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Mammalia

Genetic diversity and phylogeography of European Roe Deer, Capreolus capreolus, in Iran as inferred from mtDNA genes (Mammalia: Cervidae)

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Pages 95-105 | Received 24 Oct 2020, Accepted 10 Mar 2021, Published online: 01 Apr 2021

References

  • Baker, K. H., & Hoelzel, A. R. (2013). Evolution of population genetic structure of the British roe deer by natural and anthropogenic processes (Capreolus capreolus). Ecology and Evolution, 3, 89–102. doi: 10.1002/ece3.430
  • Clement, M., Snell, Q., Walker, P., Posada, D., & Crandall, K. (2002). TCS: estimating gene genealogies. P. 184. In: 6th International Parallel and Distributed Processing Symposium, Fort Lauderdale.
  • Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9, 772–772. doi: 10.1038/nmeth.2109
  • Esmaeili, A., & Nasrnia, F. (2014). Deforestation and the environmental Kuznets curve in Iran. Small-scale forestry, 13, 397–406. doi: 10.1007/s11842-014-9261-y
  • 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, 564–567. doi: 10.1111/j.1755-0998.2010.02847.x
  • Fu, Y. X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915–925. doi: 10.1093/genetics/147.2.915
  • Fu, Y. X., & Li, W. H. (1993). Statistical tests of neutrality of mutations. Genetics, 133, 693–709. doi: 10.1093/genetics/133.3.693
  • Gentile, G., Vernesi, C., Vicario, S., Pecchioli, E., Caccone, A., Bertorelle, G., & Sbordoni, V. (2009). Mitochondrial DNA variation in roe deer (Capreolus capreolus) from Italy: Evidence of admixture in one of the last C. c. italicus pure populations from central-southern Italy. Italian Journal of Zoology, 76, 16–27. doi: 10.1080/11250000802018725
  • Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Pp 95-98. Nucleic acids symposium series. London: Information Retrieval Ltd., c1979-c2000.
  • Hassanin, A., Delsuc, F., Ropiquet, A., Hammer, C., Van Vuuren, B. J., Matthee, C., Ruiz-Garcia, M., Catzeflis, F., Areskoug, V., & Nguyen, T. T. (2012). Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. Comptes Rendus Biologies, 335, 32–50. doi: 10.1016/j.crvi.2011.11.002
  • Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754–755. doi: 10.1093/bioinformatics/17.8.754
  • Kabiri Balajadeh, H.R., Rezaei, H.R., Naderi, S. (2013). Genetic diversity of Roe deer (Capreolus capreolus) in Golestan and Mazandaran Provinces based on mtDNA D-loop gene sequencing [In Persian]. Animal Environment, 9, 49–56.
  • Kamieniarz, R., Wolc, A., Lisowski, M., Dabert, M., Grajewski, B., Steppa, R., & Szwaczkowski, T. (2011). Inter and intra subpopulation genetic variability of roe deer (Capreolus capreolus L.) assessed by I and II class genetic markers. Folia Biologica, 59, 127–133. doi: 10.3409/fb59_3-4.127-133
  • Kashinina, N., Danilkin, A., Zvychaynaya, E., Kholodova, M., & Kiryakulov, V. (2018). On the gene pool of Roe Deer (Capreolus) of Eastern Europe: Analysis of the Cyt b gene sequence variability. Russian Journal of Genetics, 54, 825–831. doi: 10.1134/S1022795418070049
  • Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35, 1547–1549. doi: 10.1093/molbev/msy096
  • Leigh, J. W., & Bryant, D. (2015). POPART: full-feature software for haplotype network construction. Methods in Ecology and Evolution, 6, 1110–1116. doi: 10.1111/2041-210X.12410
  • Lister, A., Grubb, P., & Sumner, S. (1998). Taxonomy, morphology and evolution of European roe deer. Pp. 23-46. In: Andersen, R., Duncan, P., & Linnell, J. (Eds), The European roe deer: The biology of success. Oslo: Scandinavian University Press.
  • Liu, Z., Wang, J., Sun, Y., Hou, Z., & Teng, L. (2015). Complete mitochondrial genome of a wild Alashan Red Deer (Cervus elaphus alxaicus). Mitochondrial DNA Part A, 27, 3313–3314. doi: 10.3109/19401736.2015.1018200
  • Lorenzini, R., & Lovari, S. (2006). Genetic diversity and phylogeography of the European roe deer: the refuge area theory revisited. Biological Journal of the Linnean Society, 88, 85–100. doi: 10.1111/j.1095-8312.2006.00606.x
  • Ludt, C. J., Schroeder, W., Rottmann, O., & Kuehn, R. (2004). Mitochondrial DNA phylogeography of red deer (Cervus elaphus). Molecular Phylogenetics and Evolution, 31, 1064–1083. doi: 10.1016/j.ympev.2003.10.003
  • Lynch, M., & Crease, T. (1990). The analysis of population survey data on DNA sequence variation. Molecular Biology and Evolution, 7, 377–394.
  • Markova, A. K., Smirnov, N. G., Kozhariov, A. V., Kazantseva, N. E., Simakova, A. N., & Kitaev, L. M. (1995). Late Pleistocene distribution and diversity of mammals in Northern Eurasia (PALEOFAUNA Database). Paleontologia i evolució, 28/29, 5–143.
  • Matosiuk, M., Sheremetyeva, I., Sheremetyev, I., Saveljev, A., & Borkowska, A. (2014a). Evolutionary neutrality of mtDNA introgression: evidence from complete mitogenome analysis in roe deer. Journal of Evolutionary Biology, 27, 2483–2494. doi: 10.1111/jeb.12491
  • Matosiuk, M., Borkowska, A., Świsłocka, M., Mirski, P., Borowski, Z., Krysiuk, K., Danilkin, A. A., Zvychaynaya, E. Y., Saveljev, A. P., & Ratkiewicz, M. (2014b). Unexpected population genetic structure of European roe deer in Poland: an invasion of the mtDNA genome from Siberian roe deer. Molecular Ecology, 23, 2559–2572. doi: 10.1111/mec.12745
  • Nei, M. (1987). Molecular evolutionary genetics. New York: Columbia University Press.
  • Olivieri, C., Marota, I., Rizzi, E., Ermini, L., Fusco, L., Pietrelli, A., De Bellis, G., Rollo, F., & Luciani, S. (2014). Positioning the red deer (Cervus elaphus) hunted by the Tyrolean Iceman into a mitochondrial DNA phylogeny. PloS one, 9(7), e100136. doi: 10.1371/journal.pone.0100136
  • Poorzady, M., & Bakhtiari, F. (2009). Spatial and temporal changes of Hyrcanian forest in Iran. iForest-Biogeosciences and Forestry, 2(5), 198. doi: 10.3832/ifor0515-002
  • Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.
  • 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, 555–567. doi: 10.1534/genetics.107.083006
  • Randi, E., Alves, P., Carranza, J., Milošević-Zlatanović, S., Sfougaris, A., & Mucci, N. (2004). Phylogeography of roe deer (Capreolus capreolus) populations: the effects of historical genetic subdivisions and recent non equilibrium dynamics. Molecular Ecology, 13, 3071–3083. doi: 10.1111/j.1365-294X.2004.02279.x
  • Randi, E., Mucci, N., Pierpaoli, M., & Douzery, E. (1998). New phylogenetic perspectives on the Cervidae (Artiodactyla) are provided by the mitochondrial cytochrome b gene. Proceedings of the Royal Society of London. Series B: Biological Sciences, 265(1398), 793–801. doi: 10.1098/rspb.1998.0362
  • Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539– 542. doi: 10.1093/sysbio/sys029
  • Royo, L. J., Pajares, G., Alvarez, I., Fernández, I., & Goyache, F. (2007). Genetic variability and differentiation in Spanish roe deer (Capreolus capreolus): a phylogeographic reassessment within the European framework. Molecular Phylogenetics and Evolution, 42, 47–61. doi: 10.1016/j.ympev.2006.05.020
  • Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. E., & Sánchez-Gracia, A. (2017). DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution, 34, 3299–3302. doi: 10.1093/molbev/msx248
  • Sadeghi, M., Malekian, M., & Khodakarami, L. (2017). Forest losses and gains in Kurdistan province, western Iran: Where do we stand? The Egyptian Journal of Remote Sensing and Space Science, 20, 51–59. doi: 10.1016/j.ejrs.2016.07.001
  • Schneider, S., & Excoffier, L. (1999). Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics, 152, 1079–1089.
  • Sommer, R. S., Fahlke, J. M., Schmölcke, U., Benecke, N., & Zachos, F. E. (2009). Quaternary history of the European roe deer Capreolus capreolus. Mammal Review, 39, 1–16. doi: 10.1111/j.1365-2907.2008.00137.x
  • Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595. doi: 10.1093/genetics/123.3.585
  • 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, 4673–4680. doi: 10.1093/nar/22.22.4673
  • Tsaparis, D., Sotiropoulos, K., Legakis, A., Kotoulas, G., & Kasapidis, P. (2019). New phylogeographic insights support the distinctiveness and conservation value of the little-known Greek roe deer populations. Mammalian Biology, 96, 23–27. doi: 10.1016/j.mambio.2019.03.010
  • Vernesi, C., Pecchioli, E., Caramelli, D., Tiedemann, R., Randi, E., & Bertorelle, G. (2002). The genetic structure of natural and reintroduced roe deer (Capreolus capreolus) populations in the Alps and central Italy, with reference to the mitochondrial DNA phylogeography of Europe. Molecular Ecology, 11, 1285–1297. doi: 10.1046/j.1365-294X.2002.01534.x
  • Wada, K., Nakamura, M., Nishibori, M., & Yokohama, M. (2005). The complete nucleotide sequence of mitochondrial genome in the rein deer (Rangifer tarandus) and red deer (Cervus elaphus). GenBank: unpublished.
  • Wiehler, J., & Tiedemann, R. (1998). Phylogeography of the European roe deer Capreolus capreolus as revealed by sequence analysis of the mitochondrial control region. Acta theriologica, 43 (Suppl. 5), 187–197. doi: 10.4098/AT.arch.98-58
  • Zvychaynaya, E. Y., Volokh, A., Kholodova, M., & Danilkin, A. (2013). Mitochondrial DNA polymorphism of the European roe deer, Capreolus capreolus (Artiodactyla, Cervidae), from the South-West of Ukraine. Vestnik zoologii, 47, 27–32. doi: 10.2478/vzoo-2013-0044

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