title: The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements.
abstract: BACKGROUND
  The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds.
  
  
  RESULTS
  The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as "duplicate tRNA(Glu)-CR" and "duplicate tRNAThr-tRNA(Pro) and CR", were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication--random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea.
  
  
  CONCLUSIONS
  The duplicate tRNAThr-CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr-CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Zhou
authors.forename: Qingxian
authors.initials: Q
authors.lastname: Lin
authors.affiliation: Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, People's Republic of China. wzfang@xmu.edu.cn.
authors.forename: Wenzhen
authors.initials: W
authors.lastname: Fang
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Chen
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D001717:Birds / Q000145:classification / Q000235:genetics*; D015321:Gene Rearrangement / Q000235:genetics*; D020131:Genes, Duplicate; D054629:Genome, Mitochondrial; D024101:Mitochondrial Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D024101:Mitochondrial Proteins; D012335:RNA, Ribosomal; D012343:RNA, Transfer