بررسی تنوع ژنتیکی گرازهای وحشی ایران بر اساس توالی‌های ناحیۀ کنترل میتوکندری

نوع مقاله: مقاله پژوهشی

نویسنده

استادیار گروه شیلات و محیط‌زیست، دانشکدۀ منابع طبیعی و علوم زمین، دانشگاه شهرکرد، شهرکرد، ایران

چکیده

مدیریت و حفاظت از حیات وحش نیازمند داشتن تصویری جامع از تنوع و تغییرپذیری ژنتیکی در ساختارهای جغرافیایی است. هدف پژوهش حاضر، بررسی تنوع ژنتیکی جمعیت‌های گراز وحشی در ایران با استفاده از یک قطعۀ 572 جفت بازی از ناحیۀ کنترل میتوکندریایی در نظر گرفته شد. به این منظور، تعداد 29 نمونه متعلق به جنوب کشور توالی‌یابی شد؛ همچنین 75 توالی دیگر که به مناطق مختلف ایران مربوط بودند از بانک ژن استخراج شدند. بر اساس تحلیل‌ها، چهار کلاد جهانی متعلق به گراز وحشی شامل کلادهای شرق نزدیک 1 (NE1)، شرق نزدیک 2 (NE2)، اروپایی و آسیایی در ایران حضور دارند و کلادهای اروپایی و NE1 به‌ترتیب کمترین و بیشترین پراکنش را به خود اختصاص می‌دهند. حضور هم‌جای کلادها در مناطق مختلف کشور از مهم‌ترین جنبه‌های درخور توجه است. شمال‌غربی کشور منطقۀ تماس کلادهای اروپایی و آسیایی در نظر گرفته می‌شود. بر اساس یافته‌ها، تعداد 20 هاپلوتایپ در 104 توالی از ایران شناسایی شد. تنوع هاپلوتایپی و تنوع نوکلئوتیدی در نمونه‌های ایران به‌ترتیب حدود 882/0 (انحراف معیار= 014/0) و 0145/0 (انحراف معیار= 00047/0) محاسبه شد. بر اساس تحلیل AMOVA، اختلاف ژنتیکی بین کلادها (84/82 درصد) بیش از اختلاف ژنتیکی داخل این کلادها بود؛ علاوه‌بر‌این، نمایۀ FST نیز وجود ساختار ژنتیکی معناداری را بین کلادها تأیید کرد. هیچ‌یک از نمایه‌های Fu’s FS و
Tajima’s D، نشانه‌های مشخصی از وجود گسترش جمعیت‌شناختی ناگهانی در کلادهای گراز وحشی متعلق به ایران را تأیید نکردند.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Genetic Diversity of Wild Boar Populations from Iran based on Mitochondrial DNA Control Region Sequences

نویسنده [English]

  • Mohammad Reza Ashrafzadeh
Assistant Professor, Department of Fisheries and Environmental Sciences, Faculty of Natural Resources and Earth Sciences, Shahrekord University, Shahrekord, Iran
چکیده [English]

Abstract
Wildlife management and conservation requires a comprehensive picture of genetic variation and variability in geographic structures. The purpose of the present study was to assess the genetic relationship and diversity of Iranian wild boar populations by analyzing a 572 bp fragment of mtDNA control region. To this end, a dataset was created using our sequences (29 wild boar) together with additional 75 sequences (from the south of Iran) downloaded from GenBank. Our analyses identified four distinct maternal clades within Iranian wild boars including Near East 1 (NE1), Near East 2 (NE2), Asiatic, and European. The European and NE1 clades have the smallest and largest geographical ranges in Iran, respectively. Furthermore, all of the clades are sympatrically distributed in the northwest of the country that this area could be considered as the contact zone of the four clades. According to the results, a total of 20 haplotypes were identified among the 104 sequences belonging to wild boars from Iran. The haplotype and nucleotide diversities were estimated as about 0.882 (±0.014) and 0.0145 (±0.00047), respectively. The AMOVA results of the Iranian clades demonstrated that the proportion of variation among clades (82.84%) was higher than the variation within them (17.16%). Also, the fixation index (FST) confirmed a significant genetic structure among the boar clades. Our findings revealed no evidence for a recent demographic expansion in the Iranian wild boars.

کلیدواژه‌ها [English]

  • Genetic Variability
  • Analysis of Molecular Variance
  • Haplotype Diversity
  • Sus Scrofa

منابع

Akhani, H. (2007) Diversity, biogeography, and photosynthetic pathways of Argusia and Heliotropium (Boraginaceae) in South-West Asia with an analysis of phytogeographical units. Botanical Journal of the Linnean Society 155: 401-425.

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

Alves, E., Ovilo, C., Rodriguez, M. and Silio, L. (2003) Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations. Animal Genetics 34: 319-324.

Alves, P. C., Pinheiro, Í., Godinho, R., Vicente, J., Gortázar, C. and Scandura, M. (2010) Genetic diversity of wild boar populations and domestic pig breeds (Sus scrofa) in South-western Europe. Biological Journal of the Linnean Society 101: 797-822.

Ashrafzadeh, M. R. and Bordkhani, M. (2012) New morphometric data of wild boar (Sus scrofa Linnaeus, 1758) from the Minoo island (Iran). Romanian Journal of Biology 57: 139-153.

Ashrafzadeh, M. R., Kaboli, M. and Naghavi, M. R. (2016) Mitochondrial DNA analysis of Iranian brown bears (Ursus arctos) reveals new phylogeographic lineage. Mammalian Biology-Zeitschrift für Säugetierkunde 81: 1-9.

Ashrafzadeh, M. R., Djan, M., Szendrei, L., Paulauskas, A., Scandura, M., Bagi, Z., Ilie, D. E., Kerdikoshvili, N., Marek, P., Soós, N. and Kusza, S. (2018a) Large-scale mitochondrial DNA analysis reveals new light on the phylogeography of Central and Eastern-European Brown hare (Lepus europaeus Pallas, 1778). PloS one 13: p.e0204653.

Ashrafzadeh, M. R., Rezaei, H. R., Khalilipour, O. and Kusza, S. (2018b) Genetic relationships of wild boars highlight the importance of Southern Iran in forming a comprehensive picture of the species’ phylogeography. Mammalian Biology-Zeitschrift für Säugetierkunde 92: 21-29.

Avise, J. C. (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge.

Bandelt, H.-J., Forster, P. and Röhl, A. (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37-48.

Burg, T. M., Trites, A. W. and Smith, M. J. (1999) Mitochondrial and microsatellite DNA analyses of harbour seal population structure in the northeast Pacific Ocean. Canadian Journal of Zoology 77: 930-943.

Excoffier, L. and 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: 564-567.

Frankham, R. (1996) Relationship of genetic variation to population size in wildlife. Conservation Biology 10: 1500-1508.

Frantz, A. C., Zachos, F. E., Kirschning, J., Cellina, S., Bertouille, S., Mamuris, Z., Koutsogiannouli, E. A. and Burke, T. (2013) Genetic evidence for introgression between domestic pigs and wild boars (Sus scrofa) in Belgium and Luxembourg: a comparative approach with multiple marker systems. Biological Journal of the Linnean Society 110: 104-115.

Fu, Y.-X. (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.

Goldsworthy, S., Francis, J., Boness, D. and Fleischer, R. (2000) Variation in the mitochondrial control region in the Juan Fernandez fur seal (Arctocephalus philippii). Journal of Heredity 91: 371-377.

Gongora, J., Fleming, P., Spencer, P. B. S., Mason, R., Garkavenko, O., Meyer, J.-N., Droegemueller, C., Lee, J. H. and Moran, C. (2004) Phylogenetic relationships of Australian and New Zealand feral pigs assessed by mitochondrial control region sequence and nuclear GPIP genotype. Molecular Phylogenetics and Evolution 33: 339-348.

Greenwood, P. J. (1980) Mating systems, philopatry and dispersal in birds and mammals. Animal Behaviour 28: 1140-1162.

Hewitt, G. (2000) The genetic legacy of the Quaternary ice ages. Nature 405: 907.

Hoffman, J., Matson, C., Amos, W., Loughlin, T. and Bickham, J. (2006) Deep genetic subdivision within a continuously distributed and highly vagile marine mammal, the Steller's sea lion (Eumetopias jubatus). Molecular Ecology 15: 2821-2832.

Keis, M., Remm, J., Ho, S. Y. W., Davison, J., Tammeleht, E., Tumanov, I. L., Saveljev, A. P., Männil, P., Kojola, I. and Abramov, A. V. (2013) Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographical structure and migration patterns among brown bears in north‐western Eurasia. Journal of Biogeography 40: 915-927.

Khalilzadeh, P., Rezaei, H. R., Fadakar, D., Serati, M., Aliabadian, M., Haile, J. and Goshtasb, H. (2016) Contact Zone of Asian and European Wild Boar at North West of Iran. PloS one 11: e0159499.

Kopatz, A., Eiken, H. G., Aspi, J., Kojola, I., Tobiassen, C., Tirronen, K. F., Danilov, P. I. and Hagen, S. B. (2014) Admixture and gene flow from Russia in the recovering Northern European brown bear (Ursus arctos). PLoS One 9: e97558.

Kusza, S., Ashrafzadeh, M. R., Tóth, B. and Jávor, A. (2018) Maternal genetic variation in the northeastern Hungarian fallow deer (Dama dama) population. Mammalian Biology-Zeitschrift für Säugetierkunde 93: 21-28.

Lacy, R. C. (1997) Importance of genetic variation to the viability of mammalian populations. Journal of Mammalogy 78: 320-335.

Laikre, L., Nilsson, T., Primmer, C. R., Ryman, N. and Allendorf, F. W. (2009) Importance of genetics in the interpretation of favourable conservation status. Conservation Biology 23: 1378-1381.

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

Larson, G., Albarella, U., Dobney, K., Rowley-Conwy, P., Schibler, J., Tresset, A., Vigne, J-D., Edwards, C. J., Schlumbaum, A. and Dinu, A. (2007) Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proceedings of the National Academy of Sciences 104: 15276-15281.

Larson, G., Liu, R., Zhao, X., Yuan, J., Fuller, D., Barton, L., Dobney, K., Fan, Q., Gu, Z. and Liu, X.-H. (2010) Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. Proceedings of the National Academy of Sciences 107: 7686-7691.

Librado, P. and Rozas, J. (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.

Luetkemeier, E. S., Sodhi, M., Schook, L. B. and Malhi, R. S. (2010) Multiple Asian pig origins revealed through genomic analyses. Molecular Phylogenetics and Evolution 54: 680-686.

Maselli, V., Rippa, D., Deluca, A., Larson, G., Wilkens, B., Linderholm, A., Masseti, M. and Fulgione, D. (2016) Southern Italian wild boar population, hotspot of genetic diversity. Hystrix, the Italian Journal of Mammalogy 27: 1-8.

Meijaard, E. and Moqanaki, E. M. (2011) Sus scrofa subspecies of Iran. Suiform Soundings 11: 6-11.

Mills, L. S., Schwartz, M. K., Tallmon, D. A. and Lair, K. P. (2003) Measuring and interpreting changes in connectivity for mammals in coniferous forests. In: Mammal community dynamics in western coniferous forests: management and conservation issues: 587-613. Cambridge University Press, Cambridge.

Mouthereau, F., Lacombe, O. and Vergés, J. (2012) Building the Zagros collisional orogen: timing, strain distribution and the dynamics of Arabia/Eurasia plate convergence. Tectonophysics 532: 27-60.

Nei, M. and Kumar, S. (2000) Molecular evolution and phylogenetics. Oxford University Press, Oxford.

Ojeda, A. A. (2010) Phylogeography and genetic variation in the South American rodent Tympanoctomys barrerae (Rodentia: Octodontidae). Journal of Mammalogy 91: 302-313.

Ottoni, C., Girdland Flink, L., Evin, A., Geörg, C., De Cupere, B., Van Neer, W., Bartosiewicz, L., Linderholm, A., Barnett, R. and Peters, J. (2012) Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics. Molecular Biology and Evolution 30: 824-832.

Ricklefs, R. E. and Schluter, D. (1993) Species diversity in ecological communities: historical and geographical perspectives. The University of Chicago Press, Chicago.

Sagheb Talebi, K., Sajedi, T. and Pourhashemi, M. (2013) Forests of Iran: a treasure from the past, a hope for the future. Springer, Netherlands.

Stewart, J. R., Lister, A. M., Barnes, I. and Dalén, L. (2010) Refugia revisited: individualistic responses of species in space and time. Proceedings of the Royal Society of London B: Biological Sciences 277: 661-671.

Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30: 2725-2729.

Weir, B. S. and Cockerham, C. C. (1984) Estimating F‐statistics for the analysis of population structure. Evolution 38: 1358-1370.

Wilson, D. E. and Reeder, D. M. (2005) Mammal species of the world: a taxonomic and geographic reference. Johns Hopkins University Press, Baltimore.

Xia, X. (2013) DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Molecular Biology and Evolution 30: 1720-1728.