The Updated Phylogenies of the Phasianidae Based on Combined Data of Nuclear and Mitochondrial DNA

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 nuc...

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Main Authors:	Shen, Yong-Yi, Dai, Kun, Cao, Xue, Murphy, Robert W., Shen, Xue-Juan, Zhang, Ya-Ping
Format:	Online
Language:	English
Published:	Public Library of Science 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991718/

id	pubmed-3991718
recordtype	oai_dc
spelling	pubmed-39917182014-04-21 The Updated Phylogenies of the Phasianidae Based on Combined Data of Nuclear and Mitochondrial DNA Shen, Yong-Yi Dai, Kun Cao, Xue Murphy, Robert W. Shen, Xue-Juan Zhang, Ya-Ping Research Article 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. Public Library of Science 2014-04-18 /pmc/articles/PMC3991718/ /pubmed/24748132 http://dx.doi.org/10.1371/journal.pone.0095786 Text en © 2014 Shen et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Shen, Yong-Yi Dai, Kun Cao, Xue Murphy, Robert W. Shen, Xue-Juan Zhang, Ya-Ping
spellingShingle	Shen, Yong-Yi Dai, Kun Cao, Xue Murphy, Robert W. Shen, Xue-Juan Zhang, Ya-Ping The Updated Phylogenies of the Phasianidae Based on Combined Data of Nuclear and Mitochondrial DNA
author_facet	Shen, Yong-Yi Dai, Kun Cao, Xue Murphy, Robert W. Shen, Xue-Juan Zhang, Ya-Ping
author_sort	Shen, Yong-Yi
title	The Updated Phylogenies of the Phasianidae Based on Combined Data of Nuclear and Mitochondrial DNA
title_short	The Updated Phylogenies of the Phasianidae Based on Combined Data of Nuclear and Mitochondrial DNA
title_full	The Updated Phylogenies of the Phasianidae Based on Combined Data of Nuclear and Mitochondrial DNA
title_fullStr	The Updated Phylogenies of the Phasianidae Based on Combined Data of Nuclear and Mitochondrial DNA
title_full_unstemmed	The Updated Phylogenies of the Phasianidae Based on Combined Data of Nuclear and Mitochondrial DNA
title_sort	updated phylogenies of the phasianidae based on combined data of nuclear and mitochondrial dna
description	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.
publisher	Public Library of Science
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991718/
_version_	1612079880004960256

The Updated Phylogenies of the Phasianidae Based on Combined Data of Nuclear and Mitochondrial DNA

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