Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates

Abstract

A large number of studies in evolutionary biology utilize phylogenetic information obtained from mitochondrial DNA. Researchers place trust in this molecule and expect it generally to be a reliable marker for addressing questions ranging from population genetics to phylogenies among distantly related lineages. Yet, regardless of the phylogenetic method and weighting treatment, individual mitochondrial genes might potentially produce misleading evolutionary inferences and hence might not constitute an adequate representation neither of the entire mitochondrial genome nor of the evolutionary history of the organisms from which they are derived. We investigated the performance of all mitochondrial protein-coding genes to recover two expected phylogenies of tetrapods and mammals. According to these tests, mitochondrial protein-coding genes can be roughly classified into three groups of good (ND4, ND5, ND2, cytb, and COI), medium (COB, COIII, NDl, and ND6), and poor (ATPase 6, ND3, ATPase 8, and ND4L) phylogenetic performers in recovering these expected trees among phylogenetically distant relatives. How general our findings are is unclear. Simple length differences and rate differences between these genes cannot account for their different phylogenetic performance. The phylogenetic performance of these mitochondrial genes might depend on various factors that play a role in determining the probability of discovering the correct phylogeny such as the density of lineage creation events in time, the phylogenetic "depth" of the question, lineage-specific rate heterogeneity, and the completeness of taxa representation.

Genetic aspects of mitochondrial genome evolution

“…Furthermore, mitochondrial protein coding sequence data harbour valuable phylogenetic signal to further clarify uncertain relationships within and between phyla (Bourlat et al, 2008;Zardoya and Meyer, 1996). This review is organized as follows: We first provide an overview of the general properties of mitochondrial genomes with a focus on the aberrant structures and the variations of the genetic code in metazoan metazoan phyla.…”

Rediscovery of Protohynobius puxiongensis (Caudata: Hynobiidae) and its phylogenetic position based on complete mitochondrial genomes

“…puxiongensis by DNA analysis. The complete mitochondrial genomes have been successfully used to study phylogenetic questions for different animal groups because they have become more readily available and are expected to produce more reliable phylogenetic inference than small gene fragments (Cummings et al, 1995;Zardoya and Meyer, 1996;Zhang et al, 2008). In addition, a phylogenetic study including 8 of 10 genera of Hynobiidae has been done based on complete mitochondrial genomes by Zhang et al (2006).…”

The Phylogenetic Relationships of the Gobioninae (Teleostei: Cyprinidae) Inferred from Mitochondrial Cytochrome b Gene Sequences

“…The mitochondrial cytochrome b gene is widely used for phylogenetic analyses and is considered to be one of the most reliable mitochondrial markers for phylogenetic studies (Zardoya & Meyer, 1996). Here we use complete mitochondrial DNA cytochrome b gene sequences for 49 gobionine species to obtain a better understanding of their phylogenetic relationships and the position of this group within the cyprinids.…”