Abstract:
The interpretation of a signal sent by the mtDNA cytb gene as a molecular marker in phylogenetic and population genetic research can be complicated by cumulative influence of parallel mutations, i.e., the entropy of nucleotide sequences. Such a phenomenon impedes differentiation among the effects of hybridization, natural polymorphisms, and artifacts imposed by pseudogenes. We analyzed possible limitations in the use of the mtDNA cytb gene as a molecular marker by the example of the Apodemus genus. For this purpose, the entropy of nucleotide sequences was calculated, and probable tracts of gene conversion were sought in samples of various Apodemus species from Tibet, Korea, south of Russian Primorye, and Western Europe. Many haplotypes were identified as containing tracts of gene conversion. The high level of nucleotide sequence variability was found in species from Tibet, particularly, in A. draco, presumably due to the influence of low effective sizes of populations on the speed of point mutation accumulation and also cytochrome b role in the adaptation to unfavorable environment. The effects of hypervariability in cytb nucleotide sequences of some samplings resulting in entropy growth imitating gene conversion when compared to other species of the genus were analyzed. Examples of possible pseudogene interference among published cytb sequences are provided. It is suggested that the strategy in the use of the mtDNA cytb gene in population genetics and phylogenetics should be adapted to the degree of the gene variability. Emphasis is placed on the necessity of close control over sequencing data.
About The Authors:
A. G. Lapinski. Institute of the Biological Problems of the North, Far Eastern Branch of the RAS, Magadan, Russia; Russian Federation
L. L. Solovenchuk. Institute of the Biological Problems of the North, Far Eastern Branch of the RAS, Magadan, Russia; Russian Federation
References:
1. Abramson N.I. Filogeniya: itogi, problemy, perspektivy. Informatsionnyĭ vestnik VOGiS. 2007;11(2):307-331.
2. Grechko V.V. Problemy molekulyarnoĭ filogenetiki na primere otryada cheshuĭchatykh reptiliĭ (otryad Squamata): mitokhondrial’nye DNK markery. Molekulyar. biologiya. 2013;47(1): 61-82.
3. Dokuchaev N.E., Lapinskiĭ A.G., Solovenchuk L.L. Geneticheskaya izmenchivost’ polevykh mysheĭ (Apodemus agrarius Pallas, 1771) Dal’nego Vostoka Rossii po rezul’tatam RAPD-PCR analiza. Izv. RAN. Ser. biol. 2008;4:429-434.
4. Zykov S.V. Vnutrividovaya izmenchivost’ i mezhvidovaya differentsiatsiya mysheĭ rodov Apodemus, Mus i Sylvaemus Ural’skogo regiona po kranial’nym priznakam: Avtoref. dis. … kand. biol. nauk. Ekaterinburg: UGU im. A.M. Gor’kogo, 2011.
5. Kartavtseva I.V. Kariosistematika lesnykh i polevykh mysheĭ (Rodentia, Muridae). Vladivostok: Dal’nauka, 2002.
6. Kimura M. Molekulyarnaya evolyutsiya: teoriya neĭtral’nosti. M.: Mir, 1985.
7. Malyarchuk B.A. Gennaya konversiya mitokhondrial’nogo genoma pri mezhvidovoĭ gibridizatsii u polevok roda Clethrionomys. Biokhimiya. 2012;77(5):642-648.
8. Pereverzeva V.V., Pavlenko M.V. Raznoobrazie stroeniya gena tsitokhroma b mitokhondrial’noĭ DNK polevoĭ myshi Apodemus agrarius Pallas, 1771 iz populyatsiĭ yuga Dal’nego Vostoka Rossii. Izv. RAN. Ser. biol. 2014;1:5-16.
9. Chelomina G.N., Atopkin D.M. Molekulyarno-geneticheskie svidetel’stva glubokogo filogeneticheskogo razryva mezhdu evropeĭskoĭ i aziatskoĭ rasami maloĭ lesnoĭ myshi po dannym izmenchivosti gena tsitokhroma b mtDNK. Molekulyar. biologiya. 2010;44(5):792-803.
10. Avise J.C. Phylogeography: The History and Formation of Species. N.Y.: Harvard Univ. Press, 2000.
11. Avise J.C., Johns G.C. Proposal for a standardized temporal scheme of biological classification of extant species. Proc. Natl Acad. Sci. USA. 1999;96:7358-7363.
12. Balakirev E.S., Ayala F.J. Pseudogenes: are they «Junk» or functional DNA. Ann. Rev. Genet. 2003;37:123-151.
13. Betrán E., Rozas J., Navarro A., Barbadilla A. The estimation of the number and the length distribution of gene conversion tracts from population DNA sequence data. Genetics. 1997;146(1):89-99.
14. Bosch E., Hurles M.E., Navarro A., Jobling M.A. Dynamics of a human interparalog gene conversion hotspot. Genome Res. 2004;14:835-844.
15. Calvignac S., Konecny L., Malard F., Douady C.J. Preventing the pollution of mitochondrial datasets with nuclear mitochondrial paralogs (numts). Mitochondrion. 2011;11:246-254.
16. De Woody J.A., Chesser R.K., Baker R.J. A Translocated mitochondrial cytochrome b pseudogene in voles (Rodentia: Microtus). J. Mol. Evol. 1999;48:380-382.
17. Dubey S., Michaux J., Brünner H., Hütterer R., Vogel P. False phylogenies on wood mice due to cryptic cytochrome b pseudogene. Mol. Phylogenet. Evol. 2009;50:633-641.
18. Esposti D.M., De Vries S., Crimi M., Ghelli A., Patarnello T., Meyer A. Mitochondrial cytochrome b: evolution and structure of the protein. Biochim. Biophys. Acta. 1993;1143:243-271.
19. Fan Z., Liu S., Liu Y., Zhang X, Yue B. How Quaternary geologic and climatic events in the southeastern margin of the Tibetan Plateau influence the genetic structure of small mammals: inferences from phylogeography of two rodents, Neodon irene and A. latronum. Genetica. 2011;139(3):339-351.
20. Fan Z., Liu S., Liu Y., Lihuan L., Xiuyue Z., Bisong Y. Phylogeography of the South China field mouse (Apodemus draco) on the Southeastern Tibetan plateau reveals high genetic diversity and glacial refugia. PLoS ONE. 2012;7(5):e38184. DOI: 10.1371/journal.pone.0038184
21. Fietz K., Graves J.A., Olsen M.T. Control: a reassessment and comparison of GenBank and shromatogram mtDNA sequence variation in baltic grey seals (Halichoerus grypus). PLoS ONE. 2013;8(8):e72853. DOI:10.1371/journal.pone.0072853
22. Filippucci M.G., Macholán M., Michaux J.R. Genetic variation and evolution in the genus Apodemus (Muridae: Rodentia). Biol. J. Linnean Soc. 2002;75(3):395-419.
23. Hall T.A. BioEdit: a user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 1999;41:95-98.
24. Irwin D.M., Kocher T.D., Wilson A.C. Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 1991;32:128-144.
25. Ishii K., Charlesworth B. Associations between allozyme loci and gene arrangements due to hitch-hiking effects of new inversions. Genet. Res. 1977;30:93-106.
26. Johns G.C., Avise J.C. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b. Mol. Biol. Evol. 1998;15:1481-1490.
27. Kaneda H., Hayashi J.-I., Takahama S., Taya C., Lindahl K.F., Yonekawa H. Elimination of paternal mitochondrial DNA in intraspecific crosses during early mouse embryogenesis. Proc. Natl Acad. Sci. USA. 1995;92:4542-4546.
28. Leslie J.F., Watt W.B. Some evolutionary consequences of the molecular recombination process. Trends Genet. 1986;2:288-291. Librado P., Rozas J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25: 1451-1452.
29. Liu Q., Chen P., He K., Kilpatrick C.W., Liu S.Y., Yu F.H., Jiang X.L. Phylogeographic Study of Apodemus ilex (Rodentia: Muridae) in Southwest China. PLoS ONE. 2012;7(2):e31453.
30. Meyer A. Shortcomings of the cytochrome b gene as a molecular marker. Trends Ecol. Evol. 1994;9:278-280.
31. Michaux J.R., Chevret P., Filippucci M.G., Macholán M. Phylogeny of the genus Apodemus with a special emphasis to the subgenus Sylvaemus using the nuclear IRBP gene and two mitochondrial markers: cytochrome b and 12S rRNA. Mol. Phylogenet. Evol. 2002;23:123-136.
32. Michaux J.R., Libois R., Filippucci M.-G. So close and so different: comparative phylogeography of two small mammal species, the yellow-necked fieldmouse (Apodemus flavicollis) and the woodmouse (Apodemus sylvaticus) in the western Palearctic region. Heredity. 2005;94:52-63.
33. Oh D.J., Kim T.W., Chang M.H., Han S.H., Oh H.S., Kim S.J. Migration route estimation of the Jeju striped field mouse Apodemus agrarius chejuensis (Rodentia, Muridae). Mitochondrial DNA. 2013;24:137-144.
34. Rocha-Olivares A., Rosenblatt R.H., Vetter R.D. Molecular evolution, systematics, and zoogeography of the rockfish subgenus Sebastomus (Sebastes, Scorpaenidae) based on mitochondrial cytochrome b and control region sequences. Mol. Phyl. Evol. 1999;11(3):441-458.
35. Sakka H., Quéré J.-P., Kartavtseva I., Pavlenko M., Chelomina G., Atopkin D., Bogdanov A., Michaux J. Comparative phylogeography of four Apodemus species (Mammalia: Rodentia) in the Asian Far East: evidence of Quaternary climatic changes in their genetic structure. Biol. J. Linn. Soc. 2010;100(4):797-821.
36. Sanford J.C. Genetic Entropy and the Mystery of the Genome. N.Y.: Elim, Elim Publ., 2006.
37. Schneider T.D., Stephens R.M. Sequence logos: a new way to display consensus sequences. Nucl. Acids Res. 1990;18:6097-6100.
38. Shannon C.E. A mathematical theory of communication. Bell Syst. Tech. J. 1948;27:379-423.
39. Shitara H., Hayashi J.I., Takahama S., Kaneda H., Yonekawa H. Maternal inheritance of mouse mtDNA in interspecific hybrids: segregation of the leaked paternal mtDNA followed by the prevention of subsequent paternal leakage. Genetics. 1998;148(2):851-857.
40. Smith M.F., Thomas W.K., Patton J.L. Mitochondrial DNA-like sequence in the nuclear genome of an akodontine rodent. Mol. Biol. Evol. 1992;9(2):204-215.
41. Suzuki H., Filippucci M.G., Chelomina G.N., Sato J.J., Serizawa K., Nevo E. Biogeographic view of Apodemus in Asia and Europe inferred from nuclear and mitochondrial gene sequences. Biochem. Genet. 2008;46:329-346.
42. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011;28:2731-2739.
