Contrasting Evolutionary Dynamics and Information Content of the Avian Mitochondrial Control Region and ND2 Gene

Abstract

Mitochondrial DNA is an important tool for inference of population history in animals. A variety of mitochondrial loci have been sampled for this purpose, but many studies focus on the non-coding D-loop or control region (CR), which in at least some species appears hypermutable. Unfortunately, analyses of this region are sometimes complicated by segmental duplications, as well as by difficulties in sequencing through repeat expansions, driving many researchers to favor single-copy protein-coding or ribosomal RNA genes. Without systematic comparison, it is unclear if, how much, and what sort of information might be lost by focusing on coding regions, or conversely whether such regions might offer significant advantages over the CR. In this study, we compare the information content, both in terms of genealogy and tests of neutral equilibrium, of the mitochondrial CR and protein-coding ND2 gene of the red-winged blackbird (Agelaius phoeniceus) and its close relative the tricolored blackbird (A. tricolor). Both gene regions violate the standard infinite sites assumption central to moment-based population genetic inference, as well as exhibiting considerable among-site rate heterogeneity, obscuring significant departures from neutral equilibrium. Given the ubiquity of rate heterogeneity in mtDNA, use of more sophisticated tests that account for this should be obligatory. The two regions yield quite similar genealogical reconstructions, as well as indicating similar departures from neutral equilibrium assumptions for A. phoeniceus. However, individual Sanger-read-length fragments (∼600 bases) of the CR have significantly higher information content than comparable fragments of ND2, suggesting that limited sampling of the mitochondrial genome should focus on the CR.

Complete mitochondrial genome sequence of the Himalayan Griffon,Gyps himalayensis(Accipitriformes: Accipitridae): Sequence, structure, and phylogenetic analyses

“…ND6 and eight tRNAs are transcribed from the light strand (L), however the other 12 PCGs, 14 tRNAs, two rRNAs, and two noncoding region (CR, CCR) genes are located on the heavy (H) strand. The gene arrangement pattern of the G. himalayensis mitochondrial genome is identical to that in genera Aegypius , Buteo, and Falco , all which have the remnant CCR gene order, but differ from the standard bird gene order (Barker, Benesh, Vandergon, & Lanyon, ; Gibb et al, ; Li, Huang, et al, ). The G. himalayensis mitogenome nucleotide composition is biased toward A and T (56.14%: A = 224.55%, T = 29.49%, G = 14.37% and C = 31.59%), which is similar to that seen in the other Gyps mitogenomes (52.71%–57.65%; Table ; Haring et al, ).…”

Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific

“…The 61 WMG dataset (25) contained 363 single-nucleotide polymorphisms (SNPs), of which 154 were potentially phylogenetically informative, with 62 (17%) located in the rapidly evolving CR (32). Bayesian and maximum likelihood inference analyses of the WMG dataset supported the haplogroup framework defined by Liu et al (24) and Miao et al (25) and, importantly, produced robust support for haplogroups A-G and Z (i.e., haplogroups where multiple individuals were sequenced), as shown in Fig.…”

Multilocus genetic analyses and spatial modeling reveal complex population structure and history in a widespread resident North American passerine (Perisoreus canadensis)

“…While some studies question using a highly variable marker like control region versus ND2 or cytochrome b for phylogeographic and phylogenetic studies, previous work has shown that this marker can be used to resolve deep splits in evolutionary history among avian species (Barker, Benesh, Vandergon, & Lanyon, ) and of corvids in particular (Saunders & Edwards, ). Within a single species, some loci may not be variable enough to detect differences between populations (e.g., cytochrome b (Steeves, Anderson, McNally, Kim, & Friesen, ) versus control region (Steeves, Anderson, & Friesen, ) in masked boobies ( Sula dactylatra )).…”