–267

    Article  Google Scholar 

  44. Hoffmann GS, Johannesen J, Griebeler EM (2015) Species cross-amplification, identification and genetic variation of 17 species of deer (Cervidae) with microsatellite and mitochondrial DNA from antlers. Mol Biol Rep 42:1059–1067

    Article  CAS  Google Scholar 

  45. Hogan FE, Cooke R, Burridge CP, Norman JA (2008) Optimizing the use of shed feathers for genetic analysis. Mol Ecol Resour 8:561–567

    Article  CAS  Google Scholar 

  46. Hölzer M (2021) A decade of de novo transcriptome assembly: are we there yet? Mol Ecol Resour 21(1):11–13

    Article  Google Scholar 

  47. Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S (2018) Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol 36(4):338–345

    Article  CAS  Google Scholar 

  48. 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

    Article  CAS  Google Scholar 

  49. Kawamichi T, Liu J (1990) Capturing and marking pikas (Ochotona) with systematic ear clipping patterns. J Mammal Soc Jpn 15(1):39–43

    Google Scholar 

  50. Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust EV, Archibald JM, Bharti AK, Bell CJ, Beszteri B (2014) The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol 12(6):e1001889

    Article  CAS  Google Scholar 

  51. Khan A, Patel K, Bhattacharjee S, Sharma S, Chugani AN, Sivaraman K, Hosawad V, Sahu YK, Reddy GV, Ramakrishnan U (2020) Are shed hair genomes the most effective noninvasive resource for estimating relationships in the wild? Ecol Evol 10(11):4583–4594

    Article  Google Scholar 

  52. Khan A, Patel K, Shukla H, Viswanathan A, van der Valk T, Borthakur U, Nigam P, Zachariah A, Jhala Y, Kardos M, Ramakrishnan U (2021) Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. bioRxiv

  53. Kilpatrick CW (2002) Noncryogenic preservation of mammalian tissues for DNA extraction: an assessment of storage methods. Biochem Genet 40(1):53–62

    Article  CAS  Google Scholar 

  54. Kim GS, Kim TS, Son JS, Lai VD, Park JE, Wang SJ, Jheong WH, Mo IP (2019) The difference of detection rate of avian influenza virus in the wild bird surveillance using various methods. J Vet Sci 20(5):e56

    Article  Google Scholar 

  55. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ (2009) Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+ C)-biased genomes. Nat Methods 6(4):291–295

    Article  CAS  Google Scholar 

  56. Kumar VP, Rajpoot A, Shukla M, Kumar D, Goyal SP (2016) Illegal trade of Indian Pangolin (Manis crassicaudata): genetic study from scales based on mitochondrial genes. Egypt J Forensic Sci 6:524–533

    Article  Google Scholar 

  57. Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, Durbin R, Edwards SV, Forest F, Gilbert MTP, Goldstein MM (2018) Earth BioGenome Project: sequencing life for the future of life. Proc Natl Acad Sci 115(17):4325–4333

    Article  CAS  Google Scholar 

  58. Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. Nature 475(7357):493–496

    Article  CAS  Google Scholar 

  59. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z (2010) The sequence and de novo assembly of the giant panda genome. Nature 463(7279):311–317

    Article  CAS  Google Scholar 

  60. Li J, de Vries RP, Peng M (2020) Reference module in life science, encyclopedia of mycology

  61. Liu YC, Sun X, Driscoll C, Miquelle DG, Xu X, Martelli P, Uphyrkina O, Smith JL, O’Brien SJ, Luo SJ (2018) Genome-wide evolutionary analysis of natural history and adaptation in the world’s tigers. Curr Biol 28(23):3840–3849

    Article  CAS  Google Scholar 

  62. Longmire JL, Maltbie M, Baker RJ (1997) Use of “lysis buffer” in DNA isolation and its implication for museum collections. Museum of Texas Tech University, 163, pp 1–4

  63. de Manuel M, Barnett R, Sandoval-Velasco M, Yamaguchi N, Vieira FG, Mendoza MLZ, Liu S, Martin MD, Sinding MHS, Mak SS, Carøe C (2020) The evolutionary history of extinct and living lions. Proc Natl Acad Sci 117(20):10927–10934

    Article  CAS  Google Scholar 

  64. Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, Tomsho LP, Packard MD, Zhao F, Sher A, Tikhonov A (2008) Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456(7220):387–390

    Article  CAS  Google Scholar 

  65. Mittal P, Jaiswal SK, Vijay N, Saxena R, Sharma VK (2019) Comparative analysis of corrected tiger genome provides clues to its neuronal evolution. Sci Rep 9(1):1–11

    Article  Google Scholar 

  66. Morgera E, Tsioumani E, Buck M (2014) Unraveling the nagoya protocol: a commentary on the nagoya protocol on access and benefit-sharing to the convention on biological diversity. Martinus Nijhoff Publishers

    Book  Google Scholar 

  67. Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M (2016) The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biol 17(1):1–9

    CAS  Google Scholar 

  68. Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ, Fu B, Hims M, Ding Z, Ivakhno S, Stewart C, Ng BL (2012) Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer. Cell 148(4):780–791

    Article  CAS  Google Scholar 

  69. Murray GG, Soares AE, Novak BJ, Schaefer NK, Cahill JA, Baker AJ, Demboski JR, Doll A, Da Fonseca RR, Fulton TL, Gilbert MTP (2017) Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science 358(6365):951–954

    Article  CAS  Google Scholar 

  70. Nagy ZT (2010) A hands-on overview of tissue preservation methods for molecular genetic analyses. Org Divers Evol 10:91–105

    Article  Google Scholar 

  71. Nater A, Mattle-Greminger MP, Nurcahyo A, Nowak MG, De Manuel M, Desai T, Groves C, Pybus M, Sonay TB, Roos C, Lameira AR (2017) Morphometric, behavioral, and genomic evidence for a new orangutan species. Curr Biol 27(22):3487–3498

    Article  CAS  Google Scholar 

  72. Natesh M, Atla G, Nigam P, Jhala YV, Zachariah A, Borthakur U, Ramakrishnan U (2017) Conservation priorities for endangered Indian tigers through a genomic lens. Sci Rep 7(1):1–11

    Article  Google Scholar 

  73. Natesh M, Taylor RW, Truelove NK, Hadly EA, Palumbi SR, Petrov DA, Ramakrishnan U (2019) Empowering conservation practice with efficient and economical genotyping from poor quality samples. Methods Ecol Evol 10(6):853–859

    Article  Google Scholar 

  74. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461:272–276

    Article  CAS  Google Scholar 

  75. Oliveira R, Randi E, Mattucci F, Kurushima JD, Lyons LA, Alves PC (2015) Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris). Heredity 115(3):195–205

    Article  CAS  Google Scholar 

  76. Orkin JD, Montague MJ, Tejada-Martinez D, de Manuel M, Del Campo J, Hernandez SC, Di Fiore A, Fontsere C, Hodgson JA, Janiak MC, Kuderna LF (2021) The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. Proc Natl Acad Sci 118(7):e2010632118

    Article  CAS  Google Scholar 

  77. Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12(2):87–98

    Article  CAS  Google Scholar 

  78. Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, Baleka S, Karpinski E, Ivancevic AM, To TH, Kortschak RD, Raison JM (2018) A comprehensive genomic history of extinct and living elephants. Proc Natl Acad Sci 115(11):E2566–E2574

    Article  CAS  Google Scholar 

  79. Park PJ (2009) ChIP–seq: advantages and challenges of a maturing technology. Nat Rev Genet 10(10):669–680

    Article  CAS  Google Scholar 

  80. Perry GH, Marioni JC, Melsted P, Gilad Y (2010) Genomic-scale capture and sequencing of endogenous DNA from feces. Mol Ecol 19(24):5332–5344

    Article  CAS  Google Scholar 

  81. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7:e37135

    Article  CAS  Google Scholar 

  82. Pop M, Phillippy A, Delcher AL, Salzberg SL (2004) Comparative genome assembly. Brief Bioinform 5(3):237–248

    Article  CAS  Google Scholar 

  83. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto J-M, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65

    Article  CAS  Google Scholar 

  84. Reddy PA, Bhavanishankar M, Bhagavatula J, Harika K, Mahla RS, Shivaji S (2012) Improved methods of carnivore faecal sample preservation, DNA extraction and quantification for accurate genotyping of wild tigers. PLoS ONE 7(10):e46732

    Article  CAS  Google Scholar 

  85. Rellstab C, Dauphin B, Zoller S, Brodbeck S, Gugerli F (2019) Using transcriptome sequencing and pooled exome capture to study local adaptation in the giga-genome of Pinus cembra. Mol Ecol Resour 19(2):536–551

    Article  CAS  Google Scholar 

  86. Rice ES, Green RE (2019) Annu Rev Anim Biosci 7:17–40

    Article  CAS  Google Scholar 

  87. Robinson JA, Räikkönen J, Vucetich LM, Vucetich JA, Peterson RO, Lohmueller KE, Wayne RK (2019) Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction. Sci Adv 5(5):eaau0757

    Article  Google Scholar 

  88. Ryder O, Miller W, Ralls K, Ballou JD, Steiner CC, Mitelberg A, Romanov MN, Chemnick LG, Mace M, Schuster S (2016) Whole genome sequencing of California condors is now utilized for guiding genetic management. In: International plant and animal genome XXIV conference, San Diego, CA, 8–13 January 2016

  89. Saif R, Ejaz A, Mehmood T, Asif F, Alghanem SM, Ahmad TS (2020) Introduction to galaxy platform for NGS variant calling pipeline. Adv Life Sci 7(3):129–134

    Google Scholar 

  90. Saremi NF, Supple MA, Byrne A, Cahill JA, Coutinho LL, Dalén L, Figueiró HV, Johnson WE, Milne HJ, O’Brien SJ, O’Connell B (2019) Puma genomes from North and South America provide insights into the genomic consequences of inbreeding. Nat Commun 10(1):1–10

    CAS  Google Scholar 

  91. Scheunert A, Dorfner M, Lingl T, Oberprieler C (2020) Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing. PLoS ONE 15(3):e0226234

    Article  CAS  Google Scholar 

  92. Schnell IB, Thomsen PF, Wilkinson N, Rasmussen M, Jensen LR, Willerslev E, Bertelsen MF, Gilbert MTP (2012) Screening mammal biodiversity using DNA from leeches. Curr Biol 22(8):R262–R263

    Article  CAS  Google Scholar 

  93. Shingate P, Ravi V, Prasad A, Tay BH, Garg KM, Chattopadhyay B, Yap LM, Rheindt FE, Venkatesh B (2020) Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution. Nat Commun 11(1):1–13

    Article  CAS  Google Scholar 

  94. Smith ZD, Gu H, Bock C, Gnirke A, Meissner A (2009) High-throughput bisulfite sequencing in mammalian genomes. Methods 48(3):226–232

    Article  CAS  Google Scholar 

  95. Smith BT, Harvey MG, Faircloth BC, Glenn TC, Brumfield RT (2014) Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Syst Biol 63(1):83–95

    Article  Google Scholar 

  96. Sodhi NS, Koh LP, Brook BW, Ng PK (2004) Southeast Asian biodiversity: an impending disaster. Trends Ecol Evol 19(12):654–660

    Article  Google Scholar 

  97. Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S (2013) Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor Appl Genet 126:2699–2716

    Article  CAS  Google Scholar 

  98. Srivathsa A, Rodrigues RG, Toh KB, Zachariah A, Taylor RW, Oli MK, Ramakrishnan U (2021) The truth about scats and dogs: Next-generation sequencing and spatial capture–recapture models offer opportunities for conservation monitoring of an endangered social canid. Biol Conserv 256:109028

    Article  Google Scholar 

  99. Stratton M (2008) Nat Biotechnol 26:65–66

    Article  CAS  Google Scholar 

  100. Sun K (2020) Ktrim: an extra-fast and accurate adapter-and quality-trimmer for sequencing data. Bioinformatics 36(11):3561–3562

    Article  CAS  Google Scholar 

  101. Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S (2007) Whole-genome sequencing and assembly with high-throughput, short-read technologies. PLoS ONE 2(5):e484

    Article  CAS  Google Scholar 

  102. Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E (2012) Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol 21(8):2045–2050

    Article  CAS  Google Scholar 

  103. Van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5(3):247–252

    Article  CAS  Google Scholar 

  104. Thatte P, Chandramouli A, Tyagi A, Patel K, Baro P, Chhattani H, Ramakrishnan U (2020) Human footprint differentially impacts genetic connectivity of four wide-ranging mammals in a fragmented landscape. Divers Distrib 26:299–314

    Article  Google Scholar 

  105. Thatte P, Joshi A, Vaidyanathan S, Landguth E, Ramakrishnan U (2018) Maintaining tiger connectivity and minimizing extinction into the next century: insights from landscape genetics and spatially-explicit simulations. Biol Conserv 218:181–191

    Article  Google Scholar 

  106. Tsioumani T, Morgera E (2010) Wildlife legislation and the empowerment of the poor in Asia and Oceania. FAO legal papers online 83:1–124

  107. Utzeri VJ, Schiavo G, Ribani A, Tinarelli S, Bertolini F, Bovo S, Fontanesi L (2018) Entomological signatures in honey: an environmental DNA metabarcoding approach can disclose information on plant-sucking insects in agricultural and forest landscapes. Sci Rep 8(1):1–13

    Article  CAS  Google Scholar 

  108. Vianna JA, Fernandes FA, Frugone MJ, Figueiró HV, Pertierra LR, Noll D, Bi K, Wang-Claypool CY, Lowther A, Parker P, Le Bohec C (2020) Genome-wide analyses reveal drivers of penguin diversification. Proc Natl Acad Sci 117(36):22303–22310

    Article  CAS  Google Scholar 

  109. Vignal A, Milan D, SanCristobal M, Eggen A (2002) Genet Sel Evol 34:275

    Article  CAS  Google Scholar 

  110. Vincent AC, Sadovy de Mitcheson YJ, Fowler SL, Lieberman S (2014) The role of CITES in the conservation of marine fishes subject to international trade. Fish Fish 15(4):563–592

    Article  Google Scholar 

  111. Wheat CW (2010) Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica 138(4):433–451

    Article  CAS  Google Scholar 

  112. Wheat RE, Allen JM, Miller SDL, Wilmers CC, Levi T (2016) Environmental DNA from residual saliva for efficient noninvasive genetic monitoring of Brown Bears (Ursus arctos). PLoS ONE 11:e0165259

    Article  CAS  Google Scholar 

  113. Winker K, Glenn TC, Faircloth BC (2018) Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event. PeerJ 6:e5735

    Article  CAS  Google Scholar 

  114. Woodall LC, Jones R, Zimmerman B, Guillaume S, Stubbington T, Shaw P, Koldewey HJ (2012) Partial fin-clipping as an effective tool for tissue sampling seahorses, Hippocampus spp. J Mar Biol Assoc UK 92(6):1427–1432

    Article  Google Scholar 

  115. Worley KC, Gibbs RA (2010) Decoding a national treasure: the giant-panda genome is the first reported de novo assembly of a large mammalian genome achieved using next-generation sequencing methods. The feat reflects a trend towards ever-decreasing genome-sequencing costs. Nature 463(7279):303–305

    Article  CAS  Google Scholar 

  116. Zhao Q (2018) In: Proceedings of the 2018 5th international conference on bioinformatics research and applications, Association for Computing Machinery, New York, NY, USA, ICBRA’18, pp. 8–15. https://doi.org/10.1145/3309129.3309134

  117. Zoonomia Consortium (2020) A comparative genomics multitool for scientific discovery and conservation. Nature 587(7833):240

    Article  CAS  Google Scholar 

  118. Zulkefli NS, Kim K-H, Hwang S-J (2019) Effects of microbial activity and environmental parameters on the degradation of extracellular environmental DNA from a Eutrophic Lake. Int J Environ Resh Public Health 16:3339

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Chui Li for the information on availability of various sequencers across the region.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Anubhab Khan.

Ethics declarations

Conflict of Interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Khan, A., Tyagi, A. Considerations for Initiating a Wildlife Genomics Research Project in South and South-East Asia. J Indian Inst Sci 101, 243–256 (2021). https://doi.org/10.1007/s41745-021-00243-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s41745-021-00243-3

Navigation