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Genetic relationships of wild boars highlight the importance of Southern Iran in forming a comprehensive picture of the species’ phylogeography

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Abstract

Genetic relationships between wild boar populations in the southern regions of Iran still remain unclear. Therefore in the present study our aim was filling this gap and providing preliminary knowledge about the phylogenetic status of Iranian wild boar based on two datasets of the mtDNA control region (the 402-bp and 605-bp segments as the first and second datasets, respectively). Altogether 1063 and 490 sequences were used in the shorter and longer sequences, respectively (29 own samples and 1034 and 461 Genbank sequences from previous studies in the first and second datasets, respectively). Our findings revealed that the wild boars living in Southern Iran belong to the previously described three clades: Asian, Near Eastern 1 (NE1) and Near Eastern 2 (NE2) clades. The NE1 and NE2 clades sympatrically occupy a wide range across the southeast to southwest of Iran, whereas the Asian clade is restricted to a small area in the southeastern part of Iran. Our results propose the existence of a contact zone between the Near Eastern clades and the Asian clade in the studied area. The fixation index (FST) and the analysis of molecular variance (AMOVA) demonstrated significant genetic structure among the identified clades. Some identified haplotypes have a wide distribution, which suggests that they are probably ancestral haplotypes or are likely to be a result of recent population expansion. Overall, current research demonstrates that Iranian wild boars have an important phylogenetic position among the others in the world. In other words, Iran is a very important region for addressing some of the topical questions about phylogenetic relationships among the Eurasian wild boar clades.

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References

  • Albarella, U., Dobney, K., Rowley-Conwy, P., 2009. Size and shape of the Eurasian wild boar (Sus scrofa), with a view to the reconstruction of its Holocene history. Environ. Archaeol. 14, 103–136.

    Article  Google Scholar 

  • Alexandri, P., Triantafyllidis, A., Papakostas, S., Chatzinikos, E., Platis, P., Papageorgiou, N., Larson, G., Abatzopoulos, T.J., Triantaphyllidis, C., 2012. The Balkans and the colonization of Europe: the post-glacial range expansion of the wild boar, Sus scrofa. J. Biogeogr. 39, 713–723.

    Article  Google Scholar 

  • Allen, M.S., Matisoo-Smith, E., Horsburgh, A., 2001. Pacific ‘Babes’: issues in the origins and dispersal of Pacific pigs and the potential of mitochondrial DNA analysis. Int. J. Osteoarchaeol. 11, 4–13.

    Article  Google Scholar 

  • Alves, E., Ovilo, C., Rodriguez, M., Silio, L., 2003. Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations. Anim. Genet. 34, 319–324.

    Article  CAS  PubMed  Google Scholar 

  • Alves, P.C., Pinheiro, Í., Godinho, R., Vicente, J., Gortázar, C., Scandura, M., 2010. Genetic diversity of wild boar populations and domestic pig breeds (Sus scrofa) in South-western Europe. Biol. J. Linn. Soc. 101, 797–822.

    Article  Google Scholar 

  • Amici, A., Serrani, F., Adriani, S., 2010. Somatic variability in wild boar(Sus scrofa L.) in different areas of Central Italy. Ital. J. Anim. Sci. 9, 39–44.

    Article  Google Scholar 

  • Ashrafzadeh, M.R., Bordkhani, M., 2012. New morphometric data of wild boar (Sus scrofa Linnaeus, 1758) from the Minoo Island (Iran). Rom. J. Biol. -Zool. 57, 139–153.

    Google Scholar 

  • Ashrafzadeh, M.R., Kaboli, M., Naghavi, M.R., 2016. Mitochondrial DNA analysis of Iranian brown bears (Ursus arctos) reveals new phylogeographic lineage. Mamm. Biol. 81, 1–9.

    Article  Google Scholar 

  • Bandelt, H.J., Forster, P., Röhl, A., 1999. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37–48.

    Article  CAS  PubMed  Google Scholar 

  • Calvignac, S., Hughes, S., Hänni, C., 2009. Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa. Divers. Distrib. 15, 742–750.

    Article  Google Scholar 

  • Clutton-Brock, J., 1987. A Natural History of Domesticated Mammals. Cambridge University Press, Cambridge, UK.

    Google Scholar 

  • Dan, M., Veličković, N., Obreht, D., Kočiš, T.N., Marković, V., Stevanović, M., Beuković, M., 2013. Mitochondrial DNA control region variability in wild boars from west balkans. Genetika 45, 515–526.

    Article  Google Scholar 

  • Djamali, M., De Beaulieu, J.L., Miller, N.F., Andrieu-Ponel, V., Ponel, P., Lak, R., Sadeddin, N., Akhani, H., Fazeli, H., 2009. Vegetation history of the SE section of the Zagros Mountains during the last five millennia; a pollen record from the Maharlou Lake, Fars Province, Iran. Veg. Hist. Archaeobot. 18, 123–136.

    Article  Google Scholar 

  • Excoffier, L., Lischer, H.E., 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and WindowsMol. Ecol. Resour. 10, 564–567.

    Article  PubMed  Google Scholar 

  • Fang, M., Berg, F., Ducos, A., Andersson, L., 2006. Mitochondrial haplotypes of European wild boars with 2n = 36 are closely related to those of European domestic pigs with 2n = 38. Anim. Genet. 37, 459–464.

    Article  CAS  PubMed  Google Scholar 

  • Fonseca, C., 2004. Population Dynamics and Management of Wild Boar (Sus scrofa L.) in Central Portugal and Southeastern Poland. Ph.D. Thesis. University of Aveiro, Aveiro, Portugal.

    Google Scholar 

  • Gallo Orsi, U., Macchi, E., Perrone, A., Durio, P., 2014. Biometric data and growth rates of a wild boar population living in the Italian Alps. J. Mt. Ecol. 3, 60–63.

    Google Scholar 

  • Giuffra, E., Kijas, J., Amarger, V., Carlborg, Ö., Jeon, J.T., Andersson, L., 2000. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics 154, 1785–1791.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Groves, C.P., 1983. Pigs East of the Wallace line. J. Soc. Océanistes 39, 105–119.

    Article  Google Scholar 

  • Herre, W., Röhrs, M., 1977. Zoological considerations on the origins of farming and domestication. In: Reed, C.A. (Ed.), Origins of Agriculture. The Hague, Chicago, pp. 245–279.

    Google Scholar 

  • Huang, Y.F., Shi, X.W., Zhang, Y.P., 1999. Mitochondrial genetic variation in Chinese pigs and wild boars. Biochem. Genet. 37, 335–343.

    Article  CAS  PubMed  Google Scholar 

  • Iacolina, L., Scandura, M., Bongi, P., Apollonio, M., 2009. Nonkin associations in wild boar social units. J. Mammal. 90, 666–674.

    Article  Google Scholar 

  • Karami, M., Mohammadi, H., Cheraghi, S., 2010. Present Distribution, Abundance and Problems of Wild Pig (Sus scrofa) in Iran, Wild Pig Conference, Florida: Science and Management.

    Google Scholar 

  • Khalilzadeh, P., Rezaei, H.R., Fadakar, D., Serati, M., Aliabadian, M., Haile, J., Goshtasb, H., 2016. Contact zone of Asian and European wild boar at North West of Iran. PLoS One 11, e0159499.

    Book  Google Scholar 

  • Kijas, J., Andersson, L., 2001. A phylogenetic study of the origin of the domestic pig estimated from the near-complete mtDNA genome. J. Mol. Evol. 52, 302–308.

    Article  CAS  PubMed  Google Scholar 

  • Kim, K.I., Lee,J.H., Li, K., Zhang, Y.P., Lee, S.S., Gongora, J., Moran, C., 2002. Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism. Anim. Genet. 33, 19–25.

    Article  CAS  PubMed  Google Scholar 

  • Kusza, S., Podgórski, T., Scandura, M., Borowik, T., Jávor, A., Sidorovich, V.E., Bunevich, A.N., Kolesnikov, M., Jędrzejewska, B., 2014. Contemporary genetic structure, phylogeography and past demographic processes of wild boar Sus scrofa population in Central and Eastern Europe. PLoS One 9, e91401.

    Book  Google Scholar 

  • Larson, G., Albarella, U., Dobney, K., Rowley-Conwy, P., Schibler, J., Tresset, A., Vigne, J.D., Edwards, C.J., Schlumbaum, A., Dinu, A., 2007. Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proc. Natl. Acad. Sci. U. S. A. 104, 15276–15281.

    Article  PubMed  PubMed Central  Google Scholar 

  • Larson, G., Dobney, K., Albarella, U., Fang, M., Matisoo-Smith, E., Robins, J., Lowden, S., Finlayson, H., Brand, T., Willerslev, E., 2005. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307, 1618–1621.

    Article  CAS  PubMed  Google Scholar 

  • Lattuada, L., Quaglia, F., Iannelli, F., Gissi, C., Mantecca, P., Bacchetta, R., Polli, M., 2009. Mitochondrial DNA sequence variations in some Italian wild boar populations. J. Anim. Breed. Genet. 126, 154–163.

    Article  CAS  PubMed  Google Scholar 

  • Lemel, J., Truvé, J., Söderberg, B., 2003. Variation in ranging and activity behaviour of European wild boar Sus scrofa in Sweden. Wildl. Biol. 9, 29–36.

    Article  Google Scholar 

  • Librado, P., Rozas, J., 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452.

    Article  CAS  PubMed  Google Scholar 

  • Luetkemeier, E.S., Sodhi, M., Schook, L.B., Malhi, R.S., 2010. Multiple Asian pig origins revealed through genomic analyses. Mol. Phylogenet. Evol. 54, 680–686.

    Article  CAS  PubMed  Google Scholar 

  • Maselli, V., Rippa, D., de Luca, A., Larson, G., Wilkens, B., Linderholm, A., Masseti, M., Fulgione, D., 2016. Southern Italian wild boar population, hotspot of genetic diversity. Hystrix Ital. J. Mammal. 27 (2), https://doi.org/10.4404/hystrix-27.2-11489.

    Google Scholar 

  • Massei, G., Genov, P.V., Staines, B.W., 1996. Diet, food availability and reproduction of wild boar in a Mediterranean coastal area. ActaTheriol. 41, 307–320.

    Google Scholar 

  • Naderi, G., Kaboli, M., Koren, T., Karami, M., Zupan, S., Rezaei, H.R., Krystufek, B., 2014. Mitochondrial evidence uncovers a refugium forthe fat dormouse (Glis glis Linnaeus, 1766) in Hyrcanian forests of northern Iran. Mamm. Biol. 79, 202–207.

    Article  Google Scholar 

  • Noroozi, J., Akhani, H., Breckle, S.W., 2008. Biodiversity and phytogeography of the alpine flora of Iran. Biodivers. Conserv. 17, 493–521.

    Article  Google Scholar 

  • Nowak, R., Paradiso, J., 1999. Walker’s Mammals of the World. The Johns Hopkins University Press, Baltimore and London.

    Google Scholar 

  • Oliver, W., Leus, K., 2008. Sus scrofa. In: IUCN 2008. IUCN Red List of Threatened Species. Version 2009.1, Available at: https://doi.org/www.iucnredlist.org.

    Google Scholar 

  • Ottoni, C., Girdland Flink, L., Evin, A., Geörg, C., De Cupere, B., Van Neer, W., Bartosiewicz, L., Linderholm, A., Barnett, R., Peters, J., 2012. Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics. Mol. Biol. Evol. 30, 824–832.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peterson, A.T., 1992. Philopatry and genetic differentation in the Aphelocomajays (Corvidae). Biol. J. Linn. Soc. 47, 249–260.

    Article  Google Scholar 

  • Podgórski, T., Lusseau, D., Scandura, M., Sönnichsen, L., Jędrzejewska, B., 2014. Long-lasting, kin-directed female interactions in a spatially structured wild boar social network. PLoS One 9, e99875.

    Book  Google Scholar 

  • Posada, D., 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25, 1253–1256.

    Article  CAS  PubMed  Google Scholar 

  • Rajaei, S.H., Rödder, D., Weigand, A.M., Dambach, J., Raupach, M.J., Wägele, J.W., 2013. Quaternary refugia in southwestern Iran: insights from two sympatric moth species (Insecta, Lepidoptera). Org. Divers. Evol. 13, 409–423.

    Article  Google Scholar 

  • Ronquist, F., Huelsenbeck,J.P., 2003. MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574.

    Article  CAS  PubMed  Google Scholar 

  • Ruvinsky, A., Rothschild, M.F., 1998. Systematics and evolution of the pig. In: Genet. Pig., pp. 1–16.

    Google Scholar 

  • Sagheb Talebi, K., Sajedi, T., Pourhashemi, M., 2013. Forests of Iran: A Treasure from the Past, a Hope forthe Future. Springer Science and Business Media, Dordrech, New York.

    Google Scholar 

  • Scandura, M., Iacolina, L., Crestanello, B., Pecchioli, E., Di Benedetto, M.F., Russo, V., Davoli, R., Apollonio, M., Bertorelle, G., 2008. Ancient vs. recent processes as factors shaping the genetic variation of the European wild boar: are the effects of the last glaciation still detectable? Mol. Ecol. 17, 1745–1762.

    Article  CAS  PubMed  Google Scholar 

  • Spencer, P., Hampton, J., Lapidge, S., Mitchell, J., Lee, J., Pluske, J., 2006. assessment of the genetic diversity and structure within and among populations of wild pigs (Sus scrofa) from Australia and Papua New Guinea. J. Genet. 85, 63–66.

    Article  CAS  PubMed  Google Scholar 

  • Spitz, F., Janeau, G., 1990. Spatial strategies: an attempt to classify daily movements of wild boar. ActaTheriol. 35, 129–149.

    Google Scholar 

  • Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S., 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Velickovic, N., Djan, M., Ferreira, E., Stergar, M., Obreht, D., Maletic, V., Fonseca, C., 2015. From north to south and back: the role of the Balkans and other southern peninsulas in the recolonization of Europe by wild boar. J. Biogeogr. 42, 716–728.

    Article  Google Scholar 

  • Velickovic, N., Ferreira, E., Djan, M., Ernst, M., Vidakovic, D.O., Monaco, A., Fonseca, C., 2016. Demographic history, current expansion and future management challenges of wild boar populations in the Balkans and Europe. Heredity 117, 348–357.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vilaça, S.T., Biosa, D., Zachos, F., Iacolina, L., Kirschning, J., Alves, P.C., Paule, L., Gortazar, C., Mamuris, Z., Jędrzejewska, B., Borowik, T., 2014. Mitochondrial phylogeography of the European wild boar: the effect of climate on genetic diversity and spatial lineage sorting across Europe. J. Biogeogr. 41, 987–998.

    Article  Google Scholar 

  • Waits, L., Taberlet, P., Swenson, J.E., Sandegren, F., Franzen, R., 2000. Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos). Mol. Ecol. 9, 421–431.

    Article  CAS  PubMed  Google Scholar 

  • Watanobe, T., Ishiguro, N., Nakano, M., 2003. Phylogeography and population structure of the Japanese wild boar Sus scrofa leucomystax: mitochondrial DNA variation. Zool. Sci. 20, 1477–1489.

    Article  CAS  Google Scholar 

  • Weir, B.S., Cockerham, C.C., 1984. Estimating F-statistics forthe analysis of population structure. Evolution 38, 1358–1370.

    CAS  PubMed  Google Scholar 

  • West, B.C., Cooper, A.L., Armstrong, J.B., 2009. In: Jack, H. (Ed.), Managing Wild Pigs: A Technical Guide. Berryman Institute, Department ofWildland Resources, Utah State University, Logan, USA.

  • Wu, G.S., Yao, Y.G., Qu, K.X., Ding, Z.L., Li, H., Palanichamy, M.G., Duan, Z.Y., Li, N., Chen, Y.S., Zhang, Y.P., 2007. Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia. Genome Biol. 8, R245.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ziaie, H., 2008. A Field Guide to the Mammals of Iran, second ed. Iran Wildlife Center Press, Tehran.

    Google Scholar 

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Authors and Affiliations

  1. Department of Fisheries and Environmental Sciences, Faculty of Natural Resources and Earth Sciences, Shahrekord University, Shahrekord, 88156-48456, Iran

    Mohammad Reza Ashrafzadeh

  2. Department of Environmental Sciences, Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, 49138-15739, Iran

    Hamid Reza Rezaei

  3. Department of Environmental Sciences, Faculty of Natural Resources, Khorramshahr University of Marine Science and Technology, Khorramshahr, 43175-64199, Iran

    Olyagholi Khalilipour

  4. Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032, Debrecen, Hungary

    Szilvia Kusza

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  1. Mohammad Reza Ashrafzadeh
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  3. Olyagholi Khalilipour
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  4. Szilvia Kusza
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Ashrafzadeh, M.R., Rezaei, H.R., Khalilipour, O. et al. Genetic relationships of wild boars highlight the importance of Southern Iran in forming a comprehensive picture of the species’ phylogeography. Mamm Biol 92, 21–29 (2018). https://doi.org/10.1016/j.mambio.2018.04.001

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