Australian burrowing frogs Neobatrachus
Polyploidy or whole-genome duplications (WGDs) are characteristic for plants but are recognized as important hallmarks in the evolutionary history across the whole tree of life, including vertebrates. In order to understand complex adaptation patterns to external and internal challenges, we apply a population genomics approach to different plant and animal systems with sister diploid/tetraploid lineages and wide geography. One of such systems became a diploid-tetraploid species complex of Australian burrowing frogs Neobatrachus, amphibians living in a desert.
Neobatrachus is among the few acceptions of sexually reproducing polyploid animals with tetrasomic and mixed inheritance. Sexual reproduction is more frequent in animals compared to plants and often requires dosage compensation which can be disturbed by whole-genome duplication. This partially explains the overrepresentation of polyploidy in plants. Similarly to plants, sex chromosomes of amphibians are often undifferentiated and do not require dosage compensation, which allows these animals to tolerate genome doubling more easily. Although not sessile, ectothermic animals are also susceptible to environmental stress, which can trigger the production of unreduced gametes leading to striking associations between polyploidy instances and harsh environments. In collaboration with the Evolutionary Biology Unit of the South Australian Museum, we sequence genomes of Neobatrachus frogs to assess genetic variation and identify selected regions and adaptive changes in tetraploid compared to diploid frogs. The project aims to unravel the mechanism of polyploidy-driven adaptation in these amphibians and whether plants and animals use the same strategy to adapt their cell cycle machinery to the strong selection pressure imposed by polyploidy.
N. pelobatoides (2n). Photo credit: Stephen Mahony.
N. sutor (2n). Photo credit: Stephen Mahony.
N. wilsmorei (2n). Photo credit: Stephen Mahony.
N. albipes (2n). Photo credit: Stephen Mahony.
N. pictus (2n). Photo credit: Stephen Mahony.
N. fulvus (2n). Photo credit: Stephen Mahony.
N. kunapalari (4n). Photo credit: Stephen Mahony.
N. sudellae (4n). Photo credit: Stephen Mahony.
N. aquilonius (4n). Photo credit: Stephen Mahony.
May 11, 2020
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 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 describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond 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. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.