Low genetic variation of Persian leopard (Panthera pardus saxicolor) based on NADH5 mitochondrial gene

Document Type : Research Paper

Authors

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Abstract

Understanding phylogeography and genetic variation is a crucial to enhance conservation planning of species. Due to high level of fragmentation affecting many endangered species, unveiling their genetic status is prioritized to promote long-term persistence. Accordingly, the current investigation was carried out on a wide-ranging predator, the Persian leopard. We examined sequence variation in the mitochondrial NADH-5 gene with 550 base pairs for 38 leopards from different parts of Iran. Three closely related haplotypes were identified for the entire country. Apart from one commonly found haplotype throughout Iran, south Caucasus and Turkmenistan, two localized haplotypes were sequenced from southern Zagros and eastern Alborz. Our data supported that leopards do now show spatially differentiated genetic variation based on investigated gene in Iran as well as neighboring countries and possess lower genetic diversity comparing to other leopard subspecies or larger carnivores. It is essential to enhance conservation of the Persian leopard within southern Zagros where a specific haplotype occurs.

Keywords

Ashrafzadeh, M.R., Kaboli, M., Naghavi, M.R., 2016. Mitochondrial DNA analysis of Iranian brown bears (Ursus arctos) reveals new phylogeographic lineage. Mammalian Biology-Zeitschrift für Säugetierkunde, 81(1): 1-9.
Avise, J.C., 2000. Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge.
Bandelt, H.J., Forster, P., Röhl, A., 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular biology and evolution 16(1): 37-48.
Buzzard, P.J., Li, X. & Bleisch, W. V, 2017. The status of snow leopards Panthera uncia, and high altitude use by common leopards P. pardus, in north-west Yunnan, China. Oryx, pp.1–3.
Dubach, J., Patterson, B.D., Briggs, M.B., Venzke, K., Flammand, J., Stander, P., Scheepers, L., Kays, R., 2005. Molecular genetic variation across the southern and eastern geographic ranges of the African lion, Panthera leo. Conservation Genetics 7:15-24.
Eizirik, E., Kim, J.H., Menotti‚ÄźRaymond, M., Crawshaw, J.R., Peter, G., O’Brien, S.J., Johnson, W.E., 2001. Phylogeography, population history and conservation genetics of jaguars (Panthera onca, Mammalia, Felidae). Molecular Ecology 10(1): 65-79.
Excoffier, L., Lischer, H.E., 2010., Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10(3): 564-567.
Farhadinia, M.S., Farahmand, H., Gavashelishvili, A., Kaboli, M., Karami, M., Khalili, B., Montazamy, S., 2015. Molecular and craniological analysis of leopard, Panthera pardus (Carnivora: Felidae) in Iran: support for a monophyletic clade in Western Asia. Biological Journal of the Linnean Society, 114(4): 721-736.
Fattebert, J., Dickerson, T., Balme, G., Slotow, R., Hunter, L., 2013. Long-distance natal dispersal in leopard reveals potential for a three-country metapopulation. South African Journal of Wildlife Research, 43(1): 61-67.
Fu, Y.X., 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147(2): 915-925.
Gavashelishvili, A., Lukarevskiy, V., 2008. Modelling the habitat requirements of leopard Panthera pardus in west and central Asia. Journal of Applied Ecology 45(2): 579-588.
Hassanin, A., Ropiquet, A., Couloux, A., Cruaud, C., 2009. Evolution of the mitochondrial genome in mammals living at high altitude: new insights from a study of the tribe Caprini (Bovidae, Antilopinae). Journal of Molecular Evolution, 68(4), pp.293–310.
Jacobson, A.P., Gerngross, P., Lemeris Jr, J.R., Schoonover, R.F., Anco, C., Breitenmoser-Würsten, C., Durant, S.M., Farhadinia, M.S., Henschel, P., Kamler, J.F. and Laguardia, A., 2016. Leopard (Panthera pardus) status, distribution, and the research efforts across its range. PeerJ 4, p.e1974.
Janecka, J.E., Zhang, Y., Li, D., Munkhtsog, B., Bayaraa, M., Galsandorj, N., Wangchuk, T. R., Karmacharya, D., Li, J., Lu, Z., 2017. Range-Wide Snow Leopard Phylogeography Supports Three Subspecies. Journal of Heredity, p.esx044.
Johnson, W.E., Culver, M., Iriarte, J.A., Eizirik, E., Seymour, K.L., O’Brien, S.J., 1998. Tracking the evolution of the elusive Andean mountain cat (Oreailurus jacobita) from mitochondrial DNA. Journal of Heredity, 89, 227 –232.
Khorozyan, I.G., Baryshnikov, G.G., Abramov, A., 2006. Taxonomic status of the leopard, Panthera pardus (Carnivora, Felidae) in the Caucasus and adjacent areas. Russian Journal of Theriology 5(1): 41-52.
Librado, P., Rozas, J., 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11): 1451-1452.
Lopez, J.V., Culver, M., Stephens, J.C., Johnson, W.E., O’Brien, S.J., 1997. Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals. Molecular Biology and Evolution 14:277–286.
Miththapala, S., Seidensticker, J., O’Brien, S.J., 1996. Phylogeographic subspecies recognition in leopards (Panthera pardus): molecular genetic variation. Conservation Biology 10: 1115–1132.
Nassiri, M.R, 2, Parizadeh, S.A., Mahdavi, M., Ariannejad, H., 2011. Genetic and phylogenetic analysis of D-Loop in Persian leopard. Journal of Agricultrual Biotechnology 2(3): 81-95 (In Persian).
Nei, M., Kumar, S., 2000. Molecular evolution and phylogenetics, Oxford university press.
Nowell, K., Jackson, P., 1996. Wild cats: status survey and conservation action plan, IUCN Gland.
Ojeda, A.A., 2010. Phylogeography and genetic variation in the South American rodent Tympanoctomys barrerae (Rodentia: Octodontidae). Journal of Mammalogy, 91(2), pp.302–313.
Ramírez-Soriano, A., Ramos-Onsins, S.E., Rozas, J., Calafell, F., Navarro, A., 2008. Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination. Genetics, 179(1), pp.555–567.
Ramos-Onsins, S.E., Rozas, J., 2002. Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution, 19(12), pp.2092–2100.
Ronquist, F., Huelsenbeck, J.P., 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19(12), pp.1572–1574.
Ropiquet, A., Knight, A.T., Born, C., Martins, Q., Balme, G., Kirkendall, L., Hunter, L., Senekal, C., Matthee, C.A., 2015. Implications of spatial genetic patterns for conserving African leopards. Comptes rendus biologies, 338(11): 728-737.
Rozhnov, V.V., Lukarevsky, V.S., Sorokin, P.A., 2011. Application of molecular genetic characteristics for reintroduction of the leopard (Panthera pardus) in the Caucasus. In Doklady Biological Sciences (Vol. 437, No. 1, pp. 97-102). MAIK Nauka/Interperiodica.
Sambrook, J., Fritsch, E., Maniati, T., 1989. Molecular Cloning: a Laboratory Manual. Cold Spring Harbor Laboratory Press, New York.
Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123(3), pp.585–595.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S., 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular biology and evolution, 30(12), pp.2725–2729.
Tensen, L., Roelofs, D., Swanepoel, L.H., 2014. A note on the population structure of leopards (Panthera pardus) in South Africa. South African Journal of Wildlife Research 44(2): 193-197.
Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research, 22(22), pp.4673–4680.
Uphyrkina, O., Johnson, W.E., Quigley, H., Miquelle, D., Marker, L., Bush, M., O’Brien S.J., 2001. Phylogenetics, genome diversity and origin of modern leopard (Panthera pardus). Molecular Ecology 10: 2617–2633.
Uphyrkina, O., Miquelle, D., Quigley, H., Driscoll, C., O’Brien, S.J., 2002. Conservation genetics of the Far Eastern leopard (Panthera pardus orientalis). Journal of Heredity 93: 303–311.
Xia, X., 2013. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Molecular biology and evolution, 30(7): 1720-1728.