Ecologically diverse island-associated lizard radiation shows idiosyncratic trait diversification shifts and homogenous speciation dynamics.

A key area of interest in evolutionary biology has been understanding the role of ecological opportunity in the formation of adaptive radiations, lineages where speciation and phenotypic diversification are driven by open ecological opportunity. Evolutionary theory posits that adaptive radiations should show initial bursts of ecomorphological diversification and rapid speciation, and that these two processes are correlated. Here, we investigate and contrast these predictions across ecomorphologically diverse continental (Australia) and insular (New Caledonia and New Zealand) radiations of diplodactyloid geckos. We test two key hypotheses: (a) that island colonization and the transition to novel niche-space has resulted in increased rates of speciation and trait diversification and (b) that rates of morphological diversification are correlated across multiple trait axes. Surprisingly, we find that speciation rate is homogenous and morphological diversification rates are idiosyncratic and uncorrelated with speciation rates. Tests of morphological integration suggests that while all traits coevolve, constraint may act differentially on individual axes. This accords with a growing number of studies indicating that ecologically diverse and species-rich radiations can show limited or no evidence of exceptional regime shifts in speciation dynamics or morphological diversification, especially in continental contexts.

A new velvet gecko (Oedura: Diplodactylidae) from Groote Eylandt, Northern Territory.

Over the last decade, the combination of biological surveys, genetic diversity assessments and systematic research has revealed a growing number of previously unrecognised vertebrate species endemic to the Australian Monsoonal Tropics. Here we describe a new species of saxicoline velvet gecko in the Oedura marmorata complex from Groote Eylandt, a large island off the eastern edge of the Top End region of the Northern Territory. Oedura nesos sp. nov. differs from all congeners in combination of moderate size, and aspects of tail morphology and colouration. It has not been reported from the nearby mainland regions (eastern Arnhem Land) suggesting it may be an insular endemic, although further survey work is required to confirm this. While Groote Eylandt is recognised as a contemporary ecological refuge for declining mammal species of northern Australia, newly detected endemic species suggest it may also be of significance as an evolutionary refuge for many taxa, especially those associated with sandstone escarpments.

Relicts and radiations: Phylogenomics of an Australasian lizard clade with east Gondwanan origins (Gekkota: Diplodactyloidea).

Australasia harbors very high squamate diversity and is a center of endemicity for a number of major lineages. However, despite this diversity, the diplodactyloid geckos of Australia, New Caledonia, and New Zealand (comprised of three endemic families and >200 species) are the only extant squamates with unequivocal Mesozoic origins in the region. Diplodactyloid geckos also exhibit notable phenotypic and ecological diversity, most strikingly illustrated by the functionally limbless pygopods. Here, we present the first phylogenomic analyses of the pattern and timing of diplodactyloid evolution, based on a dataset of more than 4000 ultraconserved elements (UCEs) from 180 species. These analyses fully resolve nearly all nodes, including a number of intergeneric relationships that have proven problematic in previous studies. The hypothesis that New Caledonia and New Zealand clades represent independent post-KT boundary colonization events of Tasmantis from Australian ancestors is confirmed. Phylogenetic relationships recovered here further highlight contrasting patterns of diversity, most strikingly between insular and/or morphologically highly derived clades that have diversified rapidly, as opposed to other species poor and phylogenetically divergent relictual lineages on mainland Australia. Our new timetree suggests slightly older branching times than previous analyses and does not find a mass extinction event in the early Cenozoic. Finally, our new phylogeny highlights caudal variation across the clade. Most strikingly, the distinctive leaf-tail morphology shown by one family may in fact be plesiomorphic.

A new Gehyra (Gekkonidae: Reptilia) from New Guinea with unique caudal scalation.

We describe a new species of gekkonid gecko in the genus Gehyra from West Papua, Indonesia. Gehyra serraticauda sp. nov. keys to Gehyra, but is distinct from all known species; most notably, it is characterised by a continuous fringe of prominent acuminate lateral scales running the length of the tail, a feature shared with none of its congeners. Its robust body, intermediate size, numerous internasals, partially divided digital scansors, and the presence of well-developed popliteal folds further distinguish it from other Papuan Gehyra. The holotype of Gehyra serraticauda sp. nov. is of uncertain provenance, with the type locality listed as Fakfak, Onin Peninsula. However, the recent observation of a potential conspecific from Kaimana, Triton Bay supports the presence of this species in the region.

Sequence capture using PCR-generated probes: a cost-effective method of targeted high-throughput sequencing for nonmodel organisms.

Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of nonmodel organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes (SCPP) protocol requires no specialized equipment, is highly flexible and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25-100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies.