Multiple independent origins of mitochondrial gene order in birds

Abstract

Mitochondrial genomes of all vertebrate animals analyzed to date have the same 37 genes, whose arrangement in the circular DNA molecule varies only in the relative position of a few genes. This relative conservation suggests that mitochondrial gene order characters have potential utility as phylogenetic markers for higher-level vertebrate taxa. We report discovery of a mitochondrial gene order that has had multiple independent originations within birds, based on sampling of 137 species representing 13 traditionally recognized orders. This provides evidence of parallel evolution in mitochondrial gene order for animals. Our results indicate operation of physical constraints on mitochondrial gene order changes and support models for gene order change based on replication error. Bird mitochondria have a displaced OL (origin of light-strand replication site) as do various other Reptilia taxa prone to gene order changes. Our findings point to the need for broad taxonomic sampling in using mitochondrial gene order for phylogenetic analyses. We found, however, that the alternative mitochondrial gene orders distinguish the two primary groups of songbirds (order Passeriformes), oscines and suboscines, in agreement with other molecular as well as morphological data sets. Thus, although mitochondrial gene order characters appear susceptible to some parallel evolution because of mechanistic constraints, they do hold promise for phylogenetic studies.

Figure 1

Mitochondrial (mt) gene order from ND5 to srRNA as in nonavian vertebrate animals (including representative fish, amphibians, reptiles, and mammals) (a), as previously known for birds (b), and as in birds having the novel mt gene order reported here (c). Numbered bars denote DNA fragments that we sequenced for various bird species (see Table 1). Gene designations: ND5/ND6, NADH dehydrogenase subunits 5 and 6; CytB, cytochrome b; srRNA, small subunit rRNA; tRNAs are indicated by the corresponding one-letter amino acid code. nc, Variable length, nonprotein coding sequence. The DNA regions shown as bars below the drawings (–5) in b and c correspond to the following regions in the published Gallus gallus sequence (11): 1, positions 1–16,775 (whole mt genome); 2, 15,711–16,190; 3, 16,226–77 or 524; 4, 15,711–16,107 and 1–613; and 5, 538–1,227 and 16,108–16,190. Control region sequences were identified by the presence and relative position of conserved sequence blocks: F-box, D-box, CSB-1 (12).

Figure 2

Most parsimonious distribution of two different mitochondrial gene orders on two avian phylogenetic hypotheses. Gene order previously known for birds (11) (Fig. 1b) is shown with solid branches, and the novel gene order (Fig. 1c) is shown with cross-hatching on branches. Phylogenetic hypotheses follow published analyses by Sibley and Ahlquist based on DNA–DNA hybridization analyses (a) (20) and Cracraft based on morphological characters (b) (21). We consider the published analyses described in a and b to be more comprehensive than analysis of the limited (in taxa and characters) primary sequence data associated with sequencing of gene junctions for this study. Nonetheless, we conducted a series of phylogenetic analyses by using parsimony for the 32 species in Table 1 sequenced for fragment 1, 2, or 4, sharing about 400 bp spanning the 3′ end of Cytb and tRNA^T. All analyses, using both equal and various unequal weights for transversion substitutions versus transition substitutions, yielded most-parsimonious trees in which taxa with the novel gene order (Fig. 1c) were nonmonophyletic and scattered throughout the tree. We also conducted analyses with more than 1,900 bp of mitochondrial sequence (from the mt 12S rDNA, Cytb, ND3, and tRNA^T genes) for 15 of our Table 1 taxa, including representatives of three of the orders in which we found the novel gene order, using both equal and unequal weighting, and these also support nonmonophyly of taxa with the novel mitochondrial gene arrangement.