Definition of mtDNA Markers for Studies in Pampas Deer (Ozotoceros bezoarticus) based On Fecal Samples

Shamira De Fátima Sallum Leandro¹ , Elias Alberto Gutierrez Carnelossi² , Pedro Henrique De Faria Peres³ , Rullian César Ribeiro⁴ , José Maurício Barbanti Duarte⁵

Section:Research Paper, Product Type: Journal-Paper
Vol.9 , Issue.5 , pp.1-8, Oct-2022

Online published on Oct 31, 2022

Copyright © Shamira De Fátima Sallum Leandro, Elias Alberto Gutierrez Carnelossi, Pedro Henrique De Faria Peres, Rullian César Ribeiro, José Maurício Barbanti Duarte . This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
 

View this paper at   Google Scholar | DPI Digital Library

XML View     PDF Download

How to Cite this Paper

Abstract :
Pampas deer, Ozotoceros bezoarticus (Linnaeus, 1758), is found within a wide geographic distribution in Latin America with five subspecies recognized (O. b. bezoarticus, O. b. celer, O. b. uruguayensis, O. b. arerunguaensis and O. b. leucogaster). The limited access to biological material and the lack of genetic structure information, however, hinder the conservation strategies for the species and the management of free-living populations. Therefore, we selected informative regions and developed primers for amplification of small sequences of mitochondrial DNA (Cytochrome-b, Dloop, ND5 and COI) to provide tools for studies using non-invasive genetic sampling. We evaluated the polymorphisms and phylogenetic signal of each region and successfully amplified it in fecal DNA samples of pampas deer from Pantanal. As results we described a set of primers that allow amplified DNA present in any fecal material to be applied in different approaches of conservation genetics. The methodological approach described here will favor genetic analyses of wild populations and highlights the relevance of non-invasive sampling to assist the decision-making and conservation strategies for this species.

Key-Words / Index Term :
Odocoileini, fecal DNA, non-invasive genetic sampling, minibarcoding, conservation

References :
[1]. González, S, Duarte, J. M. B, “Speciation, evolutionary history and conservation trends of neotropical deer,” Mastozoologia Neotropical, Vol. 27, Issue.10.31687, pp.37-47, 2020.
[2]. González, S, Cosse, M, Braga, F. G, Vila, A. R, Merino, M. L, Dellafiore, C, Cartes, J. L, Maffei, L, Dixon, M. G, “Pampas deer Ozotoceros bezoarticus (Linnaeus 1758),” Funep/IUCN publisher, Brasil, pp. 119–132, 2010.
[3]. González, S, Jackson, J. J, Merino, M. L, “Ozotoceros bezoarticus,” The IUCN Red List of Threatened Species, 2016.
[4]. Weber, M, González, S, “Latin American deer diversity and conservation: a review of status and distribution,” Ecoscience, Vol.10, Issue.4, pp.443-454, 2003.
[5]. Cabrera, A, “Sobre la sistematica del venado y su variación individual y geográfica,” Revista do Museu de La Plata, Vol.3, Issue.18, pp.5-41, 1943.
[6]. González, S, Álvarez-Valin, F, Maldonado, J. E, “Morphometric differentiation of endangered Pampas deer (Ozotoceros bezoarticus), with description of new subspecies from Uruguay,” Journal of mammalogy, Vol.83, Issue.4, pp.1127-1140, 2002.
[7]. Mourão, G, Coutinho, M, Mauro, R, Campos, Z, Tomás, W, Magnusson, W, “Aerial surveys of caiman, marsh deer and Pampas deer in the Pantanal Wetland of Brazil,” Biological Conservation, Vol.92, Issue.2, pp.175-183, 2000.
[8]. Duarte, J. M. B, Piovezan, U, Zanetti, E. S, Ramos, H. G. C, “Plano de Ação Nacional para a Conservação dos Cervídeos Ameaçados de Extinção,” Instituto Chico Mendes de Conservação da Biodiversidade, Brasil, pp.128, 2012.
[9]. Klink, C. A, Machado, R. B, “Conservation of the Brazilian cerrado,” Conservation Biology, Vol.19, Issue.3, pp.707-713, 2005.
[10]. Reynolds, J, Wesson, K, Desbiez, A. L, Ochoa-Quintero, J. M, Leimgruber, P, “Using remote sensing and random forest to assess the conservation status of critical Cerrado habitats in Mato Grosso do Sul, Brazil,” Land, Vol.5, Issue.2, pp.1-12, 2016.
[11]. Françoso, R. D, Brandão, R, Nogueira, C. C, Salmona, Y. B, Machado, R. B, Colli, G. R, “Habitat loss and the effectiveness of protected areas in the Cerrado Biodiversity Hotspot,” Natureza & Conservação, Vol.13, Issue.1, pp.35-40, 2015.
[12]. González, S, Maldonado, J. E, Leonard, J. A, Vilá, C, Duarte, J. M. B, Merino, M, Brum-Zorrilla, N, Wayne, R. K, “Conservation genetics of the endangered Pampas deer (Ozotoceros bezoarticus),” Molecular Ecology, Vol.7, Issue.1, pp.47–56, 1998.
[13]. Rodrigues, F. P, Garcia, J. F, Ramos, P. R. R, Bortolozzi, J, Duarte, J. M. B, “Genetic diversity of two Brazilian populations of the Pampas deer (Ozotoceros bezoarticus, Linnaeus 1758),” Brazilian Journal of Biology, Vol.67, Issue.4, pp.805-811, 2007.
[14]. Taber, A, Beck, H, González, S, Altrichter, M, Duarte, J. M. B, Reyna-Hurtado, R, “Case Study 8 Why Neotropical Forest Ungulates Matter,” Tropical Conservation: Perspectives on Local and Global Priorities, United States of America, Vol.255, pp.255-259, 2016.
[15]. Smith, D. A, Ralls, K, Hurt, A, Adams, B, Parker, M, Davenport, B, Smith, M. C, Maldonado, J. E, “Detection and accuracy rates of dogs trained to find scats of San Joaquin kit foxes (Vulpes macrotis mutica),” Animal Conservation, Vol.6, Issue.4, pp.339–346, 2003.
[16]. [16] Waits, L. P, Paetkau, D, “Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection,” Journal of Wildlife Management, Vol.69, Issue.4, pp.1419–1433, 2005.
[17]. Beja-Pereira, A, Oliveira, R, Alves, P. C, Schwartz, M. K, Luikart, G, “Advancing ecological understandings through technological transformations in noninvasive genetics,” Molecular Ecology Resources, Vol.9, Issue.5, pp.1279-30, 2009.
[18]. Oliveira, M. L, Norris, D, Ramírez, J. F. M, Peres, P. H. F, Galetti, M, Duarte, J. M. B, “Dogs can detect scat samples more efficiently than humans: an experiment in a continuous Atlantic Forest remnant,” Zoologia, Vol.29, Issue.2, pp.183–186, 2012.
[19]. Duarte, J. M. B, Talarico, A. C, Vogliotti, A, Garcia, J. E, Oliveira, M. L, Maldonado, J. E, González, S, “Scat detection dogs, DNA and species distribution modelling reveal a diminutive geographical range for the Vulnerable small red brocket deer Mazama bororo,” Oryx, Vol.51, Issue.4, pp.656-664, 2017.
[20]. Oliveira, M. L, Do Couto, H. T. Z, Duarte, J. M. B, “Distribution of the elusive and threatened Brazilian dwarf brocket deer refined by non-invasive genetic sampling and distribution modelling,” European Journal of Wildlife Research, Vol.65, Issue.2, pp.1-9, 2019.
[21]. Oliveira, M. L, Peres, P. H. F, Gatti, A, Morales-Donoso, J. A, Mangini, P. R, Duarte, J. M. B, “Faecal DNA and camera traps detect an evolutionarily significant unit of the Amazonian brocket deer in the Brazilian Atlantic Forest,” European Journal of Wildlife Research, Vol.66, Issue.2, pp.1-10, 2020.
[22]. Monteiro, L, Bonnemaison, D, Vekris, A, Petry, K. G, Bonnet, J, Vidal, R, Cabrita, J, Mégraud, F, “Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model,” Journal of Clinical Microbiology, Vol.35, Issue.4, pp.995–998, 1997.
[23]. Duarte, J. M. B, González, S, Maldonado, J. E, “The surprising evolutionary history of South American deer,” Molecular Phylogenetics and Evolution, Vol.49, Issue.1, pp.17-22, 2008.
[24]. Hassanin, A, Delsuc, F, Ropiquet, A, Hammer, C, Van Vuuren, B. J, Matthee, C, Ruiz-Garcia, M, Catzeflis, F, Areskoug, V, Nguyen, T. T, Couloux, A, “Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes,” Comptes Rendus Biologies, Vol.335, Issue.1, pp.32-50, 2012.
[25]. Sambrook, J, Fritsch, E. F, Maniatis, T, “Molecular cloning: a laboratory manual (No. Ed. 2)”, Cold spring harbor laboratory press, United States of America, 1989.
[26]. Irwin, D. M, Kocher, T. D, Wilson, A. C, “Evolution of the cytochrome b gene of mammals,” Journal of Molecular Evolution, Vol.32, Issue. 2, pp.128–144, 1991.
[27]. Vilà, C, Amorim, I. R, Leonard, J. A, Posada, D, Castroviejo, J, Petrucci-Fonseca, F, Crandall, K. A, Ellegren, H, Wayne, R. K, “Mitochondrial DNA phylogeography and population history of the grey wolf Canis lupus,” Molecular Ecology, Vol.8, Issue.12, pp.2089-2103, 1999.
[28]. Caparroz, R, Mantellatto, A. M. B, Bertioli, D, Figueiredo, M, Duarte, J. M. B, “Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubira,” Genetics and Molecular Biology, Vol.38, Issue.3, pp.338-345, 2015.
[29]. Vrijenhoek, R, “DNA Primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan Invertebrates,” Molecular Marine Biology And Biotechnology, Vol.3, Issue.5, pp.294-299, 1994.
[30]. Hall, T. A, “BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT,” Nucleic Acids Symposium Series, Vol.41, No.95-98, 1999.
[31]. Katoh, K, Rozewicki, J, Yamada, K. D, “MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization,” Briefings in bioinformatics, Vol.20, Issue.4, pp.1160-1166, 2019.
[32]. Kumar, S, Stecher, G, Li, M, Knyaz, C, Tamura, K, “MEGA X: Genetics analysis across computing platforms,” Molecular Biology and Evolution, Vol.35, Issue.6, pp.1547-1549, 2018.
[33]. Xia, X, “DAMBE7: new and improved tools for data analysis in molecular biology and evolution,” Molecular Biology and Evolution, Vol.35, Issue.6, pp.1550-1552, 2018.
[34]. Huelsenbeck, J, Ronquist, F, “MrBayes: Bayesian inference of phylogenetic trees”, Bioinformatics, Vol.17, Issue.8, pp.754-755, 2001.
[35]. Miller, M. A, Pfeiffer, W, Schwartz, T, “Creating the CIPRES Science Gateway for inference of large phylogenetic trees,” 2010 Gateway Computing Environments Workshop (GCE). Piscataway: IEEE, pp.1-8, 2010.
[36]. Darriba, D, Taboada, G. L, Doallo, R, Posada, D, “JModelTest 2: more models, new heuristics and parallel computing,” Nature Methods, Vol.9, Issue.8, pp.772, 2012.
[37]. Glenn, T, Bavis, R, Bollback, J, “DNA extraction protocols using silica. Laboratory of molecular systematics MRC 534,” Washington: Smithsonian Institution, 1998.
[38]. Rossetti, D. F, De Toledo, P. M, “Biodiversity from a historical geology perspective: a case study from Marajó Island, lower Amazon,” Geobiology, Vol.4, Issue.3, pp.215-223, 2006.
[39]. Rocha, D. G, Vogliotti, A, Gräbin, D. M, Assunção, W. R, Cambraia, B. C, D`Amico, A. R, Portela, A. E, Sollmann, R, “New populations of Pampas deer Ozotoceros bezoarticus discovered in threatened Amazonian savannah enclaves,” Oryx, Vol.53, Issue.4, pp.748-751, 2019.
[40]. Braga, F. G, Margarido, T. C. C, Costa, L. C. M, “Depredación de venados de campo Ozotoceros bezoarticus (L.,1758) por Puma Puma concolor (L., 1771) en el estado de Paraná,” Deer Specialist Group Newsletter, Vol.20, pp. 3-4, 2005.
[41]. Mazzolli, M, Benedet, M. R, “Registro recente, redução de distribuição e atuais ameaças ao veado-campeiro Ozotoceros bezoarticus (Mammalia, Cervidae) no Estado de Santa Catarina, Brasil,” Revista Biotemas, Vol.22, Issue.2, pp.137-142, 2009.
[42]. Gilbert, C, Ropiquet, A, Hassanin, A, “Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia): Systematics, morphology, and biogeography,” Molecular Phylogenetics and Evolution, Vol.40, Issue.1, pp.101-117, 2006.
[43]. Abril, V. V, Carnelossi, E. A. G, González, S, Duarte, J. M. B, “Elucidating the Evolution of the Red Brocket Deer Mazama americana Complex (Artiodactyla; Cervidae),” Cytogenetic and Genome Research, Vol.128, Issue.1-3, pp.177-187, 2010.
[44]. Gutiérrez, E. E, Helgen, K. M, McDonough, M. M, Bauer, F, Hawkins, M. T. R, Escobedo-Morales, L. A, Patterson, B. D, Maldonado, J. E, “A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling,” ZooKeys, Vol.697, pp.87-131, 2017.
[45]. Heckberg, N. S, “The systematics of the Cervidae: a total evidence approach,” PeerJ , Vol.8, pp.e8114, 2020.
[46]. Mantellatto, A. M. B, González, S, Duarte, J. M. B, “Molecular identification of Mazama species (Cervidae: Artiodactyla) from natural history collections,” Genetics and Molecular Biology, Vol.43, Issue.2, pp.e20190008, 2020.
[47]. Sarsavan, A, Ishaque, S, Lodha, M, Gupta, A, “Molecular characterization and genetic evolutionary relationship of Staphylococcus sciuri using 16S rRNA gene sequencing from nonvenomous snake checkered keelback (Fowlea piscator, Schneider, 1799) from Western Madhya Pradesh, India,” International Journal of Scientific Research in Biological Sciences, Vol.8, Issue.4, pp.86-90, 2021.
[48]. Devaraj, V, Kesti, S. S, “Isolation and Molecular Characterization of Termite GUT Microflora,” International Journal of Scientific Research in Biological Sciences, Vol.6, Issue.3, pp.41-49, 2019.
[49]. Rava, M, Ali, R, Das, S, “Taxonomic and Phylogenetic study of Termitomyces entolomoides in western Assam”, International Journal of Scientific Research in Biological Sciences, Vol.6, Issue.1, pp.84-88, 2019.
[50]. Kim, H. R, Park, Y. C, “Intraspecific comparison of two complete mitogenome sequences from the Korean water deer (Cervidae: Hydropotes inermis argyropus),” Mitochondrial DNA Part A, Vol.27, Issue.6, pp.4101-4103, 2016.
[51]. Ambriz-Morales, P, De La Rosa-Reyna, X. F, Sifuentes-Rincon, A. M, Parra-Bracamonte, G. M, Villa-Melchor, A, Chassin-Noria, O, Arellano-Vera, W, “The complete mitochondrial genomes of nine white-tailed deer subspecies and their genomic differences,” Journal of Mammalogy, Vol.97, Issue.1, pp.234-245, 2016.
[52]. Hebert, P. D, Ratnasingham, S, deWaard, J. R, “Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species,” Proceedings of the Royal Society of London. Series B: Biological Sciences, Vol. 270, Issue.1, pp.96-S99, 2003.
[53]. González, S, “Taxonomical identification of Neotropical deer species using molecular mitochondrial markers,” 22nd International Congress of Genetics, Foz de Iguaçu-Brazil, pp.10-14, 2018.
[54]. González, S, Maldonado, J. E, Ortega, J, Talarico, A. C, Bidegaray-Batista, L, Garcia, J. E, Duarte, J. M. B, “Identification of the endangered small red brocket deer (Mazama bororo) using noninvasive genetic techniques (Mammalia; Cervidae),” Molecular Ecology Resources, Vol.9, Issue.3, pp.754-758, 2009.
[55]. Simon, C, Frati, F, Beckenbach, A, Crespi, B, Liu, H, Flook, P, “Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers,” Annals of the entomological Society of America, Vol.87, Issue.6, pp.651-701, 1994.
[56]. Struck, T. H, Nesnidal, M. P, Purschke, G, Halanych, K. M, “Detecting possibly saturated positions in 18S and 28S sequences and their influence on phylogenetic reconstruction of Annelida (Lophotrochozoa),” Molecular phylogenetics and evolution, Vol.48, Issue.2, pp.628-645, 2008.
[57]. Mackiewicz, P, Matosiuk, M, ?wis?ocka, M, Zachos, F. E, Hajji, G. M, Saveljev, A. P, Seryodkin, I. V, Farahvash, T, Rezaei, H. R, Torshizi, R. V, Ratkiewicz, S. M. M, “Phylogeny and evolution of the genus Cervus (Cervidae, Mammalia) as revealed by complete mitochondrial genomes,” Scientific Reports, Vol.12, Issue.16381, pp.1-17, 2022.
[58]. Bach, B. H, Quigley, A. B, Gaynor, K. M, McInturf, A, Charles, K. L, Dorcy, J, Brashares, J. S, “Identifying individual ungulates from fecal DNA: a comparison of field collection methods to maximize efficiency, ease, and success,” Mammalian Biology, pp.1-12, 2022.
[59]. Oliveira, M. L, Duarte, J. M. B, “Amplifiability of mitochondrial, microsatellite and amelogenin DNA loci from fecal samples of red brocket deer Mazama americana (Cetartiodactyla, Cervidae),” Genetics and Molecular Research, Vol.12, Issue.1, pp.44-52, 2013.
[60]. Bowkett, A. E, Plowman, A. B, Stevens, J. R, Davenport, T. R, Van Vuuren, B. J, “Genetic testing of dung identification for antelope surveys in the Udzungwa Mountains,” Tanzania. Conservation Genetics, Vol.1, Issue.1, pp.251-255, 2009.
[61]. Rodrigues, N. T, Saranholi, B. H, Angeloni, T. A, Pasqualotto, N, Chiarello, A. G, Galetti Jr., P. M, “DNA mini?barcoding of leporids using noninvasive fecal DNA samples and its significance for monitoring an invasive species,” Ecology and evolution, Vol.10, Issue.12, pp.5219-5225, 2020.
[62]. Haag, T, Santos, A. S, De Angelo, C, Srbek-Araujo, A. C, Sana, D. A, Morato, R. G, Salzano, F. M, Eizirik, E, “Development and testing of an optimized method for DNA-based identification of jaguar (Panthera onca) and puma (Puma concolor) faecal samples for use in ecological and genetic studies,” Genetica, Vol.136, Issue.3, pp.505-512, 2009.
[63]. Miotto, R. A, Rodrigues, F. P, Ciocheti, G, Galetti Jr, P. M, “Determination of the minimum population size of pumas (Puma concolor) through fecal DNA analysis in two protected Cerrado areas in the Brazilian southeast,” Biotropica, Vol.39, Issue.5, pp.647-654, 2007.
[64]. Caslini, C, Comin, A, Peric, T, Prandi, A, Pedrotti, L, Mattiello, S, “Use of hair cortisol analysis for comparing population status in wild red deer (Cervus elaphus) living in areas with different characteristics,” European Journal of Wildlife Research, Vol.62, Issue.6, pp.713-723, 2016.
[65]. Venegas, C, Varas, V, Vásquez, J. P, Marín, J. C, “Non-invasive genetic sampling of deer: a method for DNA extraction and genetic analysis from antlers,” Gayana, Vol.84, Issue.1, pp.67-74, 2020.
[66]. de Souza, J. N, Oliveira, M. L, Duarte, J. M. B, “A PCR/RFLP methodology to identify non-Amazonian Brazilian deer species,” Conservation Genetics Resources, Vol.5, Issue.3, pp.639-641, 2013.
[67]. Miotto, R. A, "Análise do DNA fecal para a determinação da presença e do número populacional mínimo de onças-pardas (Puma concolor, Felidae) em duas Unidades de Conservação do estado de São Paulo, o Parque Estadual do Vassununga e a Estação Ecológica de Jataí," 2006.
[68]. Oliveira, M. L, Peres, P. H. F, Grotta-Neto, F, Vogliotti, A, de Camargo, F. P, Duarte, J. M. B, “Using niche modelling and human influence index to indicate conservation priorities for Atlantic forest deer species,” Journal for nature conservation, Vol.69, pp.126262, 2022.