Phylogeographic structure across one of the largest intact tropical savannahs: Molecular and morphological analysis of Australia’s iconic frilled lizard Chlamydosaurus kingii

Genetic and geographic population structure in the malaria vector, Anopheles farauti, provides a candidate system for pioneering confinable gene-drive releases

Indoor insecticide applications are the primary tool for reducing malaria transmission in the Solomon Archipelago, a region where Anopheles farauti is the only common malaria vector. Due to the evolution of behavioural resistance in some An. farauti populations, these applications have become less effective. New malaria control interventions are therefore needed in this region, and gene-drives provide a promising new technology. In considering developing a population-specific (local) gene-drive in An. farauti, we detail the species' population genetic structure using microsatellites and whole mitogenomes, finding many spatially confined populations both within and between landmasses. This strong population structure suggests that An. farauti would be a useful system for developing a population-specific, confinable gene-drive for field release, where private alleles can be used as Cas9 targets. Previous work on Anopheles gambiae has used the Cardinal gene for the development of a global population replacement gene-drive. We therefore also analyse the Cardinal gene to assess whether it may be a suitable target to engineer a gene-drive for the modification of local An. farauti populations. Despite the extensive population structure observed in An. farauti for microsatellites, only one remote island population from Vanuatu contained fixed and private alleles at the Cardinal locus. Nonetheless, this study provides an initial framework for further population genomic investigations to discover high-frequency private allele targets in localized An. farauti populations. This would enable the development of gene-drive strains for modifying localised populations with minimal chance of escape and may provide a low-risk route to field trial evaluations.

Speciation across biomes: Rapid diversification with reproductive isolation in the Australian delicate mice

Phylogeographic studies of continental clades, especially when combined with palaeoclimate modelling, provide powerful insight into how environment drives speciation across climatic contexts. Australia, a continent characterized by disparate modern biomes and dynamic climate change, provides diverse opportunity to reconstruct the impact of past and present environments on diversification. Here, we use genomic-scale data (1310 exons and whole mitogenomes from 111 samples) to investigate Pleistocene diversification, cryptic diversity, and secondary contact in the Australian delicate mice (Hydromyini: Pseudomys), a recent radiation spanning almost all Australian environments. Across northern Australia, we find no evidence for introgression between cryptic lineages within Pseudomys delicatulus sensu lato, with palaeoclimate models supporting contraction and expansion of suitable habitat since the last glacial maximum. Despite multiple contact zones, we also find little evidence of introgression at a continental scale, with the exception of a potential hybrid zone in the mesic biome. In the arid zone, combined insights from genetic data and palaeomodels support a recent expansion in the arid specialist P. hermannsburgensis and contraction in the semi-arid P. bolami. In the face of repeated secondary contact, differences in sperm morphology and chromosomal rearrangements are potential mechanisms that maintain species boundaries in these recently diverged species. Additionally, we describe the western delicate mouse as a new species and recommend taxonomic reinstatement of the eastern delicate mouse. Overall, we show that speciation in an evolutionarily young and widespread clade has been driven by environmental change, and potentially maintained by divergence in reproductive morphology and chromosome rearrangements.

Revision of Litoria rothii (Anura: Pelodryadidae) from northern Australia

Litoria rothii is a widespread pelodryadid frog with a charismatic laughing advertisement call, distributed across the Australian Monsoon Tropics and southern New Guinea. Given its large distribution spanning well-known biogeographic barriers, variation in male advertisement calls and the prevalence of unresolved species complexes in the Australian frog fauna, we examine the genetic, morphological and acoustic diversity in the species from across its range. Our analyses reveal the presence of a previously unrecognised species in western parts of the range of L. rothii sensu lato, which we describe herein as a new species. Litoria ridibunda sp. nov. is distinguished from L. rothii on the basis of paraphyly of nuclear gene trees with L. everetti from Indonesia, colour patterns on the posterior thigh and male advertisement calls. Compared to L. rothii, the new species has a less contrasting pattern on the posterior thigh and a male advertisement call with a greater number of notes per call and a greater call duration. In particular, the magnitude of call differences between the species is highest where the ranges of the two species are in proximity in north-western Queensland. Our study further emphasises the undiagnosed diversity that remains in Australian frogs, even in relatively large, charismatic, frequently encountered species that often share human dwellings.

Whole-genome phylogeography of the blue-faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo-Z chromosome

Whole-genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long-read DNA sequencing can help clarify. Here, we report on whole-genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the blue-faced honeyeater (Entomyzon cyanotis), and the discovery and characterization of a novel neo-Z chromosome by long-read sequencing. Using short-read genome-wide SNPs, we inferred population divergence events within E. cyanotis across the Carpentarian and other biogeographic barriers during the Pleistocene (~0.3-1.7 Ma). Evidence for introgression between nonsister populations supports a hypothesis of reticulate evolution around a triad of dynamic barriers around Pleistocene Lake Carpentaria between Australia and New Guinea. During this phylogeographic survey, we discovered a large (134 Mbp) neo-Z chromosome and we explored its diversity, divergence and introgression landscape. We show that, as in some sylvioid passerine birds, a fusion occurred between chromosome 5 and the Z chromosome to form a neo-Z chromosome; and in E. cyanotis, the ancestral pseudoautosomal region (PAR) appears nonrecombinant between Z and W, along with most of the fused chromosome 5. The added recombination-suppressed portion of the neo-Z (~37.2 Mbp) displays reduced diversity and faster population genetic differentiation compared with the ancestral-Z. Yet, the new PAR (~17.4 Mbp) shows elevated diversity and reduced differentiation compared to autosomes, potentially resulting from introgression. In our case, long-read sequencing helped clarify the genomic landscape of population divergence on autosomes and sex chromosomes in a species where prior knowledge of genome structure was still incomplete.

Subspecies at crossroads: the evolutionary significance of genomic and phenotypic variation in a wide-ranging Australian lizard (Ctenotus pantherinus)

Many subspecies were described to capture phenotypic variation in wide-ranging taxa, with some later being found to correspond to divergent genetic lineages. We investigate whether currently recognized subspecies correspond to distinctive and coherent evolutionary lineages in the widespread Australian lizard Ctenotus pantherinus based on morphological, mitochondrial and genome-wide nuclear variation. We find weak and inconsistent correspondence between morphological patterns and the presumed subspecies ranges, with character polymorphism within regions and broad morphological overlap across regions. Phylogenetic analyses suggest paraphyly of populations assignable to each subspecies, mitonuclear discordance and little congruence between subspecies ranges and the distribution of inferred clades. Genotypic clustering supports admixture across regions. These results undermine the presumed phenotypic and genotypic coherence and distinctiveness of C. pantherinus subspecies. Based on our findings, we comment on the operational and conceptual shortcomings of morphologically defined subspecies and discuss practical challenges in applying the general notion of subspecies as incompletely separated population lineages. We conclude by highlighting a historical asymmetry that has implications for ecology, evolution and conservation: subspecies proposed in the past are difficult to falsify even in the face of new data that challenge their coherence and distinctiveness, whereas modern researchers appear hesitant to propose new subspecies.

Historical and future climate change fosters expansion of Australian harvester termites, Drepanotermes

Past evolutionary adaptations to Australia's aridification can help us to understand the potential responses of species in the face of global climate change. Here, we focus on the Australian-endemic genus Drepanotermes, also known as Australian harvester termites, which are mainly found in semiarid and arid regions of Australia. We used species delineation, phylogenetic inference, and ancestral state reconstruction to investigate the evolution of mound-building in Drepanotermes and in relation to reconstructed past climatic conditions. Our findings suggest that mound-building evolved several times independently in Drepanotermes, apparently facilitating expansions into tropical and mesic regions of Australia. The phylogenetic signal of bioclimatic variables, especially limiting environmental factors (e.g., precipitation of the warmest quarter), suggests that the climate exerts a strong selective pressure. Finally, we used environmental niche modeling to predict the present and future habitat suitability for eight Drepanotermes species. Abiotic factors such as annual temperature contributed disproportionately to calibrations, while the inclusion of biotic factors such as predators and vegetation cover improved ecological niche models in some species. A comparison between present and future habitat suitability under two different emission scenarios revealed continued suitability of current ranges as well as substantial habitat gains for most studied species. Human-mediated climate change occurs more quickly than these termites can disperse into newly suitable habitat; however, their role in stabilizing arid ecosystems may allow them to mitigate effects on some other organisms at a local level.