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Doughty, P.

Publications and source records attributed to Doughty, P..

2 recordsLinked to original sources

Integrating Genomics, Collections, and Community Science to Reveal Speciation in a Variable Monitor Lizard (Varanus tristis)

--The accurate characterization of species diversity is a vital prerequisite for ecological and evolutionary research, as well as conservation. Thus, it is necessary to generate robust hypotheses of species limits based on the inference of evolutionary processes. Integrative species delimitation, the inference of species limits based on multiple sources of evidence, can provide unique insight into species diversity and the processes behind it. However, the application of integrative approaches in non-model organisms is often limited by the amount of data that is available. Here, we show how data relevant for species delimitation can be bolstered by incorporating information from tissue collections, museum specimens, and observations made by the wider community. We show how to integrate these data under a hypothesis-driven, integrative framework by identifying the processes generating genetic and phenotypic variation in Varanus tristis, a widespread and variable complex of Australian monitor lizards. Using genomic, morphometric (linear and geometric), coloration, spatial, and environmental data we show that disparity in this complex is inconsistent with intraspecific variation and instead suggests that speciation has occurred. Based on our results, we identify the environmental factors that may have been responsible for the geographic sorting of variation. Our workflow provides a guideline for the integrative analysis of several types of data to identify the occurrence and causes of speciation. Furthermore, our study highlights how community science and machine learning--two tools used here--can be used to accelerate taxonomic research.

evolutionary biology↗

Whole genome duplication potentiates inter-specific hybridisation and niche shifts in Australian burrowing frogs Neobatrachus

Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less well-understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We resolve the phylogenetic relationships among Neobatrachus species and provide further support that the three polyploid species have independent autotetraploid origins. We document higher genetic diversity in tetraploids, resulting from widespread gene flow specifically between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and current isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate variation on frogs with differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which in turn corresponds to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow into tetraploid lineages specifically. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.

evolutionary biology↗