Mitochondrial rate variation among lineages of passerine birds

Abstract

The order Passeriformes comprises the majority of extant avian species. Analyses of molecular data have provided important insights into the evolution of this diverse order. However, molecular estimates of the evolutionary and demographic timescales of passerine species have been hindered by a lack of reliable calibrations. This has led to a reliance on the application of standard substitution rates to mitochondrial DNA data, particularly rates estimated from analyses of the gene encoding cytochrome b (CYTB). To investigate patterns of rate variation across passerine lineages, we used a Bayesian phylogenetic approach to analyse the protein-coding genes of 183 mitochondrial genomes. We found that the most commonly used mitochondrial marker, CYTB, has low variation in rates across passerine lineages. This lends support to its widespread use as a molecular clock in birds. However, we also found that the patterns of among-lineage rate variation in CYTB are only weakly related to the evolutionary rate of the mitochondrial genome as a whole. Our analyses confirmed the presence of mutational saturation at third codon positions across the protein-coding genes of the mitochondrial genome, reinforcing the view that these sites should be excluded in studies of deep passerine relationships. The results of our analyses have provided information that will be useful for molecular-clock studies of passerine evolution.

Body mass‐corrected molecular rate for bird mitochondrial DNA

“…). Using data sets composed of passerines, Nguyen & Ho () also detected fast evolution for ND genes; however, CYTB was reported as clearly the slowest genes which is not the case in our analysis. The observed variation might be a consequence of the variation in evolutionary constraint among genes, as the ND genes are known to be less constrained than the COX genes (Mishmar et al .…”

“…; Ksepka & Clarke ; Prum et al . ) and are not suited to the fast‐evolving nucleotide sequences of the mitochondrial genome (Nguyen & Ho ). To make use of these ancient calibrations, we performed a molecular dating analysis with the amino acid sequences because they are less prone to saturation (Brown et al .…”

“…Moreover, the molecular divergence is moderate, with the maximal divergence between any two species at 14%. It is important to limit the divergence as third codon position can saturate rapidly due to their fast rate of evolution, leading to an inaccurate branch length estimates (Nguyen & Ho ). Using the parameters from Table , the mass‐corrected substitution rates vary between 0.0116 (0.0097–0.0149) subst/sites/Myr for third codon position and 0.0140 (0.0116–0.0177) subst/sites/Myr for third codon position for the calibration sets 2 and 4, respectively.…”

“…; Jarvis et al . ; Nguyen & Ho ). Indeed, the broader picture is that variation in substitution rates is the rule rather than the exception across the tree of life (Bromham et al .…”

Mitochondrial substitution rates estimation for molecular clock analyses in modern birds based on full mitochondrial genomes

“…Despite of its widespread use, the validity of this standard molecular clock for any mtDNA loci in any bird lineage has been heavily criticized (Garcia-Moreno, 2004; Lovette, 2004; Pereira & Baker, 2006; Ho, 2007). Previous analyses of the mtDNA of birds highlight a lack of “standard” rates, finding variation between the different mtDNA genes as well as across different avian lineages (Pereira & Baker, 2006; Pacheco et al ., 2011; Lavinia et al ., 2016; Nabholz et al ., 2016; Nguyen & Ho, 2016). Some of these studies also attempted to calibrate the molecular rates of the different protein-coding mitochondrial genes across the avian phylogeny using complete mitochondrial genomes (Pereira & Baker, 2006; Pacheco et al ., 2011; Nabholz et al ., 2016).…”