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PLOS BLOGS DNA Science

DNA Study Adds Branch to North American Mammoth Family Tree

An international team has assembled billions of DNA snippets from molars that three mammoths left in the permafrost of northeastern Siberia, at widely different times. The research reveals an unrecognized ancestor that contributed half of the genome of the mammoth species that came to North America some 1.5 million years ago. The report appears in Nature.

The timescale of the study paints a portrait of mammoth evolution, perhaps even capturing a glimmer of speciation. The finding also sets back the clock of ancient DNA analysis; a horse that lived 780,000 to 560,000 years ago holds the record.

The three mammoth specimens were excavated in the 1970s from different locations in Siberia, dating from half a million to roughly 1.2 million years ago. They reside at the Geological Institute, Russian Academy of Sciences, in Moscow. The permafrost helped to preserve the DNA.

The Land Bridge Where It Happened

The common ancestor of mammoths and African elephants lived on the African continent about 4.2 million years ago. By the early Pleistocene epoch (2.6 million years ago to 11,700 years ago), two types of mammoths were in eastern Siberia: southern mammoths and steppe mammoths. Two of the three animals described in the new paper are steppe mammoths, Adycha from 1.34 million years ago and Chukochya from 870,000 years ago.

The steppe mammoths branched into the Columbian mammoth about 1.5 million years ago and then diverged again, spawning the familiar woolly mammoth of Flintstones fame about 700,000 years ago. The woollies stayed in Siberia, but the Columbian mammoths wound up here. Ten species of mammoth are recognized.

“Several years ago, we aimed to recover genomes from before and after origin of the woolly mammoth. We expected that the two oldest steppe mammoths were the direct ancestors of the woolly mammoth. This ancestral relationship is indeed what we found for a one million-year-old specimen, but it was surprising to find another, of a previously unknown genetic lineage of mammoth, that diversified more than 1.2 million years ago. We call it Krestovka,” explained Tom van der Valk from the Centre for Palaeogenetics in Stockholm at a webinar for reporters the day before the paper published.

Krestovka’s ancestors may have branched from the family tree 2.66 to 1.78 million years ago and the animals may have lived as long ago as 1.65 million years – dates are very uncertain on such a vast time scale. The other half of the genome of the Columbian mammoths came from steppe mammoths on the move.

The story stitched into the DNA pieces indicates that steppe mammoths bred with Krestovka’s ancestors. The beasts stayed in Siberia for awhile, and then some of them crossed the land bridge arising from the Bering Strait, lumbering into North America some 100,000 years ago. Shortly after, another large breeding event introduced about 12 percent more woolly mammoth DNA into the Columbia mammoth genome. All told, some half a million of the beasts came from there to here over the millennia.

The initial 50:50 split of two ancestral genomes that the new research unveils is unusual, a little too neat not to mean something. “What is different in our study is that most others find hybridization has resulted in 95% from one genome. The best comparison is the Neanderthal and human genomes, which share on average 2% (of their differences). But the hybridization resulting in the Columbia mammoth was much cleaner, with half from either ancestral species,” explained Love Dalén, also from the Centre for Palaeogenetics, at the webinar. The 50:50 split reflects hybrid animals mating with each other, the researchers suggest, perpetuating the proportion, rather than the more common backbreeding with members of the past generation.

The most recent mammoths to leave fossil evidence traversed the land bridge about 5,600 years ago, on St. Paul Island in Alaska.

“Deep-time Paleogenomics” Probes Ancient DNA

Dating the specimens relies on two sources of information. Other fossils found in the same rock layer (“biostratigraphy”) provide clues and context. Of great value are remains of rodents such as voles, pikas, and lemmings. Not only is their anatomy well studied, but their DNA freezes fast and is preserved, because of small body size.

Comparing DNA sequences provides a “molecular clock” when mutation rates of specific genes are known, converting DNA differences into a time machine of sorts that deduces how long ago genetic change likely occurred. Teeth are the best place to get ancient DNA.

“We chose teeth because only on teeth can we identify the species of mammoth we are working on. We knew one specimen was an early woolly and the other two were from ancestral types of steppe mammoths,” explained Dalén.

Experts in mammoth dentition compare the height of the crowns, enamel thickness, and the number and density of flat dentine plates underneath the enamel. The ancient DNA came from the tooth interiors, a common practice in paleogenomics to preserve the outer structure.

“Mammoth teeth are very large, but we use very small amounts of powder to get the genomes out from the teeth, like a pinch of salt. We recovered DNA from mammoth remains up to 1.2 million years old. It was extremely degraded into very small pieces, so we had to sequence billions of ultrashort DNA sequences to passel this genome together,” said Dalén. The algorithm compared that information to DNA from remains of more modern mammoth species and from close contemporary relatives, elephants.

“Previous understanding of what genomes look like allowed us to map back our tiny fragments to the correct mammoth. We had the opportunity from tiny pieces of DNA to make quite large inferences about the evolution and history of these other specimens,” said van der Valk. And Dalén offered a vivid analogy. “The reference genomes from the elephant are like the cover of the puzzle box, so we had an idea of what to expect.”

The algorithm also filters out DNA snippets common to large groups, such as all mammals, as well as pieces from contaminating microbes. It’s a little like ignoring common words like “and” and “to” in comparing documents and removing errant cut-and-pastes from other work.

Comparison of the amino acid sequences of the proteins encoded in the genomes of the mammoths and elephants revealed that adaptations to the cold were already part of the mammoth family tree before a million years ago, in the steppe mammoths. The adaptations, which are changes that fuel evolution, affected retaining heat, circadian rhythms, and growth of the trademark shaggy hair.

What is the bigger picture? Summed up van der Valk, “We don’t think there was one rapid burst of adaptation that led to evolution of the woolly mammoth, but rather a gradual process over time as steppe mammoths accumulated adaptations to colder environments. That increased up to the late Pleistocene mammoths.”

CODA
I was happy to blog this week about something other than COVID, and then realized that I didn’t really get away from it. For the mammoth story and the continuing saga of humanity versus the novel coronavirus illustrate that we can never completely know or understand nature.




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