Understanding the joint evolutionary and ecological underpinnings of sympatry among close relatives remains a key challenge in biology. This problem can be addressed through joint phylogenomic and phenotypic analysis of complexes of closely related lineages within, and across, species and hence representing the speciation continuum. For a complex of tropical geckos from northern Australia-Gehyra nana and close relatives-we combine mtDNA phylogeography, exon-capture sequencing, and morphological data to resolve independently evolving lineages and infer their divergence history and patterns of morphological evolution. Gehyra nana is found to include nine divergent lineages and is paraphyletic with four other species from the Kimberley region of north-west Australia. Across these 13 taxa, 12 of which are restricted to rocky habitats, several lineages overlap geographically, including on the diverse Kimberley islands. Morphological evolution is dominated by body size shifts, and both body size and shape have evolved gradually across the group. However, larger body size shifts are observed among overlapping taxa than among closely related parapatric lineages of G.nana, and sympatric lineages are more divergent than expected at random. Whether elevated body size differences among sympatric lineages are due to ecological sorting or character displacement remains to be determined.

Recent advances in molecular genetic techniques and increased fine scale sampling in the Australian Monsoonal Tropics (AMT) have provided new impetus to reassess species boundaries in the Gehyra nana species complex, a clade of small-bodied, saxicolous geckos which are widely distributed across northern Australia. A recent phylogenomic analysis revealed eight deeply divergent lineages that occur as a series of overlapping distributions across the AMT and which, as a whole, are paraphyletic with four previously described species. Several of these lineages currently included in G. nana are phenotypically distinct, while others are highly conservative morphologically. Here we use an integrated approach to explore species delimitation in this complex. We redefine G. nana as a widespread taxon with complex genetic structure across the Kimberley of Western Australia and Top End of the Northern Territory, including a lineage with mtDNA introgressed from the larger-bodied G. multiporosa. We describe four new species with more restricted distributions within the G. nana complex. The new species are phylogenetically divergent and morphologically diagnosable, and include the relatively cryptic G. paranana sp. nov. from the western Northern Territory, the large-bodied G. pseudopunctata sp. nov. from the southern Kimberley ranges, G. granulum sp. nov., a small-bodied form with granules on the proximal lamellae from the north-west and southern Kimberley ranges and the small-bodied G. pluraporosa sp. nov. restricted to the northern Kimberley. Our revision largely stabilises the taxonomy of the G. nana complex, although further analyses of species limits among the remaining mostly parapatric lineages of G. nana sensu stricto are warranted.

The tropical savannah landscapes of Australia's north, though previously overshadowed by the biodiverse rainforests of the Wet Tropics, are themselves now attracting interest for their biological significance and uniqueness. The Einasleigh Uplands region of north-east Queensland is home to a diverse group of mammals and reptiles and was previously recognised for its importance in shaping speciation in birds. Here we add a small saxicoline gecko to a growing list of recently described reptiles that are endemic to this region. Phylogenetic analyses including Gehyra species from the arid zone and the monsoonal tropics reveal that small Gehyra geckos in this area, while closely resembling Gehyra nana from the Top End and Kimberley, form a clade that is geographically isolated and phylogenetically distant from the G. nana complex. Instead, the Einasleigh Uplands taxon is sister to a large, arboreal species within the arid zone clade. It is readily distinguished from all lineages within the G. nana complex, its closest relative G. purpurascens, and all other rock-dwelling species from the arid zone by a combination of its very small body size, few subdigital lamellae, and mid tan to golden dorsal coloration with a pattern of scattered pale ocelli and irregular dark-brown blotches on a stippled background. We therefore describe this taxon as a new Australian species of Gehyra, Gehyra einasleighensis sp. nov., based on a combination of phylogenetic separation, morphological characters and discrete geographic distribution.

Australia's lizard fauna is among the most diverse in the world. Yet for the continent's vast northern Monsoonal Tropics, recent genomic and morphological evidence indicate that current taxonomy significantly underestimates actual biological diversity. Apparently widespread species typically contain ancient phylogenetic divisions or confounded taxonomic boundaries. Resolving the distributions and relationships across tropical species complexes reveals higher diversity than is recognised taxonomically and may warrant substantial taxonomic changes. For conservation assessments however, we need not wait for revised taxonomy, because phylogenetically informed analyses can use the best available data to inform conservation priorities now, independent of taxonomy.We present results of a large-scale conservation analysis based on comparative phylogeography of ten genera of lizards in two families (Gekkonidae and Scincidae) across the "Top End" of northern Australia, an ecologically and topographically diverse landscape recognised for its high biodiversity and indigenous cultural values. We combine the distributions and phylogeny of evolutionary lineages across multiple species complexes to estimate phylogenetic endemism, a measure of the extent to which evolutionary diversity is geographically concentrated. We demonstrate new methods for conservation assessment to incorporate phylogenetic diversity both within and across species, and for cases where taxonomy is uncertain or incomplete.We identify five hotspots of endemism, some previously known such as the Arnhem Plateau but others that are newly identified such as the Wessel & English Company Islands and the Darwin-Litchfield area. We find that, weighted by range size, the 28% of the region within protected areas holds 44% of the region's sampled phylogenetic diversity. (C) 2016 Elsevier Ltd. All rights reserved.

Ongoing fieldwork and molecular research continues to reveal that the monsoonal tropics of northern Australia contain more vertebrate species than currently recognised. Here we focus on two morphologically distinctive, yet unrecognised forms in the genus Gehyra from the southern Kimberley region and surrounding deserts. We base our descriptions on a combination of unpublished genetic data and a morphological examination of voucher specimens. We recognise and re-describe G. kimberleyi, a species with a broad distribution extending over most of the south-west Kimberley, across the Great Sandy Desert and into the far northern Pilbara. This species has been previously assigned to G. pilbara owing to its frequent occurrence on termite mounds and short snout, but can be distinguished from G. pilbara and other regionally sympatric Gehyra by its moderate body size, moderate number of pre-cloacal pores in males (12-17) and aspects of dorsal colouration. We also describe G. girloorloo sp. nov., a small rock-dwelling species with a short snout, low number of pre-cloacal pores in males (8-11) and pinkish-grey dorsal colouration with alternating series of indistinct pale spots and irregular transversely-aligned dark blotches. The new species appears to be restricted to a relatively small region of exposed limestone karst in the south-west Kimberley and is entirely circumscribed by morphologically similar congeners.

Ongoing fieldwork and molecular research continues to reveal that the monsoonal tropics of northern Australia contain more vertebrate species than currently recognised. Here we focus on two morphologically distinctive, yet unrecognised forms in the genus Gehyra from the southern Kimberley region and surrounding deserts. We base our descriptions on a combination of unpublished genetic data and a morphological examination of voucher specimens. We recognise and redescribe G. kimberleyi, a species with a broad distribution extending over most of the south-west Kimberley, across the Great Sandy Desert and into the far northern Pilbara. This species has been previously assigned to G. pilbara owing to its frequent occurrence on termite mounds and short snout, but can be distinguished from G. pilbara and other regionally sympatric Gehyra by its moderate body size, moderate number of pre-cloacal pores in males (12–17) and aspects of dorsal colouration. We also describe G. girloorloo sp. nov., a small rock-dwelling species with a short snout, low number of pre-cloacal pores in males (8–11) and pinkish-grey dorsal colouration with alternating series of indistinct pale spots and irregular transversely-aligned dark blotches. The new species appears to be restricted to a relatively small region of exposed limestone karst in the south-west Kimberley and is entirely circumscribed by morphologically similar congeners.

Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics include vast, ecologically intact savanna‐woodland plains interspersed with ancient sandstone uplands. Although recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock‐restricted taxa. To provide a baseline for ongoing comparative analyses, we tested for phylogeographic structure in an ecologically generalized and widespread taxon, the gecko Heteronotia binoei. We apply coalescent analyses to multilocus sequence data (mitochondrial DNA and eight nuclear DNA introns) from individuals sampled extensively and at fine scale across the region. The results demonstrate surprisingly deep and geographically nested lineage diversity. Several intra‐specific clades previously shown to be endemic to the region were themselves found to contain multiple, short‐range lineages. To infer landscapes with concentrations of unique phylogeographic diversity, we probabilistically estimate the ranges of lineages from point data and then, combining these estimates with the nDNA species tree, estimate phyloendemism across the region. Highest levels of phyloendemism occur in northern Top End, especially on islands, across the topographically complex Arnhem escarpment, and across the sandstone ranges of the western Gulf region. These results drive home that deep phylogeographic structure is prevalent in tropical low‐dispersal taxa, even ones that are ubiquitous across geography and habitats.