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Woolly Mammoth Genomes Provide Pre-Extinction Population Clues

Late Pleistocene woolly mammoths.

NEW YORK (GenomeWeb) – A Current Biology paper published online today described demography and diversity patterns detected using the genomes of two woolly mammoths that lived tens of thousands of years apart.

An international team led by investigators at the Swedish Museum of Natural History sequenced an almost 45,000-year-old woolly mammoth specimen from Siberia and another woolly mammoth that lived on Wrangel Island an estimated 4,300 years ago — not long before the woolly mammoth became extinct.

Using the two newly sequenced woolly mammoth genomes, the researchers detected a decline in genetic diversity and a rise in sequences associated with inbreeding in the representative from the isolated Wrangel Island population, though the reasons for woolly mammoth die offs in the few hundred years that followed remain murky.

"We still cannot really say what was the cause of the extinction," first author Eleftheria Palkopoulou told GenomeWeb.

"We find lower genetic variation and we find signals of inbreeding, but … there doesn't seem to [have been] very intense inbreeding, in terms of close relatives mating with each other," explained Palkopoulou, who was completing her PhD in paleogenetics with Stockholm University and the Swedish Museum of Natural History when the study was done. She is currently a postdoctoral researcher at Harvard University.

Archeological studies suggest woolly mammoth numbers were robust as recently as the Middle or Late Pleistocene period, she and her colleagues noted. Nevertheless, the animals all but disappeared towards the end of the Pleistocene and start of the Holocene period around 11,000 years ago, with just a few island populations remaining.

The newly sequenced Wrangel Island mammoth represents the last of these island holdout populations, which persisted until around 4,000 years ago.

For their genome sequencing study, Palkopoulou and her colleagues initially took a crack at sequencing DNA from 10 Wrangel Island mammoths, narrowing in on three samples with more than 50 percent endogenous woolly mammoth DNA.

The sample containing the highest woolly mammoth DNA levels, a mammoth molar radiocarbon dated to around 4,300 years old, was selected for full genome sequencing. After treating it to remove uracil bases formed through cytosine deamination during ancient DNA degradation, the researchers sequenced genomic DNA with the Illumina HiSeq 2500 and aligned the reads to the African savanna elephant reference genome.

Collaborators in Canada used a similar approach to sequence DNA from a woolly mammoth soft tissue sample from Siberia's Oimyakon district. The Oimyakon sample is believed to be some 44,800 years old, placing it within a large woolly mammoth population that spanned continental Europe in the Late Pleistocene period.

In the case of the Wrangel Island individual, more than three-quarters of the woolly mammoth reads aligned to the elephant genome, covering it to an average depth of 11.2-fold. A slightly lower proportion of the Oimyakon mammoth sequences aligned (around 64 percent), producing just over 17-fold coverage of genome, on average.

Mitochondrial genome sequences suggested the two woolly mammoths belonged to maternal lineages previously believed to have diverged more than a million years ago. Based on X chromosome and autosomal chromosome sequences, though, authors of the new analysis estimated that this divergence was far more recent at roughly 50,000 years ago.

"Both of these analyses showed that, in contrast to what the mitochondrial DNA had shown, the two … populations represented by these two individuals seem to have split recently, close in time to when the Oimyakon individual died," Palkopoulou said. "That suggests they're more likely to be from the same population."

Investigators used the genomic DNA to glean other demographic patterns, too. Along with an anticipated population bottleneck coinciding with the end of the last Ice Age and woolly mammoth isolation on islands such as Wrangel, the team used heterozygosity patterns across the genome to identify a more ancient bottleneck that pinched off woolly mammoth populations some 250,000 to 300,000 years.

Researchers have not yet pinpointed a particular event that may have caused this population contraction, Palkopoulou said. "We're not sure if it had something to do with climate," she explained. "It definitely didn't have anything to do with human hunting. So it's a little bit puzzling why this population bottleneck happened."

Finally, the genome analyses revealed diminished genetic variation in the Wrangel Island specimen, which had one-fifth fewer heterozygous sequences than found in its Late Pleistocene counterpart from Siberia. These and other data are consistent with smaller Wrangel Island population sizes and more frequent inbreeding in the lead-up to extinction.

Even so, more research is needed to chart the trajectory of the decline, Palkopoulou said, noting that the "woolly mammoth managed to survive [on Wrangel Island] for 6,000 years and then all of a sudden it disappeared about 4,000 years ago."

Swedish team members are in the process of screening Wrangel Island samples to find those most amenable to genome sequencing in the hopes of untangling the details of mammoth extinction.