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Data from: Body mass-corrected molecular rate for bird mitochondrial DNA

posted on 2022-06-11, 04:19 authored by Benoit Nabholz, Robert Lanfear, Jérome Fuchs
Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per million years, that is that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species and correlate with life history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species’ body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently published data sets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds.

Usage Notes

Full nucleotide sequences alignmentAlignments of the 12 H-stranded protein-coding genes (i.e. all the protein-coding genes except NADH-dehydrogenase 6, ND6) for 475 speciesmito.fastaPhylogenetic treePhylogenetic tree of 475 species following the topology of Prum et al. (2015)mito.treeChronogram Calibration sets 2Chronogram estimated using the calibration sets 2 (see table 1 of Nabholz et al. 2016)Chronogram_Calibration_sets_2.treeChronogram Calibration sets 4Chronogram estimated using the calibration sets 4 (see table 1 of Nabholz et al. 2016)Chronogram_Calibration_sets_4.treeR script to convert branch length in divergence datesA R script to compute the mass-corrected substitution rate and compute the divergence dates. This program convert branch length in divergence dates by computing the mass-corrected molecular rates as described in Nabholz et al. 2016. Header of the script contains useful informations.applyMassCorrectedRates.RHarrier_Oatley_2015This dataset is used as the first working example in Nabholz et al. 2016Xiphorhynchus_Rocha_2015This dataset is used as the second working example in Nabholz et al. 2016


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