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.

Diversification across biomes in a continental lizard radiation

“…Resolving the diversity and relationships of lineages in the G. variegata group has previously proved intractable, despite the use of karyotypic, allozyme, morphological, mtDNA, and small-scale nuclear datasets (King 1979;Moritz 1986Moritz , 1992Heinicke et al 2011;Sistrom et al 2013;Sistrom et al 2014). As for the AMT nana clade , the much-improved resolution and largely consistent estimates of phylogeny for the AAZ radiation of Gehyra emphasize the value of phylogenomic datasets with comprehensive sampling of taxa for resolving the diversity of radiating taxa (Blom et al 2017).…”

“…) and many species relationships remain poorly resolved despite considerable effort (Sistrom et al. ). The variegata group has radiated extensively across the Australian arid zone (AAZ) and monsoonal tropics (AMT) since the Miocene (Heinicke et al.…”

Crypsis and convergence: integrative taxonomic revision of the Gehyra australis group (Squamata: Gekkonidae) from northern Australia

“…The gekkonid lizards in the genus Gehyra from Australia show conservative body form, variable appearance and have been a test case for implementing new methods to document species diversity (King, 1979(King, , 1982Sistrom, Donnellan & Hutchinson, 2013;Sistrom et al, 2014;Ashman et al, 2018;Kealley et al, 2018;Moritz et al, 2018;summarised in Doughty et al, 2018a). The various genetic techniques have led to increasingly finer resolution of phylogenetic structure, and have recently resulted in major revisions of Gehyra species-groups from the Australian arid zone and the Australian Monsoonal Tropics (AMT) such that the number of recognised species has nearly doubled from 22 to 43 Doughty et al, 2018aDoughty et al, , 2018bKealley et al, 2018).…”

Spots before the eyes: revision of the saxicoline geckos of the Gehyra punctata (Squamata: Gekkonidae) species complex in the Pilbara region of Western Australia

“…Recently, progress has been made resolving the affinities of Gehyra to other gekkonine geckos (Heineke et al 2011;Gamble et al 2012;Sistrom et al 2014) and delimiting species boundaries (Horner 2005;Sistrom et al 2009Sistrom et al , 2013Oliver et al 2010Oliver et al , 2016Doughty et al 2012Doughty et al , 2018Hutchinson et al 2014). As pointed out 35 years ago, taxonomic progress on Gehyra has been particularly hindered by the loss of colour patterns in preservative and that 'too few specimens from too few localities have been examined ' (p. 739).…”

“…-F.J. Mitchell on Gehyra (1965, p. 302) Gehyra is a 'taxonomist's nightmare'… -M. King (1979, p. 376) Geckos of the genus Gehyra are among the most taxonomically confusing within the Australian herpetofauna owing to their conservative body form, widely varying characters within taxa, remote locations for many species complexes and poor preservation of colour patterns in museum specimens Sistrom et al 2009Sistrom et al , 2014Doughty et al 2012Doughty et al , 2018Kealley et al 2018). Recently, progress has been made resolving the affinities of Gehyra to other gekkonine geckos (Heineke et al 2011;Gamble et al 2012;Sistrom et al 2014) and delimiting species boundaries (Horner 2005;Sistrom et al 2009Sistrom et al , 2013Oliver et al 2010Oliver et al , 2016Doughty et al 2012Doughty et al , 2018Hutchinson et al 2014).…”