Phylogeography of the gray red-backed vole <i>Craseomys rufocanus</i> (Rodentia: Cricetidae) across the distribution range inferred from nonrecombining molecular markers

Abramson, N.I.; Petrova, T.V.; Dokuchaev, N.E.; Obolenskaya, E.V.; Lissovsky, A.A.

Russian Journal of Theriology. Main page

Phylogeography of the gray red-backed vole Craseomys rufocanus (Rodentia: Cricetidae) across the distribution range inferred from nonrecombining molecular markers
Abramson N.I., Petrova T.V., Dokuchaev N.E., Obolenskaya E.V., Lissovsky A.A.
P. 137-156
A range-wide phylogeographic study of the gray red-backed vole (Craseomys rufocanus), was carried out using cytochrome b and cytochrome oxidase subunit I of mtDNA and a fragment of the Y-chromosome SRY gene. The results, based on 271 specimens from 81 localities over the majority of the species distribution, demonstrate that there are four main mitochondrial lineages with partly sympatric distribution. Spatial distribution of SRY haplotypes generally coincides with the mitochondrial distribution, being different mainly in details. However one of the mitochondrial lineages is not reflected in Y-chromosome based data. Most of the genetic diversity of C. rufocanus is allocated within the south-eastern part of the range, where representatives of all discovered mtDNA lineages and most of the SRY haplogroups have been found. The observed genetic structure could be explained by repeated glacial fragmentation of the species range together with following dispersion from several refugia.

DOI: 10.15298/rusjtheriol.11.2.04

References

Abramson N.I. & Lissovsky A.A. 2012. Subfamily Arvicolinae // Pavlinov I.Ya. & Lissovsky A.A. (eds.). The Mammals of Russia: A Taxonomic and Geographic Reference. Moscow: KMK Scientific Press. P.220-276.

Abramson N.I., Rodchenkova E.N. & Kostygov A.Yu. 2009. Genetic variation and phylogeography of the bank vole (Clethrionomys glareolus, Arvicolinae, Rodentia) in Russia with special reference to the introgression of the mtDNA of a closely related species, red-backed vole (Cl. rutilus) // Russian Journal of Genetics. Vol.45. P.533-545.

Agadjanian A.K. & Serdyuk N.V. 2005. History of mammalian communities and paleogeography of the Altai Mountains in the Paleolithic // Paleontological Journal. Vol.39. P.S645-S821.

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

Bennett K.D. 1997. Evolution and Ecology: the Pace of Life. Cambridge: Cambridge University Press. 241 p.

Borodin A.V. 1988. [History of voles of the genus Clethrionomys in the West Siberia Lowland] // Borodin A.V. (ed.). [Modern Status and History of Animals from the West Siberia Lowland]. Sverdlovsk: USSR Academy of Sciences, Ural Branch. P.23-31 [in Russian].

Excoffier L., Laval G. & Schneider S. 2006. Arlequin ver. 3.1: an integrated software package for population genetics data analysis. Bern: CMPG, University of Bern.

Fedorov V.B., Goropashnaya A.V., Boeskorov G.G. & Cook J.A. 2008. Comparative phylogeography and demographic history of the wood lemming (Myopus schisticolor): implications for late Quaternary history of the taiga species in Eurasia // Molecular Ecology. Vol.17. P.598-610.

Fu Y. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection // Genetics. Vol.147. P.915-925.

Galkina L.I. 1977. [Formation of anthropogenic rodents (Rodentia) of south-east of Western Siberia] // Yudin B.S. (ed.). [Fauna and Systematics of Vertebrates in Siberia]. Novosibirsk: Nauka. P.141-156 [In Russian].

Galkina L.I. & Foronova I.V. 1980. [The Anthropogene theriofauna from the Bachatskii Quarry of the Kuznetsk Depression (Kuznetsk Coal Field)] // Yudin B.S. (ed.). [Fauna and Ecology of Vertebrates of Siberia]. Novosibirsk: Nauka. P.176-188. [in Russian]

Gromov I.M. & Erbajeva M.A. 1995. [The Mammals of Russia and Adjacent Territories Lagomorphs and Rodents]. Sankt-Peterburg: Zoological Institute of Russian Academy of Sciences. 520 p. [In Russian]

Hall T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT // Nucleic Acids Symposium Series. Vol.41. P.95-98.

Hasegawa M., Kishino H. & Yano T.A. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA // Journal of Molecular Evolution. Vol.22. P.160-174.

Hewitt G.M. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation // Biological Journal of the Linnean Society. Vol.58. P.247-276.

Hewitt G.M. 2004. Genetic consequences of climatic oscillations in the Quaternary // Philosophical Transactions of the Royal Society of London. Vol.359. P.183-195.

Ho S.Y.W., Phillips M.J., Cooper A. & Drummond A.J. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times // Molecular Biology and Evolution. Vol.22. P.1561-1568.

Ivanova N.V., Zemlak T.S., Hanner R.H. & Hebert P.D.N. 2007. Universal primer cocktails for fish DNA barcoding // Molecular Ecology Notes. Vol.7. P.544-548.

Iwasa M.A., Kartavtseva I.V., Dobrotvorsky A.K., Panov V.V. & Suzuki H. 2002. Local differentiation of Clethrionomys rutilus in northeastern Asia inferred from mitochondrial gene sequences // Mammalian Biology. Vol.67. P.157-166.

Iwasa M.A., Utsumi Y., Nakata K., Kartavtseva I.V., Nevedomskaya I.A., Norihisa K. & Suzuki H. 2000. Geographic patterns of cytochrome b and SRY gene lineages in the gray red-backed vole Clethrionomys rufocanus from Far East Asia including Sakhalin and Hokkaido // Zoological Science. Vol.17. P.477-484.

Jobb G. 2008. TREEFINDER. Version of October, 2008. Munich, Germany. Available via http://www.treefinder.de/

Kowalski K. & Hasegawa Y. 1976. Quaternary rodents from Japan // Bulletin of the National Science Museum, Ser. C. (Geology). Vol.2. No.1. P.31-66.

Kulik I.L. 1972. [Taiga faunistic complex of Eurasian mammals] // Byulleten' Moskovskogo Obshchestva Estestvoipytatelei. Otdel Biologicheskii. T.77. No.4. P.11-24 [In Russian].

Lebedev V.S., Bannikova A.A., Tesakov A.S. & Abramson N.I. 2007. Molecular phylogeny of the genus Alticola (Cricetidae, Rodentia) as inferred from the sequence of the cytochrome b gene // Zoologica Scripta. Vol.36. P.547-563.

Lee M.-Y., Lissovsky A.A., Park S.-K., Obolenskaya E.V., Dokuchaev N.E., Zhang Y.-P., Yu L., Kim Y.-J., Voloshina I., Myslenkov A., Choi T.-Y., Min M.-S. & Lee H. 2008. Mitochondrial cytochrome b sequence variations and population structure of Siberian chipmunk (Tamias sibiricus) in northeastern Asia and population substructure in South Korea // Molecules and Cells. Vol.26. P.566-575.

Librado P. & Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data // Bioinformatics. Vol.25. P.1451-1452.

Markova A. & van Kolfschoten T. (eds.). 2008. Evolution of the European Ecosystems during Pleistocene-Holocene Transition (24-8 kyr BP). Moscow: KMK Scientific Press. 556 p.

Musser G.G. & Carleton M.D. 2005. Superfamily Muroidea // Wilson D.E. & Reeder D.M. (eds.). Mammal Species of the World: A Taxonomic and Geographic Reference, 3rd ed. Baltimore: Johns Hopkins University Press. Vol.2. P.894-1531.

Miller S.A., Dykes D.D. & Polesky H.F. 1988. A simple salting out procedure for extracting DNA from human nucleated cells // Nucleic Acids Research. Vol.16. P.1215.

Ognev S.I. 1950. [Mammals of the USSR and Adjacent Countries (Mammals of Eastern Europe and Northern Asia). Rodents. Vol.7. Microtinae]. Moskva, Leningrad: Izdatel'stvo AN SSSR Publ. 706 p. [in Russian]. Translated as: Ognev S.I. 1964. Mammals of the USSR and adjacent countries: Rodents. Vol.7. Jerusalem: Jean Salkind Publisher. 640 p.

Ohdachi S., Dokuchaev N.E., Hasegawa M. & Masuda R. 2001. Intraspecific phylogeny and geographical variation of six species of northeastern Asiatic Sorex shrews based on the mitochondrial cytochrome b sequences // Molecular Ecology. Vol.10. P.2199-2213.

Peterson G.I. & Masel J. 2009. Quantitative prediction of molecular clock and Ka/Ks at short timescales // Molecular Biology and Evolution. Vol.26. P.2595-2603.

Ronquist F. & Huelsenbeck J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models // Bioinformatics. Vol.19. P.1572-1574.

Shenbrot G.I. & Krasnov B.R. 2005. An Atlas of the Geographic Distribution of the Arvicoline Rodents of the World (Rodentia, Muridae: Arvicolinae). Sofia: Pensoft. 350 p.

Sinclair A.H., Berta P., Palmer M.S., Hawkins J.R., Griffiths B.L., Smith M.J., Foster J.W., Frischauf A.M., Lovell-Badge R. & Goodfellow P.N. 1990. A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif // Nature. Vol.346. P.240-244.

Skiba L.A. 1975. [The history of development of vegetation of Kamchatka in the end of Coenozoic] // Trudy Geologicheskogo Instituta AN SSSR. Vol.276. P.1-70 [in Russian].

Suzuki H., Minato S., Sakurai S., Tsuchiya K. & Fokin I.M. 1997. Phylogenetic position and geographic differentiation of the Japanese dormouse, Glirulus japonicus, revealed by variations among rDNA, mtDNA and the SRY gene // Zoological Science. Vol.14. P.167-173.

Swofford D.L. 1998. PAUP. Phylogenetic Analysis Using Parsimony (and Other Methods). Sunderland, Massachusetts: Sinauer Associates.

Tamura K. & Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees // Molecular Biology and Evolution. Vol.10. P.512-526.

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. Vol.22. P.4673-4680.

Velichko A.A. (ed.). 2009. [Paleoclimates and Paleoenvironments of Extra-tropical Regions of the Northern Hemisphere. Late Pleistocene - Holocene. Atlas-Monograph]. Moskva: GEOS. 119 p. [in Russian]

Volkova V.S. & Babushkin A.E. (eds.). 2000. [Unified Regional Stratigraphic Scheme of Quaternary Deposits of West Siberian Plain]. Novosibirsk: SNIIGGIMS. 64 p. [in Russian]

West K.J. 2000. Plant Life of the Quaternary Cold Stages. Cambridge: Cambridge University Press. 332 p.

Zazhigin V.S. 1980. [Late Pliocene and Anthropogene rodents of the south of western Siberia] // Trudy Geologicheskogo Instituta AN SSSR. Vol.339. P.1-156 [in Russian].

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