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

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^Glu to tRNA^Phe. Genetic distances between species ranged from 1.80% (between <i>Carduelis pinus</i> and <i>Carduelis spinus</i>) to 25.34% (between <i>Carduelis sinica</i> and <i>Coccothraustes vespertinus</i>). The average genetic distances among the species within the genera varied from 5.11% (<i>Leucosticte</i>) to 14.31% (<i>Carpodacus</i>). 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 <i>Carpodacus, Carduelis</i> and <i>Serinus</i>.