title: False phylogenies on wood mice due to cryptic cytochrome-b pseudogene.
abstract: The phylogeny and phylogeography of the Old World wood mice (subgenus Sylvaemus, genus Apodemus, Muridae) are well-documented. Nevertheless, the distributions of species, such as A. fulvipectus and A. ponticus remain dubious, as well as their phylogenetic relationships with A. sylvaticus. We analysed samples of Apodemus spp. across Europe using the mitochondrial cytochrome-b gene (cyt-b) and compared the DNA and amino-acid compositions of previously published sequences. The main result stemming from this study is the presence of a well-differentiated lineage of Sylvaemus including samples of various species (A. sylvaticus, A. fulvipectus, A. ponticus) from distant locations, which were revealed to be nuclear copies of the mitochondrial cyt-b. The presence of this cryptic pseudogene in published sequences is supported by different pathways. This has led to important errors in previous molecular trees and hence to partial misinterpretations in the phylogeny of Apodemus.
authors.affiliation: School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia. sylvain.dubey@bio.usyd.edu.au
authors.forename: Sylvain
authors.initials: S
authors.lastname: Dubey
authors.forename: Johan
authors.initials: J
authors.lastname: Michaux
authors.forename: Harald
authors.initials: H
authors.lastname: Brünner
authors.forename: Rainer
authors.initials: R
authors.lastname: Hutterer
authors.forename: Peter
authors.initials: P
authors.lastname: Vogel
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D045303:Cytochromes b / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics; D005060:Europe; D019143:Evolution, Molecular; D050259:Genes, Mitochondrial; D014644:Genetic Variation; D006239:Haplotypes; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D051189:Murinae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D011544:Pseudogenes; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial; D045303:Cytochromes b