Keywords
noninvasive genetic sampling
PCR
rDNA
16S
species identification
How to Cite
Abstract
Fecal analysis is a useful tool for studying the species identity of rare mammals. The possibility of using non-invasive biological materials in molecular genetic studies of rare bovids is shown, using the example of the markhor and Siberian ibex of Uzbekistan. Field work including noninvasive genetic sampling collection was carried out in the study area in spring and autumn 2022-2023 in the Hissar, Surkhan State Reserves and Ugam-Chatkal State National Natural Park and Termez zoo in Uzbekistan. We used species-specific 16S rRNA mitochondrial gene fragments for polymerase chain reaction amplification for species identification. The results of the molecular analysis with the 16S rRNA mitochondrial gene allowed the identification of Capra sibirica, C. falconeri and C. hircus belonging to the subfamily Caprinae using a noninvasive genetic sampling method. This method is quite easy to use, while avoiding direct contact with the animal, which minimizes the degree of impact on the object being studied and does not require significant material and labor costs for researchers. We believe that noninvasive genetic sampling is emerging as one of the most effective and accurate methods for estimating the population size of animals, and we recommend considering this approach for endangered and rare species. The protocol developed could be a valuable tool in the management and conservation of the Capra species occurring on the Uzbekistan.
References
Bach BH, Quigley AB, Gaynor KM, McInturff A, Charles KL, Dorcy J, Brashares JS (2022) Identifying individual ungulates from fecal DNA: a comparison of field collection methods to maximize efficiency, ease, and success. Mammalian Biology 102: 863–874. https://doi.org/10.1007/s42991-021-00176-5
Bellemain E, Swenson JE, Tallmon D, Brunberg S, Taberlet P (2005) Estimating population size of elusive animals with DNA from hunter-collected feces: four methods for brown bears. Conservation Biology 19: 150–161. https://doi.org/10.1111/j.1523-1739.2005.00549.x
Canu A, Mattioli L, Santini A, Apollonio M, Scandura M (2017) ‘Video-scats’: combining camera trapping and non-invasive genotyping to assess individual identity and hybrid status in gray wolf. Wildlife Biology 4: 00355. https://doi.org/10.2981/wlb.00355
Caragiulo A, Isabela Dias-Freedman I, Clark JA, Rabinowitz S, Amato G (2013) Mitochondrial DNA sequence variation and phylogeography of Neotropic pumas (Puma concolor). Mitochondrial DNA 25(4): 304–312. https://doi:10.3109/19401736.2013.800486
Ferreira CM, Sabino-Marques H, Barbosa S, Costa P, Encarnacao C, Alpizar-Jara R, Pita R, Beja P, Mira A, Searle JB, Pauperio J, Alves PC (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
Furnas BJ, Landers RH, Hill S, Itoga SS, Sacks BN (2018) Integrated modeling to estimate population size and composition of mule deer. Journal of Wildlife Management 82: 1429–1441. https://doi.org/10.1002/jwmg.21507
Gebremedhin B, Ficetola GF, Naderi S, Rezaei HR, Maudet C, Rioux D, Luikart G, Flagstad O, Thuiller W, Taberlet P (2009) Combining genetic and ecological data to assess the conservation status of the endangered Ethiopian walia ibex. Animal Conservation 12: 89–100. https://doi.org/10.1111/j.1469-1795.2009.00238.x
Hammer SE, Schwammer HM, Suchentrunk F (2016) Evidence for introgressive hybridization of captive markhor (Capra falconeri) with domestic goat: Cautions for reintroduction. Mammalian Biology 81: 7. https://doi.org/10.1016/j.mambio.2016.07.021
Heptner VG, Nasimovitch AA, Bannikov AA (1988) Mammals of the Soviet Union: Artiodactyla and Perissodactyla. Vol. 1. Smithsonian Institution Press, Washington DC, 1147 pp.
Kierepka EM, Unger SD, Keiter DA, Beasley JC, Olin ER, Cunningham FL, Piaggio AJ (2016) Identification of robust microsatellite markers for wild pig fecal DNA. Journal of Wildlife Management 80: 1120–1128. https://doi.org/10.1002/jwmg.21102
Kuchboev AE, Krücken J (2022) Prevalence, infection intensity and molecular diagnosis of mixed infections with Metastrongylus spp. (Metastrongylidae) in wild boars in Uzbekistan. Pathogens 11(11): 1316. https://doi.org/10.3390/pathogens11111316
Kuchboev AE, Krucken J, Karimova RR, Ruziev BH, Von Samson-Himmelstjerna G (2015) Molecular phylogeny and diagnosis of species of the family Protostrongylidae from caprine hosts in Uzbekistan. Parasitology Research 114(4): 1355–1364. https://doi.org/10.1007/s00436-015-4313-6
Kurose N, Masuda R, Tatara M (2005) Fecal DNA Analysis for identifying species and sex of sympatric Carnivores: A noninvasive method for conservation on the Tsushima Islands, Japan. Journal of Heredity 96(6): 688–697. https://doi.org/10.1093/jhered/esi124
Lampa S, Mihoub JB, Gruber B, Klenke R, Henle K (2015) Non-invasive genetic mark-recapture as a means to study population sizes and marking behaviour of the elusive Eurasian otter (Lutra lutra). PLoS ONE 10: e0125684. https://doi.org/10.1371/journal.pone.0125684
Lounsberry ZT, Forrester TD, Olegario MJ, Brazeal JL, Wittmer HU, Sacks BN (2015) Estimating sex-specific abundance in fawning areas of a high-density Columbian black-tailed deer population using fecal DNA. Journal of Wildlife Management 79: 39–49. https://doi.org/10.1002/jwmg.817
McCarthy MP, Best MJ, Betts RA (2010) Climate change in cities due to global warming and urban effects. Geophysical Research Letters 37: 1–5. https://doi.org/10.1029/2010GL042845
Newediuk L, Vander Wal E (2022) Predicting the individual identity of non-invasive faecal and hair samples using biotelemetry clusters. Mammalian Biology 102: 685–700. https://doi.org/10.1007/s42991-021-00173-8
Nguyen LT, Schmidt HA, Haeseler A, Minh BQ (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating Maximum-likelihood phylogenies. Molecular Biology Evolution 32(1): 268–274. https://doi.org/10.1093/molbev/msu300
Phoebus I, Boulanger J, Eiken HG, Fløystad I, Graham K, Hagen SB, Sorensen A, Stenhouse G (2020) Comparison of grizzly bear hair-snag and scat sampling along roads to inform wildlife population monitoring. Wildlife Biology 3: 1–12. https://doi.org/10.2981/wlb.00697
Quasim S, McDonald AJ, Sarre SD (2018) Towards more efficient large-scale DNA-based detection of terrestrial mammal predators from scats. Mammalian Research 63: 387–393. https://doi.org/10.1007/s13364-018-0369-x
Ramón-Laca VA, Soriano L, Gleeson D, Godoy JA (2015) A simple and effective method for obtaining mammal DNA from faeces. Wildlife Biology 21: 195–203. https://doi.org/10.2981/wlb.00096
Reading R, Michel S, Suryawanshi K, Bhatnagar YV (2020) Capra sibirica. In: The IUCN Red List of Threatened Species: e.T42398A22148720. https://dx.doi.org/10.2305/IUCN.UK.2020-2.RLTS.T42398A22148720.en
Sobirov KhF, Kuchboev AE, Amirov OO, Karimova R, Abdullaev A (2022) Molecular identification of rare species of wild sheep (Ovis ammon severtzovi and Ovis vignei arkal) in Uzbekistan. Bulletin of Karshi State University 2(1): 102–106. [In Uzbek]
Sokolov VI (1959) Fauna of USSR. Vol. 1(3). Mammals: Ungulate (Orders Perissodactyla and Artiodactyla). Academy Sciences of USSR, Moscow, 79-81 p. [In Russian]
Voronova N, Levykina S (2019) Biological diversity and DNA barcoding. Science and innovation 8(198): 13–18. [In Russian]
Werhahn KJ, Trinka E, Dobesberger J, Unterberger I, Baum P, Deckert-Schmitz M, Kniess T, Schmitz B, Bernedo V, Ruckes C, Ehrlich A, Krämer G (2015) Arandomized, double-blind comparison of antiepileptic drug treatment in the elderly with new-onset focal epilepsy. Epilepsia 56(3): 450–459. https://doi.org/10.1111/epi.12926
Acta Biologica Sibirica is a golden publisher, as we allow self-archiving, but most importantly we are fully transparent about your rights.
Authors may present and discuss their findings ahead of publication: at biological or scientific conferences, on preprint servers, in public databases, and in blogs, wikis, tweets, and other informal communication channels.
ABS allows authors to deposit manuscripts (currently under review or those for intended submission to ABS) in non-commercial, pre-print servers such as ArXiv.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License (CC BY 4.0) that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).