A Robust Test System for DNA Identification of Raccoon Dogs

A. E. Hrebianchuk; Гребенчук А. Е.; O. N. Lukashkova; Лукашкова О. Н.; S. A. Kotava; Котова С. А.; I. S. Tsybovsky; Цыбовский И. С.

doi:10.31857/S0016675823050065

A Robust Test System for DNA Identification of Raccoon Dogs

Authors: Hrebianchuk A.E.¹, Lukashkova O.N.², Kotava S.A.², Tsybovsky I.S.³
Affiliations:
1. State Forensic Examination Committee of the Republic of Belarus
2. Scientific and Practical Center of the State Forensic Examination Committee of the Republic Belarus
3. RUP “BelJurZabespjachjenne”
Issue: Vol 59, No 5 (2023)
Pages: 584-600
Section: МАТЕМАТИЧЕСКИЕ МОДЕЛИ И МЕТОДЫ
URL: https://ogarev-online.ru/0016-6758/article/view/134591
DOI: https://doi.org/10.31857/S0016675823050065
EDN: https://elibrary.ru/FNOVHT
ID: 134591

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Abstract
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Abstract

To establish a system for DNA identification of biological samples of the raccoon dog (Nyctereutes procyonoides), we carried out a study of polymorphism of 39 microsatellite loci and three sex loci specific to various species of the Canidae family. This resulted in the development of the NPlex test system, which includes 14 autosomal STRs and two sex loci. The test system has been validated for use in forensic identification of racoon dogs based on biological traces (such as traces of blood and secretions, fragments of muscle tissue or bones, dermis and hair, etc.) found at crime scenes, as well as for establishing biological relationship of animals of this species. Validation efforts were performed in accordance with the protocol of the Scientific Working Group on DNA Analysis Methods.

Keywords

microsatellites, identification, Canidae family, forensics, illegal hunting.

References

Yan S.Q., Li Y.M., Bai C.Y. et al. Development and characterization of polymorphic microsatellite markers for Chinese raccoon dog (Nyctereutes procyonoides procyonoides) // Genet. Mol. Res. 2013. V. 12. P. 6351–6355. https://doi.org/10.4238/2013.December.6.2
Hong Y., Kim K.S., Lee H., Min M.S. Population genetic study of the raccoon dog (Nyctereutes procyonoides) in South Korea using newly developed 12 microsatellite markers // Genes & Genet. Systems. 2013. V. 88. № 1. P. 69–76. https://doi.org/10.1266/ggs.88.69
Paulauskas A., Griciuvienė L., Juknelyte S. et al. Genetic diversity and population structure of raccoon dog (Nyctereutes procyonoides) in invaded areas // XMAT. 2014. P. 78. Antalya, Turkey. https://www.neobiota.eu/wp/wp-content/uploads/NEOBIOTA-2014-Abstract-Book.pdf
Nørgaard L.S., Mikkelsen D.M.G., Elmeros M. et al. Population genomics of the raccoon dog (Nyctereutes procyonoides) in Denmark: Insights into invasion history and population development // Biol. Invasions. 2017. V. 19. № 5. P. 1637–1652. https://doi.org/10.1007/s10530-017-1385-5
Oh S.Y., Kim S.A., Kim J.Y. et al. Detection of antibodies against the rabies virus in Korean raccoon dogs (Nyctereutes procyonoides koreensis) // J. Zoo and Wildlife Med. 2012. V. 43. № 1. P. 174–176. https://doi.org/10.1638/2011-0063.1
Kido N., Itabashi M., Takahashi M., Futami M. Epidemiology of sarcoptic mange in free-ranging raccoon dogs (Nyctereutes procyonoides) in Yokohama // Jap. Veter. Parasitology. 2013. V. 191. № 1–2. P. 102–107. https://doi.org/10.1016/j.vetpar.2012.07.026
Bagrade G., Deksne G., Ozoliņa Z. et al. Echinococcus multilocularis in foxes and raccoon dogs: an increasing concern for Baltic countries // Parasites & Vectors. 2016. V. 9. № 1. P. 1–9. https://doi.org/10.1186/s13071-016-1891-9
Griciuvienė L., Paulauskas A., Radzijevskaja J. et al. Impact of anthropogenic pressure on the formation of population structure and genetic diversity of raccoon dog Nyctereutes procyonoides // Curr. Zool. 2016. V. 62. № 5. P. 413–420. https://doi.org/10.1093/cz/zow038
Kauhala K., Kowalczyk R. Invasion of the raccoon dog Nyctereutes procyonoides in Europe: history of colonization, features behind its success, and threats to native fauna // Curr. Zool. 2011. V. 57. № 5. P. 584–598. https://doi.org/10.1093/czoolo/57.5.584
Lever C. Naturalized Mammals of the World. London: Longman, 1985. Available from: https://www.cabi.org/isc/abstract/19860537058
Deinet S., Ieronymidou C., McRae L. et al. Wildlife comeback in Europe: The recovery of selected mammal and bird species // Final Rep. to Rewilding Europe by ZSL, BirdLife International and the European Bird Census Council. London, UK, 2013. Available from: https://rewildingeurope.com/wp-content/uploads/20-13/11/Wildlife-Comeback-in-Europe-the-recovery-of-selected-mammal-and-bird-species.pdf
Sillero-Zubiri C., Hoffmann M., Macdonald D.W. Canids: Foxes, wolves, jackals, and dogs // Status Survey and Conservation Action Plan. 2004. V. 95. Gland, Switzerland: IUCN, available from: https://www.carnivoreconservation.org/files/actionplans/canids.pdf
Boom R.C.J.A., Sol C.J., Salimans M.M. et al. Rapid and simple method for purification of nucleic acids // J. Clin. Microbiol. 1990. V. 28. № 3. P. 495–503. https://doi.org/10.1128/jcm.28.3.495-503.1990
Benson D.A., Karsch-Mizrachi I., Lipman D.J. et al. GenBank // Nucl. Acids Res. 2005. V. 34. P. D16–D20. https://doi.org/10.1093/nar/gkj157
Hall T., Biosciences I., Carlsbad C. BioEdit: An important software for molecular biology // GERF Bull. Biosci. 2011. V. 2. № 1. P. 60–61. https://www.researchgate.net/profile/Ahmed-Alzohairy/publication/2585-65830_BioEdit_An_important_software_for_molecular_biology/links/0deec528a87d3f2ee0000000/BioEdit-An-important-software-for-molecular-biology.pdf
Peakall R.O.D., Smouse P.E. GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research // Mol. Ecol. Notes. 2006. V. 6. № 1. P. 288–295. https://doi.org/10.1093/bioinformatics/bts460
Excoffier L., Lischer H. An integrated software package for population genetics data analysis // Comput. and Mol. Popul. Genet. Lab (CMPG). 2006. Berne, Switzerland: Institute Zool., Univ. Berne, PMID: 19325852.
Van Oosterhout C., Hutchinson W.F., Wills D.P., Shipley P. MICRO-CHECKER: Software for identifying and correcting genotyping errors in microsatellite data // Mol. Ecol. Notes. 2004. V. 4. № 3. P. 535–538. https://doi.org/10.1111/j.1471-8286.2004.00684.x
Marshall T.C., Slate J.B.K.E., Kruuk L.E.B., Pemberton J.M. Statistical confidence for likelihood – based paternity inference in natural populations // Mol. Ecol. 1998. V. 7. № 5. P. 639–655. https://doi.org/10.1046/j.1365-294x.1998.00374.x
Pritchard J.K., Stephens M., Donnelly P. Inference of population structure using multilocus genotype data // Genetics. 2000. V. 155. № 2. P. 945–959. https://doi.org/10.1534/genetics.116.195164
Earl D.A., VonHoldt B.M. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method // Conservation Genet. Res. 2012. V. 4. № 2. P. 359–361. https://doi.org/10.1007/s12686-011-9548-7
Lischer H.E., Excoffier L. PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs // Bioinformatics. 2012. V. 28. № 2. P. 298–299. https://doi.org/10.1093/bioinformatics/btr642
DeNise S., Johnston E., Halverson J. et al. Power of exclusion for parentage verification and probability of match for identity in American kennel club breeds using 17 canine microsatellite markers // Animal Genet. 2004. V. 35. № 1. P. 14–17. https://doi.org/10.1046/j.1365-2052.2003.01074.x
Caniglia R., Fabbri E., Greco C. et al. Forensic DNA against wildlife poaching: Identification of a serial wolf killing in Italy // Forensic Sci. Int. Genet. 2010. V. 4. № 5. P. 334–338. https://doi.org/10.1016/j.fsigen.2009.10.012
Dayton M., Koskinen M.T., Tom B.K. et al. Developmental validation of short tandem repeat reagent kit for forensic DNA profiling of canine biological material // Croatian Med. J. 2009. V. 50. № 3. P. 268–285. https://doi.org/10.3325/cmj.2009.50.268
Whiteside H.M., Dawson D.A., Soulsbury C.D., Harris S. Mother knows best: Dominant females determine offspring dispersal in red foxes (Vulpes vulpes) // PLoS One. 2011. V. 6. № 7. P. e22145. https://doi.org/10.1371/journal.pone.0022145
Seddon J.M. Canid-specific primers for molecular sexing using tissue or non-invasive samples // Conservation Genet. 2005. V. 6. № 1. P. 147–149. https://doi.org/10.1007/s10592-004-7734-9
Botstein D., White R.L., Skolnick M., Davis R.W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms // Am. J. Hum. Genet. 1980. V. 32. № 3. P. 314. PMID: 6247908.