title: The updated phylogenies of the phasianidae based on combined data of nuclear and mitochondrial DNA.
abstract: The phylogenetic relationships of species in the Phasianidae, Order Galliformes, are the object of intensive study. However, convergent morphological evolution and rapid species radiation result in much ambiguity in the group. Further, matrilineal (mtDNA) genealogies conflict with trees based on nuclear DNA retrotransposable elements. Herein, we analyze 39 nearly complete mitochondrial genomes (three new) and up to seven nuclear DNA segments. We combine these multiple unlinked, more informative genetic markers to infer historical relationships of the major groups of phasianids. The nuclear DNA tree is largely congruent with the tree derived from mt genomes. However, branching orders of mt/nuclear trees largely conflict with those based on retrotransposons. For example, Gallus/Bambusicola/Francolinus forms the sister-group of Coturnix/Alectoris in the nuclear/mtDNA trees, yet the tree based on retrotransposable elements roots the former at the base of the tree and not with the latter. Further, while peafowls cluster with Gallus/Coturnix in the mt tree, they root at the base of the phasianids following Gallus in the tree based on retrotransposable elements. The conflicting branch orders in nuclear/mtDNA and retrotransposons-based trees in our study reveal the complex topology of the Phasianidae.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China; Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China.
authors.forename: Yong-Yi
authors.initials: YY
authors.lastname: Shen
authors.affiliation: Xinjiang Institute of Ecology and Geography, the Chinese Academy of Sciences, Urumqi, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Dai
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China; University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Cao
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China; Department of Natural History, Royal Ontario Museum, Toronto, Canada.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Murphy
authors.affiliation: Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China.
authors.forename: Xue-Juan
authors.initials: XJ
authors.lastname: Shen
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China; Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China.
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Zhang
mesh_terms: D000818:Animals; D003370:Coturnix; D004272:DNA, Mitochondrial; D066264:Datasets as Topic; D046094:Galliformes / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D018626:Retroelements
chemical_list: D004272:DNA, Mitochondrial; D018626:Retroelements
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