For over two decades, assessments of geographic variation in mtDNA and small numbers of nuclear loci have revealed morphologically similar, but genetically divergent, intraspecific lineages in lizards from around the world. Subsequent morphological analyses often find subtle corresponding diagnostic characters to support the distinctiveness of lineages, but occasionally do not. In recent years it has become increasingly possible to survey geographic variation by sequencing thousands of loci, enabling more rigorous assessment of species boundaries across morphologically similar lineages. Here we take this approach, adding new, geographically extensive SNP data to existing mtDNA and exon capture datasets for the Gehyra australis and G. koira species complexes of gecko from northern Australia. The combination of exon-based phylogenetics with dense spatial sampling of mitochondrial DNA sequencing, SNP-based tests for introgression at lineage boundaries and newly-collected morphological evidence supports the recognition of nine species, six of which are newly described here. Detection of discrete genetic clusters using new SNP data was especially convincing where candidate taxa were continuously sampled across their distributions up to and across geographic boundaries with analyses revealing no admixture. Some species defined herein appear to be truly cryptic, showing little, if any, diagnostic morphological variation. As these SNP-based approaches are progressively applied, and with all due conservatism, we can expect to see a substantial improvement in our ability to delineate and name cryptic species, especially in taxa for which previous approaches have struggled to resolve taxonomic boundaries.

Aim Birds are often coloured yellow, olive, orange or red by carotenoids, which are plant pigments that are ingested with food. Here we test whether there are consistent patterns of intraspecific geographic variation in male carotenoid‐based plumage coloration linked to latitude, temperature, precipitation and primary productivity. It has been suggested that patterns of geographic variation should be different for yellow, compared to the metabolically derived red carotenoid‐based coloration, but this has not been tested. Location Australia. Taxa Forty‐nine randomly selected species of Australian passerine birds (Passeriformes), 30 with yellow and 19 with red carotenoid‐based plumage coloration. Methods Carotenoid‐based plumage patches of male museum specimens were measured using reflectance spectrometry, and spectra analysed using models of avian colour vision. For each species, we used linear models to determine whether geographic variation in carotenoid‐based colour correlated with latitude, temperature, precipitation or primary productivity. To determine whether effects are consistent across species, we used phylogenetic meta‐analyses. Results Although spatial environmental effects on carotenoid‐based plumage coloration varied across species, overall, species tended to have more saturated carotenoid‐based coloration at lower latitudes, and warmer regions. These effects applied mainly to resident species (as opposed to migratory or nomadic) and were stronger for red compared to yellow carotenoid‐based colours. We found no consistent effects of precipitation or primary productivity. Main conclusions Geographic variation in male carotenoid‐based plumage coloration of Australian passerines is unlikely to be caused by variation in plant productivity (the ultimate source of carotenoids), and may be better explained by latitudinal gradients in the intensity of sexual selection or predation risk. Alternatively, temperature effects on red carotenoid‐based coloration may be driven by the hypothesized link between carotenoid and cellular metabolism. Latitudinal and temperature effects have the potential to generate perceivable differences in coloration across realistic spatial scales, contributing to divergence in visual signals.