Structure and variation of the Fringillidae (Aves: Passeriformes) mitochondrial DNA control region and their phylogenetic relationship

Abstract

The control region is the major noncoding segment of animal mitochondrial DNA. To infer the structure and variation of Fringillidae mitochondrial DNA control region, the entire control region sequences of 25 species were analyzed. The length of the control region sequences was very conserved (1230 ± 18) and can be separated into three domains. The frequency of both substitutions and gaps was highest in the third domain and lowest in the central region. The control region has the same flanking gene order from tRNA to tRNA. Genetic distances between species ranged from 1.80% (between Carduelis pinus and Carduelis spinus) to 25.34% (between Carduelis sinica and Coccothraustes vespertinus). The average genetic distances among the species within the genera varied from 5.11% (Leucosticte) to 14.31% (Carpodacus). The average genetic distances showed insignificantly negative correlation with ts/tv. Domain III is the most variable of the three domains among all the genera. The control region of Fringillidae contains a putative TAS element and the highly conserved CSB-1, and F, E, D, C boxes. However, neither CSB-2 nor CSB-3 could be unambiguously identified in the Fringillidae. The maximum likelihood method was used to construct a phylogenetic tree. Control region analysis demonstrated that some currently recognized genera may be polyphyletic, including Carpodacus, Carduelis and Serinus.

Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications

“…material 8: Table S2), with C-skew being more obvious. This C-skew was consistent with findings in other reported avian CRs (e.g., Huang et al 2017).…”

“…The proportions of variable sites among the three domains were 3.6%, 2.4% and 9.0%, respectively. Thus, most variation was found in domain III, similar to the findings of previous studies (Ruokonen and Kvist 2002;Huang et al 2017). A poly-C sequence was found near the 5' end of CR domain I in M. flava, with a sequence of CCCCCCCCCCTTCCCCCCCC, and this sequence was relatively conserved in the sampled mitogenome CRs (Suppl.…”

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

“…Key mtDNA molecular markers that have been used since the dawn of genetics include cytochrome b (MT-CYB), cytochrome c oxidase subunit I (MT-CO1), NADH dehydrogenase subunit 6 (MT-ND6), and 16S rRNA [19][20][21]. Thanks to its fast evolutionary rate, highly polymorphic nature, the non-coding CR has also been used in both present and ancient DNA studies [22] to resolve the phylogenetic history of closely related species [23,24].…”

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

“…Key mtDNA molecular markers that have been used since the dawn of genetics include cytochrome b (cob), cytochrome c oxidase subunit I (coi), NADH dehydrogenase subunit 6 (nad6), and 16S rRNA [19][20][21] . Thanks to its fast evolutionary rate, highly polymorphic nature, the non-coding CR has also been used in both present and ancient DNA studies 22 to resolve the phylogenetic history of closely related species 23,24 .…”