New Research Provides Insights into Platypus Population Structure and History

The platypus (Ornithorhynchus anatinus) is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian family tree. The unique creature had its genome sequenced a decade ago, revealing its unique genetic makeup and its divergence from the rest of the mammals around 160 million years ago. Now, a greater effort to understand its ecological and population history has been made possible by the first, whole-scale genome sequencing of 57 platypuses from Queensland, New South Wales, and Tasmania.

A pair of platypuses (Ornithorhynchus anatinus). Image credit: Heinrich Harder.

This population-scale, whole-genome sequencing study of the platypus is one of the largest such studies of non-human mammals, and the first for a non-placental mammal.

“Our analyses provide insights into the population structure and levels of diversity in this species not previously possible and estimate the relatedness between individuals,” said study co-lead author Dr. Peter Donnelly, from the Wellcome Centre for Human Genetics and the Department of Statistics at the University of Oxford, UK.

“For example, we found that more than half of our samples had a least a third-degree relative amongst the other individuals sampled from the same river. Additionally, there were 26 pairs of second- or third-degree relatives, in all cases from the same river or creek, or closely connected waterways, involving 28 of our 57 samples.”

Dr. Donnelly and colleagues were able to estimate vital evolutionary forces at work including platypus mutation rates, divergence times, and population sizes throughout its history.

“We estimated the de novo mutation rate in the platypus, the first estimate in a non-placental mammal,” said study first author Dr. Hilary Martin, also from the University of Oxford.

“We found it to be middle of the road for mammals, lower than humans and chimpanzees but higher than laboratory bred mice.”

“The relative ordering of the point estimates is consistent with the observation that mutation rates in mammals are negatively correlated with body mass and generation time.”

The study also estimated that the platypus population most likely last shared a common ancestor nearly one million years ago.

“The deepest branch on the population tree separated three separate groups: the samples from Tasmania (an island to the south of Australia that separated from the mainland around 12,000 years ago); those from north Queensland (in the far north); and the remaining samples, which are from central Queensland and New South Wales,” said co-lead author Dr. Jaime Gongora, from the University of Sydney, Australia.

“We think it is most likely that there were three ancestral populations (Tasmania, North Queensland and North New South Wales/Central Queensland) which all coalesced around the same time, about 800,000 years ago.”

“The central Queensland samples likely shared an ancestral population with the North New South Wales samples about 300,000 years ago. This implies that there has been extensive population structure in platypus samples across Australia over a long time period.”

“Interestingly, the divergence times we have estimated predate the earliest fossil evidence for platypus,” Dr. Donnelly said.

“This finding does not necessarily contradict fossil evidence but suggests that the modern platypus extends back to the Early to Middle Pliocene. This could be consistent with it having evolved from the giant platypus species, Obdurodon tharalkooschild.”

In addition, the team found evidence of past population bottlenecks, particularly in North Queensland around 10,000 years ago, and identified modern populations (especially near the Carnarvon River) that would be aided by conservation efforts.

The Queensland bottleneck likely reflects the historical and current isolation and paucity of suitable habitat for platypus between North (Australian Wet Tropics) and Central Queensland, known as the ‘Burdekin gap’ (named for the Burdekin River).

“This hot and dry area is currently climatically unsuitable for platypus and has long acted as a barrier to genetic exchange,” Dr. Gongora said.

The study is published in the journal Molecular Biology and Evolution.

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Hilary C. Martin et al. Insights into Platypus Population Structure and History from Whole-Genome Sequencing. Molecular Biology and Evolution, published online March 20, 2018; doi: 10.1093/molbev/msy041