A mammoth bottleneck prior to extinction

Here’s to back-to-back posts on extinct mammalian genomes!
Woolly mammoth genomes are all the rage. How do I know? Just check out the new book, pre-print, and paper that were recently published.

In Current Biology, Eleftheria Palkopoulou and colleagues deeply sequenced¹ the genomes of two woolly mammoth specimens dated ~40,000 years apart in order to understand the population demographics of the species prior to its extinction. The older sample, from northern Siberia, was ~44,800 years old, while the more recent sample was ~4,300 years old and from from Wrangel Island – the home to the last known population of woolly mammoths ~4,000 years ago (yes, this means the ~4,300 sample was one of the last mammoths on earth!).
Using magic pairwise sequentially Markovian coalescent (PSMC) models, the researchers identified two mammoth bottlenecks (double entendre fully intended). The first, occurred ~285,000 years ago and was evident in both mammoth genomes². The second, more recent bottleneck, was only present in the Wrangel Island mammoth sample and was estimated to have occurred ~12,000 years ago (with a fair bit of uncertainty: 8,000–71,000 years). They then scanned the genomes for stretches that had an excess of homozygosity (aptly called: runs of homozygosity (ROH)) and, in combination with measures of heterozygosity, concluded that the population of mammoths on Wrangel Island had a drastic reduction in genetic diversity, which may have led to decreased fitness and ultimately extinction.
In fact this diversity was so low that it fell: “close to that observed in humans, bonobos, eastern lowland gorillas, and western chimpanzees, which have also experienced dramatic declines in population size during their history as inferred from PSMC analyses.” Scary, that these great apes with very low effective population sizes are comparable to the last living mammoths, right?

Resolving the divergence time of the two major mammoth clades


Another finding from the Palkopoulou et al. has to do with the estimate of the divergence time between the two major mammoth lineages (cleverly named “clade I” and “clade II”). A previous study had estimated that the divergence time to be 1-2 million years ago and even hypothesized that they were two different species! The Current Biology study found two converging lines of evidence that suggested that the divergence time was ~50,000 years ago, which provides some strong evidence against the “two different species of mammoth” possibility. Palkopoulou et al. explain the large difference in the two estimates:

The observed discordance between nuclear and mtDNA estimates of divergence is not surprising if we consider the biology and natural history of the Elephantidae. Females are largely non-dispersing, and this tends to produce deeper coalescent times for mtDNA lineages compared to nuclear coalescent dates.

Overall, this study is the first of its kind to examine the genomes of two members of a species at two different time periods (importantly one just prior to extinction), which shed light on the demography of the species before it went extinct.

Our finding of an overall reduced genome-wide diversity in one of the last surviving mammoths constitutes the first direct observation of genetic stochasticity in a species shortly before its extinction.

Footnotes:

¹ As with many ancient DNA projects, they couldn’t just sequence the first sample they found: they had to screen DNA extracted from 10 extinct mammoth samples before they found one suitable for sequencing. Really makes you appreciate working with extant species, right?
² Note that if the authors had just used PSMC on each sample and estimated the population bottlenecks they would have found support for a bottleneck ~245,000 years ago in the older sample and 285,000 years ago in the more recent, Wrangel Island. Any idea why? It’s because the samples died ~40,000 years apart, which means that the Wrangel Island mammoth’s genome had another ~40,000 years of mutation. So what did the authors do? They just shifted PSMC plots of the older genome ~40,000 years to the right until they matched up with the Wrangel Island plot. This is pretty cool and also something that is not without precedent.
REFERENCES

Palkopoulou E, Mallick S, Skoglund P, Enk J, Rohland N, Li H, Omrak A, Vartanyan S, Poinar H, Götherström A, Reich D & Dalén L (2015) Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth. Curr. Biol.
Lynch V, Bedoya-Reina OC, Ratan A, Sulak M, Drautz-Moses DI, Perry GH, Miller W & Schuster SC (2015) Elephantid genomes reveal the molecular bases of Woolly Mammoth adaptations to the arctic, Cold Spring Harbor Labs Journals.