Dragons in the tropics - Phylogeography and speciation in Diporiphora lizards and common geographic breaks in co-distributed taxa

Co-distributed taxa can respond both similarly or differently to the same climatic and geological events, resulting in a range of phylogeographic patterns across the region. Using a nested approach on a taxonomically diverse yet morphologically conservative group of agamid lizards, we first aimed to evaluate more precisely the extent of phylogeographic structuring within the genus. Then, focusing on four lineages within the more widespread species, we assessed the impact of biogeographic barriers on phylogeographic structuring and demographic history of species, comparing to patterns previously observed in co-distributed taxa. These species occur in the Australian Monsoonal Tropics, a vast tropical savanna system with high richness and endemism associated with environmental heterogeneity and past climate fluctuations. The employment of genomic data helped to determine the relationships between specific taxa that were previously difficult to place. We found a local influence of biogeographic and climatic breaks on population dynamics, analogous to other species. We detected high levels of population structure in the West Kimberley and Arnhem Plateau, which are already known for high endemism. However, we also highlighted unique lineages in areas that have been overlooked until recently, in the South Kimberley and West Top End. Climatic and geographical features in the Arnhem Plateau act as a soft barrier between populations in the east and west regions of the Top End. These observations reflect patterns observed for other vertebrates across this rich biome, indicating how climatic variation, species' ecology, and landscape features interact to shape regional diversity and endemism.

Plio–Pleistocene vicariance across arid Australia in the ‘Spiny Knob-tailed Geckos’ (

Across Australia’s monsoon tropics and vast arid zone isolated regions or ‘islands’ of upland or rocky habitat are home to disjunct populations of many taxa of plants and animals. Comparative analyses of lineages that occur across these habitat islands provide opportunities to understand when and how environmental change drove isolation and diversification across arid Australia. Here we present an analysis of mitochondrial genetic diversity across disjunct populations of geckos in the Nephrurus asper group. Dating analyses suggest that disjunct and genetically divergent populations spanning the northern half of Australia diverged through the Plio–Pleistocene. Based on the timing of divergence and current habitat associations we hypothesise that species in this lineage were isolated by the expansion of unsuitable arid-zone habitats from the late Pliocene onwards. Across most areas, these barriers appear to be sandy or stony deserts. However, in eastern Australia genetically divergent populations are separated by grassland on flat vertisol-dominated soils (‘blacksoils’), suggesting that these habitats also expanded during the late Pliocene aridification. Finally, we show that western Queensland populations formerly referred to N. asper are genetically divergent and diagnosable on the basis of colour pattern and, herein, recognise these populations as a distinct species. https://zoobank.org/urn:lsid:zoobank.org:pub:9508CAAA-D014-452D-A3DA-325851615FA7

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

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.

On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation

Background

Congruent patterns in the distribution of biodiversity between regions or habitats suggest that key factors such as climatic and topographic variation may predictably shape evolutionary processes. In a number of tropical and arid biomes, genetic analyses are revealing deeper and more localised lineage diversity in rocky ranges than surrounding habitats. Two potential drivers of localised endemism in rocky areas are refugial persistence through climatic change, or ecological diversification and specialisation. Here we examine how patterns of lineage and phenotypic diversity differ across two broad habitat types (rocky ranges and open woodlands) in a small radiation of gecko lizards in the genus Gehyra (the australis group) from the Australian Monsoonal Tropics biome.

Results

Using a suite of approaches for delineating evolutionarily independent lineages, we find between 26 and 41 putative evolutionary units in the australis group (versus eight species currently recognised). Rocky ranges are home to a greater number of lineages that are also relatively more restricted in distribution, while lineages in open woodland habitats are fewer, more widely distributed, and, in one case, show evidence of range expansion. We infer at least two shifts out of rocky ranges and into surrounding woodlands. Phenotypic divergence between rocky ranges specialist and more generalist taxa is detected, but no convergent evolutionary regimes linked to ecology are inferred.

Conclusions

In climatically unstable biomes such as savannahs, rocky ranges have functioned as zones of persistence, generators of diversity and a source of colonists for surrounding areas. Phenotypic divergence can also be linked to the use of differing habitat types, however, the extent to which ecological specialisation is a primary driver or secondary outcome of localised diversification remains uncertain.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1408-1) contains supplementary material, which is available to authorized users.