Conspicuously concealed: revision of the arid clade of theGehyra variegata(Gekkonidae) group in Western Australia using an integrative molecular and morphological approach, with the description of five cryptic species

Abstract

The methods used to detect and describe morphologically cryptic species have advanced in recent years, owing to the integrative nature of molecular and morphological techniques required to elucidate them. Here we integrate recent phylogenomic work that sequenced many genes but few individuals, with new data from mtDNA and morphology from hundreds of gecko specimens of the Gehyra variegata group from the Australian arid zone. To better understand morphological and geographical boundaries among cryptic forms, we generated new sequences from 656 Gehyra individuals, largely assigned to G. variegata group members over a wide area in Western Australia, with especially dense sampling in the Pilbara region, and combined them with 566 Gehyra sequences from GenBank, resulting in a dataset of 1,222 specimens. Results indicated the existence of several cryptic species, from new species with diagnostic morphological characters, to cases when there were no useful characters to discriminate among genetically distinctive species. In addition, the cryptic species often showed counter-intuitive distributions, including broad sympatry among some forms and short range endemism in other cases. Two new species were on long branches in the phylogram and restricted to the northern Pilbara region: most records of the moderately sized G. incognita sp. nov. are near the coast with isolated inland records, whereas the small-bodied saxicoline G. unguiculata sp. nov. is only known from a small area in the extreme north of the Pilbara. Three new species were on shorter branches in the phylogram and allied to G. montium. The moderately sized G. crypta sp. nov. occurs in the western and southern Pilbara and extends south through the Murchison region; this species was distinctive genetically, but with wide overlap of characters with its sister species, G. montium. Accordingly, we provide a table of diagnostic nucleotides for this species as well as for all other species treated here. Two small-bodied species occur in isolated coastal regions: G. capensis sp. nov. is restricted to the North West Cape and G. ocellata sp. nov. occurs on Barrow Island and other neighbouring islands. The latter species showed evidence of introgression with the mtDNA of G. crypta sp. nov., possibly due to recent connectivity with the mainland owing to fluctuating sea levels. However, G. ocellata sp. nov. was more closely related to G. capensis sp. nov. in the phylogenomic data and in morphology. Our study illustrates the benefits of combining phylogenomic data with extensive screens of mtDNA to identify large numbers of individuals to the correct cryptic species. This approach was able to provide sufficient samples with which to assess morphological variation. Furthermore, determination of geographic distributions of the new cryptic species should greatly assist with identification in the field, demonstrating the utility of sampling large numbers of specimens across wide areas.

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

“…Our analysis of mtDNA recovered many groups that corresponded to the allozyme groups from the initial pilot study, as well as many other described taxa, including those in other recent Gehyra studies (Figure 1; Ashman et al 2018;Kealley et al 2018;Moritz et al 2018). A conspicuous feature of the phylogram was the recovery of two major clades that roughly consisted of small and large-bodied forms of G. punctata s.l.…”

“…media species-group', comprises two major groups and is sister to a different group of small-bodied species in the arid clade of the G. variegata group that included G. variegata, G. pilbara, G. montium and G. versicolor (Figure 1; Kealley et al 2018). The two major groups within this lineage showed different levels of genetic structure within them, with one (G. media sp.…”

“…Preliminary mtDNA phylograms generated by Sistrom et al (2013) and for this study informed the study of Ashman et al (2018), who drew samples from within mtDNA lineages and used exon capture techniques to carry out a detailed phylogenomic assessment of nearly all Gehyra species that firmly established independently-evolving lineages. Similar to Kealley et al (2018), we use the findings of Ashman et al (2018) based on few individuals per lineage and coupled them with our expanded mtDNA sampling to provide sufficient genotyped specimens for morphological analyses and for mapping distributions.…”

“…However, the two species of reddish-brown spotted Gehyra from the Pilbara were synonymised by Storr (1982) in his description of G. purpurascens and G. montium from the Central Ranges. The reddish, spotted G. montium presumably had been previously referred to G. punctata as early as Fry's 1914 publication and so necessitated a redescription (although recent work has found the Central Ranges to contain several more Gehyra species, as well as discovering that G. montium extends across the western deserts and is widespread in the Pilbara [Sistrom et al 2013;Hutchinson et al 2014;Kealley et al 2018]). Without commenting on the type specimens of either taxa, Storr (1982) synonymised G. fenestra with G. punctata based on an overlap of characters, concluding his characteristically brief paper with: 'I suspect that Mitchell's concept of G. punctata was partly based on Pilbara specimens of G. variegata and/or G. pilbara.…”

“…-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).…”