Complete mitochondrial genome of the Japanese wood pigeon, Columba janthina janthina (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.

The mitochondrial genome of a giant water bug Lethocerus deyrollei (Hemiptera: Belostomatidae) from South Korea

A giant water bug Lethocerus deyrollei (Hemiptera: Belostomatidae) is a large, predatory, and nocturnal hemipteran insect, which has been considered threatened and thus enrolled as an endangered species in South Korea and Japan. Here, we characterized the complete mitochondrial genome of L. deyrollei, which has a circular form with 19,295 bp in length, which is the longest when compared to those of the 111 hemipteran species reported so far. Its longest genome size is due to the extremely extended CR (4686 bp), which is much longer than those of China and Japan. It consisted of a total of 37 genes (13 PCGs, 22 tRNA genes, and two rRNA genes) and one control region (CR). The genome composition and gene order were identical to those previously reported from the same species of China and Japan with over 99.7% sequence similarities except for CR and trnI. The nucleotide composition was highly A + T biased, accounting for 71% of the whole mitochondrial genome, as in other species of Nepoidea. Based on the aa sequences of 13 PCGs, we reconstructed a maximum likelihood tree, which indicated that the three mitochondrial genomes of L. deyrollei from South Korea, China, and Japan are grouped, and also Lethocerus, Belostomatidae, Nepoidea, Nepomorpha, Heteroptra are strong monophyletic groups, respectively.

Complete mitogenomic and phylogenetic characteristics of the speckled wood-pigeon (Columba hodgsonii)

The speckled wood-pigeon, Columba hodgsonii, is mainly distributed in Bhutan, China, India, Laos, Myanmar, Nepal, Pakistan, and Thailand. Although there are several studies on birds in the family Columbidae, no study has focused on C. hodgsonii, a member of this family. Therefore, this study aimed to clarify the phylogenetic status of C. hodgsonii. The complete mitochondrial genome (mitogenome) of C. hodgsonii was sequenced and characterized and compared with those of other Columba species. The C. hodgsonii mitogenome was found to be 17,477 bp in size and contained 13 PCGs, two rRNAs, 22 tRNAs, and one CR. Of the 37 genes encoded by the C. hodgsonii mitogenome, 28 were on the heavy strand and nine were on the light strand. Twelve PCGs were initiated by ATN codons and one PCG harbored an incomplete termination codon (T-). The base composition of C. hodgsonii PCGs was A = 29.44%, T = 24.37%, G = 12.43%, and C = 33.76%. For the whole mitogenome, including PCGs, rRNAs, tRNAs, and the control region, the AT-skew was positive, and the GC-skew was negative. Phylogenetic analysis based on the base sequences of 13 PCGs from 28 Columbidae species and one outgroup using maximum likelihood and Bayesian inference indicated that C. hodgsonii belongs to the genus Columba and that the family Columbidae is monophyletic.

Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation

BACKGROUND

Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group's evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context.

RESULTS

We used ancient DNA and next generation sequencing approaches to assemble complete mitochondrial genomes for eleven pigeons, including the extinct Ryukyu wood pigeon (Columba jouyi), the thick-billed ground dove (Alopecoenas salamonis), the spotted green pigeon (Caloenas maculata), the Rodrigues solitaire (Pezophaps solitaria), and the dodo (Raphus cucullatus). We used a Bayesian approach to infer the evolutionary relationships among 24 species of living and extinct pigeons and doves.

CONCLUSIONS

Our analyses indicate that the earliest radiation of the Columbidae crown group most likely occurred during the Oligocene, with continued divergence of major clades into the Miocene, suggesting that diversification within the Columbidae occurred more recently than has been reported previously.