Comparison Of Mitochondrial Genomes And Genealogical Studies On 7 Species

Galliformes is an important group of birds, and closely related to human life. The phylogenetic relationship within Galliformes still remains controversial, partly because specific clades within this order underwent rapid radiations, although a series of phylogenetic investigations have been undertaken with different types of data. In recent years, mitochondrial genome sequence has been widely used in different levels of analyses focusing on Galliformes, and was proved as a powerful tool in resolving the evolution history of Galliformes. Here we sequenced mitochondrial genomes of seven Galliformes species (Arborophila ardens, Francolinus pintadeanus, Bonasa sewerzowi, Crossoptilon mantchuricum, Crossoptilon crossoptilon, Perdix perdix and Tetraogallus himalayensis), comparative genomic and phylogenomic analyses were carried out on Galliformes mitochondrial genomes combined with other Galliformes data. The main results are shown below: 1. The complete mitochondrial genome sequences of seven Galliformes species are 16,658-16,730 bp in size. All of them share the same 37 typical metazoan genes (13 protein-coding genes,22 transfer RNA genes and 2 ribosomal RNA genes), and a control region. The composition and gene order of these seven mitochondrial genomes are consistent with other previously published Galliformes species.2. The features of mitochondrial genome (e.g. nucleotide composition, base skew, codon usage, secondary structure of RNA, structure of D-loop) are similar within genera {Arborophila, Bonasa, Crossoptilon, Perdix and Tetraogallus). The Ka/Ks values are less than 1, except for some genes in Crossoptilon.3. The mitochondrial genome sequences of Galliformes are 16,658-16,841 bp in size, with the average length 16,705 bp. The length of Gallus mitochondrial genomes is larger than others, Galliformes species reveal much higher A+T content than G+C, and contain a weak A-skew and an obvious C-skew. The genes coded by J-strand have A/C-skews, while genes coded by N-strand include T/G-skews. There are obvious A/C-skews in the third codon of protein-coding genes.4. The protein-coding genes of Galliformes mitochondrial genomes prefer to choose the codon with NNM pattern. There are similai conservation among the three domains of 12S rRNA. In the six domains of 16S rRNA, the domain IV and V are the more conserved region, while the domain VI and III are more varied. All tRNAs can be folded into the typical cloverleaf secondary structures except for tRNASer(AGY), which lacks of DHU arm. The conservation of domain II is higher than domain I and III in D-loop. Besides, there are tandem repeat sequences in D-loop of some Galliformes.5. The genetic distance (P-distance) values based on mitochondrial genomes are between 0.001 and 0.197 in Galliformes species. The P-distance values of intra-genus are less than that of inter-genus except for Coturnix.6. According to the phylogenetic analyses, the phylogenetic relationships of seven families in Galliformes are ((((((Tetraoninae+Meleagrididae)+Phasianidae) +Odontophoridae)+Numididae)+Cracidae)+Megapodiidae). Megapodiidae forms the basal position of Galliformes. Tetraoninae and Meleagrididae are nested within Phasianidae. The clade (Arborophila+Caloperdix oculeus) is basal in Phasianidae. The monophyly of pheasant and partridge is not supported.7. The history of Galliformes differentiation can be dated back to the late Cretaceous. The origin and differentiation of Phasianidae occur in the Eocene. The diversification of genera within Phasianidae began in early Eocene, and the diversity expanded in the Oligocene and Miocene. The uplift of QTP (Qinghai-Tibet Plateau) and Quaternary climatic fluctuation affected the origin and evolution of some Phasianidae species, such as Crossoptilon.8. The phylogenetic informations of mitochondrial genome are mainly from protein-coding genes, and the third codon contains higher phylogenetic signal. The partitioned mitochondrial datasets used to reconstruct Galliformes phylogeny should consider gene type, code chain and different codon position.