title: Evaluating evolutionary history in the face of high gene tree discordance in Australian Gehyra (Reptilia: Gekkonidae).
abstract: Species tree methods have provided improvements for estimating species relationships and the timing of diversification in recent radiations by allowing for gene tree discordance. Although gene tree discordance is often observed, most discordance is attributed to incomplete lineage sorting rather than other biological phenomena, and the causes of discordance are rarely investigated. We use species trees from multi-locus data to estimate the species relationships, evolutionary history and timing of diversification among Australian Gehyra-a group renowned for taxonomic uncertainty and showing a large degree of gene tree discordance. We find support for a recent Asian origin and two major clades: a tropically adapted clade and an arid adapted clade, with some exceptions, but no support for allopatric speciation driven by chromosomal rearrangement in the group. Bayesian concordance analysis revealed high gene tree discordance and comparisons of Robinson-Foulds distances showed that discordance between gene trees was significantly higher than that generated by topological uncertainty within each gene. Analysis of gene tree discordance and incomplete taxon sampling revealed that gene tree discordance was high whether terminal taxon or gene sampling was maximized, indicating discordance is due to biological processes, which may be important in contributing to gene tree discordance in many recently diversified organisms.
authors.affiliation: 1] South Australian Museum, North Terrace, Adelaide, South Australia, Australia [2] Australian Centre for Evolutionary Biology and Biodiversity, The University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: M
authors.initials: M
authors.lastname: Sistrom
authors.affiliation: 1] South Australian Museum, North Terrace, Adelaide, South Australia, Australia [2] Australian Centre for Evolutionary Biology and Biodiversity, The University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: M
authors.initials: M
authors.lastname: Hutchinson
authors.affiliation: 1] South Australian Museum, North Terrace, Adelaide, South Australia, Australia [2] School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: T
authors.initials: T
authors.lastname: Bertozzi
authors.affiliation: 1] South Australian Museum, North Terrace, Adelaide, South Australia, Australia [2] Australian Centre for Evolutionary Biology and Biodiversity, The University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: S
authors.initials: S
authors.lastname: Donnellan
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D063147:Animal Distribution; D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D005075:Biological Evolution; D019295:Computational Biology; D019143:Evolution, Molecular; D016013:Likelihood Functions; D008116:Lizards / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity