Estimation of divergence times for major lineages of galliform birds: Evidence from complete mitochondrial genome sequences

Abstract

Determining an absolute timescale for avian evolutionary history has been recently challenged by the relaxed molecular clock methods, that rates of molecular evolution can vary significantly among organisms. In this study, we used relaxed molecular clocks to date the divergence of major lineages of Galliformes based on complete mitochondrial genomes. A nucleotide dataset of 13 concatenated protein-coding genes from 22 species of Galliformes was used to investigate the evolutionary divergences within the group. Using Gallus bravardi, Schaubortyx and Gallinuloides fossils as calibration points, divergence times analyses were performed with four relaxed molecular clock methods as follows: (1) Bayesian method of Multidivtime; (2) Bayesian Markov chain Monte Carlo (MCMC) analysis of the Bayesian evolutionary analysis by sampling trees (BEAST); (3) local rate minimum deformation method (LRMD) of TREEFINDER; and (4) nonparametric rate smoothing (NPRS) of TREEFINDER. The various relaxed clock methods all indicated that (1) Megapodiidae originated in the Late Cretaceous; (2) Numididae, Phasianidae, Arborophilinae and Coturnicinae originated in the Eocene of Palaeogene; (3) Pavoninae and Gallininae originated at the Eocene-Oligocene boundary; (4) Phasianinae and Meleagridinae originated in the Oligocene; (5) divergence times estimation among most genera of Phasianidae were much older than those of the previous studies. Our results might provide a more likely time scale for evolutionary history of the galliform birds.