Structural conservation and variation in the mitochondrial control region of fringilline finches (Fringilla spp.) and the greenfinch (Carduelis chloris)

We sequenced the entire control region and portions of flanking genes(tRNA(Phe), tRNA(Glu), and ND6) in the common chaffinch (Fringillacoelebs), blue chaffinch (F. teydea), brambling (F. montifringilla), andgreenfinch (Carduelis chloris). In these finches the control region issimilar in length (1,223-1,237 bp) and has the same flanking gene order asin other birds, and contains a putative TAS element and the highlyconserved CSB-1 and F, D, and C boxes recognizable in most vertebrates.Cloverleaf-like structures associated with the TAS element at the 5' endand CSB-1 at the 3' end of the control region may be involved with the stopand start of D-loop synthesis, respectively. The pattern of nucleotide andsubstitution bias is similar to that in other vertebrates, and consequentlythe finch control region can be subdivided into a central, conserved G-richdomain (domain II) flanked by hypervariable 5'-C-rich (domain I) and3'-AT-rich (domain III) segments. In pairwise comparisons among finchspecies, the central domain has unusually low transition/transversionratios, which suggests that increased G + T content is a functionalconstraint, possibly for DNA primase efficiency. In finches the relativerates of evolution vary among domains according to a ratio of 4.2 (domainIII) to 2.2 (domain I) to 1 (domain II), and extensively among sites withindomains I and II. Domain I and III sequences are extremely useful inrecovering intraspecific phylogeographic splits between populations inAfrica and Europe, Madeira, and a basal lineage in Nefza, Tunisia. DomainII sequences are highly conserved, and are therefore only useful inconjunction with sequences from domains I and III in phylogenetic studiesof closely related species.