The complete mitochondrial genome of the Fancy Pigeon, Columba livia (Columbiformes: Columbidae)

The mitochondrial genome and phylogenetic characteristics of the Thick-billed Green-Pigeon, Treron curvirostra: the first sequence for the genus

Members of the genus Treron (Columbidae) are widely distributed in southern Asia and the Indo-Malayan Region but their relationships are poorly understood. Better knowledge of the systematic status of this genus may help studies of historical biogeography and taxonomy. The complete mitochondrial genome of T.curvirostra was characterized, a first for the genus. It is 17,414 base pairs in length, containing two rRNAs, 22 tRNAs, 13 protein coding genes (PCGs), and one D-loop with a primary structure that is similar to that found in most members of Columbidae. Most PCGs start with the common ATG codon but are terminated by different codons. The highest value of the Ka/Ks ratio within 13 PCGs was found in ATP8 with 0.1937, suggesting that PCGs of the mitochondrial genome tend to be conservative in Columbidae. Moreover, the phylogenetic relationships within Columbidae, which was based on sequences of 13 PCGs, showed that (T.curvirostra + Hemiphaganovaeseelandiae) were clustered in one clade, suggesting a potentially close relationship between Treron and Hemiphaga. However, the monophyly of the subfamilies of Columbidae recognized by the Interagency Taxonomic Information System could not be corroborated. Hence, the position of the genus Treron in the classification of Columbidae may have to be revised.

Complete mitogenome of Treron sphenurus (Aves, Columbiformes): the first representative from the genus Treron, genomic comparisons and phylogenetic analysis of Columbidae

The wedge-tailed green pigeon (Treron sphenurus) has a protective value in the evolution of the family Columbidae. In this study, the complete mitogenome of T. sphenurus from Baise City, China, which represents the first sequenced species of the genus Treron in Tribe Treronini, is reported. This was accomplished using PCR-based methods and a primer-walking sequencing strategy with genus-specific primers. The mitogenome was found to be 18,919 bp in length comprising 37 genes, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. In terms of structure and composition, many similarities were found between the T. sphenurus and Hemiphaga novaeseelandiae (New Zealand pigeon) mitogenomes. This was further supported by phylogenetic analysis showing that T. sphenurus has a close evolutionary relationship with H. novaeseelandiae. The complete mitogenome of T. sphenurus reported here is expected to provide valuable molecular information for further studies on the phylogeny of the genus Treron and for analyses of the taxonomic status of the family Columbidae.

Near-complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data

Species of the order Crocodylia are mostly large, predatory and semi-aquatic reptiles. Crocodylia, the closest living relatives of birds, first appeared in the Late Cretaceous period. In the present study, the complete mitochondrial (mt) genomes of 19 Crocodylia species, including two species (Melanosuchus niger and Caiman yacare) that have not been previously sequenced for mitogenomes, were processed through Illumina sequencing to offer genetic resources and compare with the mitogenomes of Crocodylia species reported previously. In addition, a high-resolution phylogenetic tree of nearly all current recognized species of Crocodylia is constructed based on mitogenomic data. Phylogenetic analyses support monophyly of three families: Alligatoridae (four genera: Alligator, Caiman, Melanosuchus and Paleosuchus), Crocodylidae (three genera: Crocodylus, Mecistops and Osteolaemus) and Gavialidae (two genera: Gavialis and Tomistoma). The tree topology is generally similar to previous studies. Molecular dating suggests that the first split within Crocodylia date back to the Upper Cretaceous (approx. 86.75 Mya). The estimated time to the most recent common ancestor (TMRCA) of Alligatoridae is 53.33 Mya and that of Crocodylidae and Gavialidae is 50.13 Mya, which might be closely linked to climate changes during the Late Palaeocene and Early Eocene. Additionally, this study proves that the diversification rate within Crocodylia began to increase from the Late Eocene (about 36 Mya) and two diversification peak periods of Crocodylia (0–10 Mya and 10–20 Mya) are disclosed, which is roughly consistent with the estimated crocodylian species richness through time. Combining all these clues, we can suggest that climate fluctuation may have played a decisive role in the speciation of Crocodylia.