Non-invasive genetic sampling in wildlife research

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Genetic analysis is being used in wildlife research to estimate species abundance, effective population size, hybridization, to detect pathogens, and for other applications. Traditionally, DNA samples for genetic analysis have been obtained from blood or tissue samples, either through invasive or lethal means.[1] Since the early 1990s, researchers have started implementing non-invasive DNA sampling methods (sensu lato), meaning not penetrating the skin barrier[2], for example by using faeces or hair.[3]

Non-invasive genetic sampling might be more cost-effective and – depending on the method – can require less time effort than both invasive genetic sampling and other wildlife research methods.[4] A disadvantage of non-invasively obtained samples is that they often contain lower quality and quantity of DNA in comparison with tissue samples. This issue can be, nevertheless, overcome with optimized protocols and specialized extraction kits.[5][6][7]

Examples of non-invasive genetic sampling application in wildlife research

DNA material Example study Species
Non-invasive methods requiring capture or contact with the animal Buccal swab Gallardo et al. 2012[8] Amphibian
Handel et al. 2006[9] Bird
Reid et al. 2012[10] Fish
Cloacal swab Wang et al. 2008[11] Bird
Mucci et al. 2014[12] Reptile
Skin swab Pichlmuller et al. 2013[13] Amphibian
Player et al. 2017[14] Bat
Taslima et al. 2017[15] Fish
Régnier et al. 2011[16] Mollusc
Non-invasive methods not requiring capture Breath sample Pirotta et al. 2017[17] Cetacean
Egg shell Maia et al. 2017[18] Bird
Hu and Wu 2008[19] Reptile
Exuviae Petersen et al. 2007[20] Arachnid
Ozana et al. 2020[21] Insect
Faeces Boston et al. 2012[22] Bat
Dai et al. 2015 [23] Bird
Rutledge et al. 2009[24] Carnivore
Hunt et al. 2006[25] Cetacean
Fernando et al. 2003 [26] Elephant
Scriven et al. 2013[27] Insect
Zemanova and Ramp 2021[28] Marsupial
Perry et al. 2010[29] Primate
Mitelberg et al. 2019[30] Reptile
Ferreira et al. 2018[31] Rodent
Powell et al. 2019[32] Ungulate
Saliva left on food or twigs Monge et al. 2020[33] Bird
Stewart et al. 2018[34] Primate
Shed antlers Lopez and Beier 2012[35] Ungulate
Shed feathers Olah et al. 2016[36] Bird
Shed hair Khan et al. 2020[37] Carnivore
Henry et al. 2011[38] Lagomorph
Shed skin Swanson et al. 2006[39] Carnivore
Horreo et al. 2015[40] Reptile
Spider web Blake et al. 2016[41] Arachnid
Urine Valiere and Taberlet 2000[42] Carnivore
Ozga et al. 2021[43] Primate


This page was created and edited by Miriam A. Zemanova --MZ21917 (talk) 15:41, 18 February 2022 (UTC)

References

  1. ↑ Zemanova MA (2019): Poor implementation of non-invasive sampling in wildlife genetics studies. Rethinking Ecology 4: 119-132. https://doi.org/10.3897/rethinkingecology.4.32751.
  2. ↑ Lefort MC, et al. (2019): Blood, sweat and tears: a review of non-invasive DNA sampling. bioRxiv: 385120. https://doi.org/10.1101/385120.
  3. ↑ Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang JL (2018): Genetic and genomic monitoring with minimally invasive sampling methods. Evolutionary Applications 11: 1094-1119. https://doi.org/10.1111/eva.12600.
  4. ↑ Zemanova MA (2021): Non-invasive genetic assessment is an effective wildlife research tool when compared with other approaches. Genes 12: 1672. https://doi.org/10.3390/genes12111672.
  5. ↑ Russello MA, Waterhouse MD, Etter PD, Johnson EA (2015): From promise to practice: pairing non-invasive sampling with genomics in conservation. PeerJ 3: e1106. https://doi.org/10.7717/peerj.1106.
  6. ↑ Schmidt DA, Campbell NR, Govindarajulu P, Larsen KW, Russello MA (2020): Genotyping-in-Thousands by sequencing (GT-seq) panel development and application to minimally invasive DNA samples to support studies in molecular ecology. Molecular Ecology Resources 20: 114-124. https://doi.org/10.1111/1755-0998.13090.
  7. ↑ Spitzer R, Norman AJ, Konigsson H, Schiffthaler B, Spong G (2020): De novo discovery of SNPs for genotyping endangered sun parakeets (Aratinga solstitialis) in Guyana. Conservation Genetics Resources 12: 631-641. https://doi.org/10.1007/s12686-020-01151-x.
  8. ↑ Gallardo CE, Correa C, Morales P, Saez PA, Pastenes L, Mendez MA (2012): Validation of a cheap and simple nondestructive method for obtaining AFLPs and DNA sequences (mitochondrial and nuclear) in amphibians. Molecular Ecology Resources 12: 1090-1096. https://doi.org/10.1111/1755-0998.12013.
  9. ↑ Handel CM, Pajot LM, Talbot SL, Sage GK (2006): Use of buccal swabs for sampling DNA from nestling and adult birds. Wildlife Society Bulletin 34: 1094-1100. https://www.jstor.org/stable/4134320.
  10. ↑ Reid SM, Kidd A, Wilson CC (2012): Validation of buccal swabs for noninvasive DNA sampling of small-bodied imperiled fishes. Journal of Applied Ichthyology 28: 290-292. https://doi.org/10.1111/j.1439-0426.2011.01889.x.
  11. ↑ Wang R, Soll L, Dugan V, Runstadler J, Happ G, Slemons RD, Taubenberger JK (2008): Examining the hemagglutinin subtype diversity among wild duck-origin influenza A viruses using ethanol-fixed cloacal swabs and a novel RT-PCR method. Virology 375: 182-189. https://doi.org/10.1016/j.virol.2008.01.041.
  12. ↑ Mucci N, Mengoni C, Berti E, Randi E (2014): Cloacal swab sampling is a reliable and harmless source of DNA for population and forensic genetics in tortoises. Conservation Genetics Resources 6: 845-847. https://doi.org/10.1007/s12686-014-0251-3.
  13. ↑ Pichlmuller F, Straub C, Helfer V (2013): Skin swabbing of amphibian larvae yields sufficient DNA for efficient sequencing and reliable microsatellite genotyping. Amphibia-Reptilia 34: 517-523. https://doi.org/10.1163/15685381-00002909.
  14. ↑ Player D, Lausen C, Zaitlin B, Harrison J, Paetkau D, Harmston E (2017): An alternative minimally invasive technique for genetic sampling of bats: wing swabs yield species identification. Wildlife Society Bulletin 41: 590-596. https://doi.org/10.1002/wsb.803.
  15. ↑ Taslima K, Taggart JB, Wehner S, McAndrew BJ, Penman DJ (2017): Suitability of DNA sampled from Nile tilapia skin mucus swabs as a template for ddRAD-based studies. Conservation Genetics Resources 9: 39-42. https://doi.org/10.1007/s12686-016-0614-z.
  16. ↑ Régnier C, Gargominy O, Falkner G, Puillandre N (2011): Foot mucus stored on FTA® cards is a reliable and non-invasive source of DNA for genetics studies in molluscs. Conservation Genetics Resources 3: 377-382. https://doi.org/10.1007/s12686-010-9345-8.
  17. ↑ Pirotta V, Smith A, Ostrowski M, Russell D, Jonsen ID, Grech A, Harcourt R (2017): An economical custom-built drone for assessing whale health. Frontiers in Marine Science 4: 425. https://doi.org/10.3389/fmars.2017.00425.
  18. ↑ Maia TA, Vilaca ST, da Silva LR, Santos FR, Dantas GPD (2017): DNA sampling from eggshells and microsatellite genotyping in rare tropical birds: case study on Brazilian merganser. Genetics and Molecular Biology 40: 808-812. https://doi.org/10.1590/1678-4685-gmb-2016-0297.
  19. ↑ Hu Y, Wu XB (2008): Eggshell membranes as a noninvasive sampling for molecular studies of Chinese alligators (Alligator sinensis). African Journal of Biotechnology 7: 3022-3025. https://www.ajol.info/index.php/ajb/article/view/59219
  20. ↑ Petersen SD, Mason T, Akber S, West R, White B, Wilson P (2007): Species identification of tarantulas using exuviae for international wildlife law enforcement. Conservation Genetics 8: 497-502. https://doi.org/10.1007/s10592-006-9173-2.
  21. ↑ Ozana S, Pyszko P, Dolny A (2020): Determination of suitable insect part for non-lethal DNA sampling: case study of DNA quality and regeneration capability of dragonflies. Insect Conservation and Diversity 13: 319-327. https://doi.org/10.1111/icad.12400.
  22. ↑ Boston ESM, Puechmaille SJ, Scott DD, Buckley DJ, Lundy MG, Montgomery IW, Prodöhl PA, Teeling EC (2012): Empirical assessment of non-invasive population genetics in bats: comparison of DNA quality from faecal and tissue samples. Acta Chiropterologica 14: 45-52. https://doi.org/10.3161/150811012X654259.
  23. ↑ Dai Y, Lin Q, Fang W, Zhou X, Chen X (2015): Noninvasive and nondestructive sampling for avian microsatellite genotyping: a case study on the vulnerable Chinese egret (Egretta eulophotes). Avian Research 6 (art. 24): 24. https://doi.org/10.1186/s40657-015-0034-x.
  24. ↑ Rutledge LY, Holloway JJ, Patterson BR, White BN (2009): An improved field method to obtain DNA for individual identification from wolf scat. Journal of Wildlife Management 73: 1430-1435. https://doi.org/10.2193/2008-492.
  25. ↑ Hunt KE, Rolland RA, Kraus SD, Wasser SK (2006): Analysis of fecal glucocorticoids in the North Atlantic right whale (Eubalaena glacialis). General and Comparative Endocrinology 148: 260-272. https://doi.org/10.1016/j.ygcen.2006.03.012.
  26. ↑ Fernando P, Vidya TNC, Rajapakse C, Dangolla A, Melnick DJ (2003): Reliable noninvasive genotyping: fantasy or reality? Journal of Heredity 94: 115-123. https://doi.org/10.1093/jhered/esg022.
  27. ↑ Scriven JJ, Woodall LC, Goulson D (2013): Nondestructive DNA sampling from bumblebee faeces. Molecular Ecology Resources 13: 225-229. https://doi.org/10.1111/1755-0998.12036.
  28. ↑ Zemanova MA, Ramp D (2021): Genetic structure and gene flow in eastern grey kangaroos in an isolated conservation reserve Diversity 13: 570. https://doi.org/10.3390/d13110570.
  29. ↑ Perry GH, Marioni JC, Melsted P, Gilad Y (2010): Genomic-scale capture and sequencing of endogenous DNA from feces. Molecular Ecology 19: 5332-5344. https://doi.org/10.1111/j.1365-294X.2010.04888.x.
  30. ↑ Mitelberg A, Vandergast AG, Nussear KE, Dutcher K, Esque TC (2019): Development of a genotyping protocol for Mojave Desert tortoise scat. Chelonian Conservation and Biology 18: 123-132. https://doi.org/10.2744/ccb-1394.1.
  31. ↑ Ferreira CM, et al. (2018): Genetic non-invasive sampling (gNIS) as a cost-effective tool for monitoring elusive small mammals. European Journal of Wildlife Research 64: 46. https://doi.org/10.1007/s10344-018-1188-8.
  32. ↑ Powell C, Butler F, O’Reilly C (2019): The development of real-time PCR assays for species and sex identification of three sympatric deer species from noninvasive samples. Conservation Genetics Resources 11: 465-471. https://doi.org/http://dx.doi.org/10.1007/s12686-018-1041-0.
  33. ↑ Monge O, Dumas D, Baus I (2020): Environmental DNA from avian residual saliva in fruits and its potential uses in population genetics. Conservation Genetics Resources 12: 131-139. https://doi.org/10.1007/s12686-018-1074-4.
  34. ↑ Stewart FA, Piel AK, Luncz L, Osborn J, Li Y, Hahn BH, Haslam M (2018): DNA recovery from wild chimpanzee tools. PLoS ONE 13: e0189657. https://doi.org/10.1371/journal.pone.0189657.
  35. ↑ Lopez RG, Beier P (2012): Weathered antlers as a source of DNA. Wildlife Society Bulletin 36: 380-382. https://doi.org/10.1002/wsb.138.
  36. ↑ Olah G, Heinsohn RG, Brightsmith DJ, Espinoza JR, Peakall R (2016): Validation of non-invasive genetic tagging in two large macaw species (Ara macao and A. chloropterus) of the Peruvian Amazon. Conservation Genetics Resources 8: 499-509. https://doi.org/10.1007/s12686-016-0573-4.
  37. ↑ 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? Ecology and Evolution 10: 4583-4594. https://doi.org/10.1002/ece3.6157.
  38. ↑ Henry P, Henry A, Russello MA (2011): A noninvasive hair sampling technique to obtain high quality DNA from elusive small mammals. Jove-Journal of Visualized Experiments 49: e2791. https://doi.org/10.3791/2791.
  39. ↑ Swanson BJ, Kelly BP, Maddox CK, Moran JR (2006): Shed skin as a source of DNA for genotyping seals. Molecular Ecology Notes 6: 1006-1009. https://doi.org/10.1111/j.1471-8286.2006.01473.x.
  40. ↑ Horreo JL, Pelaez ML, Fitze PS (2015): Skin sheds as a useful DNA source for lizard conservation. Phyllomedusa 14: 73-77. https://doi.org/10.11606/issn.2316-9079.v14i1p73-77.
  41. ↑ Blake M, McKeown NJ, Bushell MLT, Shaw PW (2016): DNA extraction from spider webs. Conservation Genetics Resources 8: 219-221. https://doi.org/10.1007/s12686-016-0537-8.
  42. ↑ Valiere N, Taberlet P (2000): Urine collected in the field as a source of DNA for species and individual identification. Molecular Ecology 9: 2150-2152. https://doi.org/10.1046/j.1365-294x.2000.01114-2.x.
  43. ↑ Ozga AT, Webster TH, Gilby IC, Wilson MA, Nockerts RS, Wilson ML, Pusey AE, Li Y, Hahn BH, Stone AC (2021): Urine as a high-quality source of host genomic DNA from wild populations. Molecular Ecology Resources 21: 170-182. https://doi.org/10.1111/1755-0998.13260.
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