Insights into Platypus Population Structure and History from Whole-Genome Sequencing

Abstract

The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10−9/bp/generation (95% CI 4.1 × 10−9–1.2 × 10−8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.

A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data

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The platypus: evolutionary history, biology, and an uncertain future

“…3). The surge in research in the 21st century was driven by more researchers and new technological developments, including smaller telemetry and data logging devices, use of passive integrated transponder tags (“microchipping”) for permanent marking (Grant and Whittington 1991), as well as DNA technologies and sequencing (Warren et al 2008; Martin et al 2018; Fig. 3).…”

Genome‐wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

“…Assessing genomic variation is a key step when studying natural populations, as patterns of genome‐wide variation are pertinent to identify signatures imprinted by demographic or adaptive processes. Accordingly, genotyping approaches based on whole‐genome sequencing have been developed to generate hundreds of thousands of SNPs (Alonso‐Blanco et al, ; Branca et al, ; Martin et al, ; Qiu et al, ), but SNPs are representative of only one type of molecular variation. In particular, the last decade has offered a deeper understanding of the diversity, abundance and global significance of TEs on the evolution of functional host genomes (Biemont & Vieira, ; Kidwell & Lisch, ), and surveys of their distribution in natural populations are needed (Bonchev & Parisod, ).…”