Mammoth Genomes Shatter Record for Oldest DNA Sequences

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Mammoth Genomes Shatter Record for Oldest DNA Sequences Feb 17, 2021 19:47:04 GMT

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Post by Admin on Feb 17, 2021 19:47:04 GMT

Scientists have recovered DNA from mammoth fossils found in Siberian permafrost that are more than a million years old. This DNA—the oldest genomic evidence recovered to date—illuminates the evolutionary history of woolly mammoths and Columbian mammoths. It also raises the prospect of recovering DNA from other organisms this ancient—including extinct members of the human family.

Ever since the recovery of two short DNA sequences from a recently extinct zebra subspecies known as the quagga in 1984, researchers have been working to get ever larger amounts of DNA from ever older remains. Advances in ancient DNA extraction and sequencing methods eventually brought to light genomes of creatures from deeper time, including cave bears and Neandertals. In 2013, investigators announced that they had retrieved DNA from a 700,000-year-old horse fossil—by far the oldest genomic data ever obtained. But as astonishingly old as that genetic material was, some experts predicted that sequenceable DNA should survive more than a million years in fossils preserved in frozen environments.

The new findings, published today in Nature, bear that prediction out. Tom van der Valk and Love Dalén of the Center for Paleogenetics in Stockholm and their colleagues obtained DNA from molar teeth belonging to three mammoths from different time periods. Mammoth species can be distinguished on the basis of dental characteristics. One tooth, discovered in deposits thought to be around 700,000 years old, looked like that of an early woolly mammoth, Mammuthus primigenius. The other two teeth—one dated to around one million years ago and the other to 1.2 million years ago or more—resembled molars of the steppe mammoth, Mammuthus trogontherii.

The genetic material extracted from the teeth was highly degraded, having fragmented into lots of tiny pieces over the millennia. To reassemble the pieces and help filter out any DNA from microbes or other contaminants, the researchers used the genomes of modern-day elephants as guides, much as someone solving a jigsaw puzzle might refer to the image on the box. In all they recovered billions of DNA base pairs from the youngest fossil (the woolly mammoth)—about 70 to 80 percent of the genome. They got hundreds of millions of base pairs constituting around 25 to 30 percent of the genome of the second oldest mammoth. The oldest fossil yielded the least DNA, but the team still sequenced around 60 million base pairs from it—enough to provide insights into mammoth evolution.

The fossil record of mammoths indicates that they arose around five million years ago in Africa and spread across much of the world, evolving into number of species and enduring for millions of years before going extinct just a few thousand years ago. Comparing the new genomic data to genomes of younger mammoths, the researchers confirmed their expectation that the woolly mammoth evolved from the steppe mammoth, and they showed that it gradually acquired its adaptations to the extreme cold of ice age Siberia.

The results also revealed surprises about another branch of the mammoth family tree. The oldest mammoth the team sampled turned out to belong to a previously unknown lineage that was ancestral to the mammoths that colonized North America 1.5 million years ago during the early Pleistocene epoch and gave rise to the Columbian mammoth that inhabited temperate regions of North and Central America. The Columbian mammoth may have been the product of interbreeding between woolly mammoths and members of the lineage to which the researchers’ oldest fossil specimen belonged, they suggest.

Outside experts say the work represents a significant advance in ancient DNA research. “It’s an exciting study revealing DNA survival beyond what many in the field would have predicted being the upper limit just a decade ago,” remarks Eske Willerslev of the University of Copenhagen, whose team recovered the 700,000-year-old horse genome in 2013. He and his colleagues were among the researchers who calculated that DNA more than a million years old could survive in permafrost conditions. “Now this has been proven,” he says.

“This is a very exciting study, not only because it pushes back the age of the oldest DNA yet recovered, but because the DNA that the team obtained from these very ancient mammoths provides important insights into early mammoth populations and into the origins of later mammoths both in Europe and the Americas,” says Janet Kelso of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Mammoths are not the only creatures of interest from this time period. Dalén, van der Valk and their colleagues note that many modern-day mammal and bird species got their start in the Early and Middle Pleistocene. At a press teleconference on February 16, Dalén said that the team is starting projects looking into some of these species, including horses, musk ox and various rodents.

Can scientists expect to recover DNA from similarly ancient human ancestors? The human fossil record spans up to seven million years. The oldest human DNA comes from remains dated to 430,000 years ago. “We know that environmental conditions matter a lot for the preservation of DNA. The extraordinary preservation of these mammoth specimens is likely thanks to the fact that they have been ‘on-ice’—frozen in Northern Siberia since the death of these mammoths,” says Kelso, who has studied a number of ancient human genomes. “The ancient humans that have been discovered so far are not found in such ideal conditions, and our view back into the human past is unfortunately therefore still limited.”

But all hope is not lost. “Every year there are new innovations in methods,” Dalén said at the press teleconference. “Maybe a number of years in the future the methods will be there to recover DNA from human nonpermafrost specimens that are getting close to a million years old.” Alternatively, he added, “it is quite possible that in the future someone will find human remains frozen in permafrost of that age.”

Million-year-old DNA sheds light on the genomic history of mammoths
Tom van der Valk

Abstract
Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780–560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.

www.nature.com/articles/s41586-021-03224-9

Last Edit: Feb 17, 2021 22:08:40 GMT by Admin

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Mammoth Genomes Shatter Record for Oldest DNA Sequences Feb 17, 2021 22:07:09 GMT

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Post by Admin on Feb 17, 2021 22:07:09 GMT

Genomic DNA extracted from a trio of tooth specimens excavated in the 1970s has identified a new kind of mammoth that gave rise to a later North American species. The findings were published in Nature on 17 February1.

“I love the paper. I’ve been waiting for that paper for, what, eight years now,” says Ludovic Orlando, an ancient-DNA specialist at the Centre for Anthropobiology and Genomics of Toulouse in France, who co-led a 2013 effort that sequenced the previous oldest ancient DNA — a genome from a 560,000-to-780,000-year-old horse leg bone2. “I’m pleased to lose this record, because it was a heavy one,” he says.

Researchers had suspected that ancient DNA could survive beyond one million years, if the right sample could be found. Once an organism dies, its chromosomes shatter into pieces that get shorter over time. Eventually, the DNA strands become so small that — even if they can be extracted — they lose their information content.

Orlando’s team found that fragments as short as 25 DNA letters in their horse bone, from the Canadian Yukon Territory, could still be interpreted. They estimated that million-year-old remains preserved in the constant cold of permafrost — which slows DNA fragmentation — should also contain DNA fragments of that length. “My only doubt: does such a sample exist?” Orlando says.

Decadal dream
Love Dalén, an evolutionary geneticist at the Swedish Museum of Natural History (SMNH) in Stockholm, had been dallying with the idea of sequencing very old mammoth remains since he first encountered a collection of them, in 2007. The samples his team sequenced, one from an early woolly mammoth (Mammuthus primigenius) and two assigned to a precursor known as steppe mammoths (Mammuthus trogontherii), had been excavated by the Russian palaeontologist Andrei Sher.

Dalén hoped that DNA from the samples could capture the evolution of woolly mammoths and other species in action, but he was sceptical because of previous bad experiences with much younger remains found in permafrost. “It’s not like everything found in the permafrost always works. The vast majority of samples have crap DNA,” he says.

And indeed, two of the three mammoth molars from Sher’s excavations, retrieved from sediments more than than one million years old, contained so little DNA that Dalén says he would have discarded them had they been younger.

But thanks to advances in sequencing technology and bioinformatics, his team managed to obtain 49 million base pairs of nuclear DNA from the oldest sample, found near a village called Krestovka, and 884 million base pairs from another tooth, called Adycha. Analysis of the DNA suggested that the Krestovka sample was 1.65 million years old, and the Adycha sample around 1.3 million (see ‘Ancient genomes’). The third sample, a 600,000-year-old woolly mammoth tooth dubbed Chukochya, produced nearly 3.7 billion base pairs of DNA, more than the length of its 3.1-billion-base-pair genome.

From their shape, the two oldest teeth looked like they belonged to steppe mammoths, a European species that researchers think pre-dated woolly mammoths and Columbian mammoths (Mammuthus columbi), a North American species. But their genomes painted a more complicated picture. The Adycha specimen was part of the lineage that gave rise to woolly mammoths, but the Krestovka specimen clearly was not.

Dalén’s team found that it belonged to an entirely new lineage. “We can’t say it’s a different species, but it sure looks like it,” he says. Although the Krestovka sample is from Russia, he suspects the lineage became isolated from other steppe mammoths in North America. The team found that Columbian mammoths trace half their ancestry to the Krestovka mammoth lineage, and the other half to woolly mammoths. Dalén estimates that the two lineages mixed more than 420,000 years ago.

The idea that new species can form through mixing — and not just splitting from a single parent species — is gaining currency among evolutionary biologists. But this is the first evidence for ‘hybrid speciation’ from ancient DNA, says Orlando. “This is amazing.”

Hendrik Poinar, an ancient-DNA specialist at McMaster University in Hamilton, Canada, says different mammoth species probably routinely hybridized when glacial expansion brought them together. His team has found evidence that later woolly and Columbian mammoths occasionally interbred.

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Mammoth Genomes Shatter Record for Oldest DNA Sequences Feb 18, 2021 0:50:45 GMT

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Post by Admin on Feb 18, 2021 0:50:45 GMT

The future of ancient DNA
Even though researchers have long been expecting a million-year-old genome, crossing that threshold is important, says Viviane Slon, a palaeogeneticist at Tel Aviv University in Israel. “There’s a difference between what we think is possible and actually showing it.”

Tom van der Valk, a bioinformatician at the University of Uppsala in Sweden who led the mammoth-tooth work with evolutionary biologists Patrícia Pečnerová and David Díez-del-Molino at the SMNH, hopes that it will encourage other labs. “It is a symbolic barrier that I hope can inspire and motivate other groups that have ideas about really deep-time sequencing.”

By crossing the million-year threshold, ancient-DNA researchers might be able to access the early histories of other mammals big and small, says Dalén. Very old permafrost samples of musk oxen, moose and lemmings are now on his lab’s radar.

The mammoth DNA does not represent the oldest biomolecular information from the fossil record. In 2016, researchers reported protein sequences from 3.8-million-year-old ostrich eggshells from Tanzania3, and in 2019 another team decoded proteins from a 1.77-million-year-old rhinoceros tooth from Georgia4. Protein sequences tend to be much less informative about an organism’s ancestry than DNA. But protein molecules are much hardier, so researchers can use them to glean insights from very old fossils found in places with no permafrost. The ostrich and rhino samples both come from archaeological sites famous for hominin remains.

The chances of finding million-year-old remains of ancient human relatives in the permafrost are very low, researchers say. But Dalén thinks that the right environment, such as a deep cave, could yield samples that old. Early Neanderthal remains from a Spanish cave dated to 430,000 years ago represent the oldest DNA from an ancient human relative discovered so far5. “Finding a hominin in the sort of ideal context for preservation as permafrost would be would be a dream,” says Slon.

As for the likely age limit of ancient DNA, Dalén says that’s easy to determine: “2.6 million years. That’s the limit of the permafrost. Before that, it was too warm.”

doi: doi.org/10.1038/d41586-021-00436-x

References
1.van der Valk, T. et al. Nature doi.org/10.1038/s41586-021-03224-9 (2021).

2.Orlando, L. et al. Nature 499, 74–78 (2013).

3.Demarchi, B. et al. eLife 5, e17092 (2016).

4.Cappellini, E. et al. Nature 574, 103–107 (2019).

5.Meyer, M. et al. Nature 531, 504–507 (2016).

Last Edit: Feb 18, 2021 3:32:49 GMT by Admin

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Mammoth Genomes Shatter Record for Oldest DNA Sequences Feb 23, 2021 5:16:27 GMT

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Post by Admin on Feb 23, 2021 5:16:27 GMT

Scientists have successfully sequenced the genome of an extinct cave bear using a 360,000-year-old bone—the oldest genome of any organism from a non-permafrost environment.

The work, involving Nottingham Trent University and the University of Potsdam in Germany, has revealed a new evolutionary history for the giant cave bear, which became extinct about 25,000 years ago.

As part of the study, the team found that cave bears and their living relatives—the brown bear and polar bear—diverged from a common ancestor about 1.5 million years ago.

They also found that many significant events in bear evolution may have been driven by major global climate change about one million years ago, when cold phases—or ice ages—became longer and more intense and warm phases much shorter.

The sample analyzed by the researchers was from a cave bear which inhabited the Southern Caucasus, in what is now Georgia, around the Middle Pleistocene.

The oldest DNA sequences have previously come from permafrost environments where DNA is much better preserved.

For this study, however, the researchers wanted to push back the time limit of paleogenome sequencing much further into warmer, temperate zones, which were home to a far greater range of species.

Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears

Axel Barlow 13
Johanna L.A. Paijmans
Federica Alberti
Love Dalén
Gennady Baryshnikov
Michael Hofreiter

Published:February 15, 2021
DOI:https://doi.org/10.1016/j.cub.2021.01.073

Summary
Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.1　As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.

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Mammoth Genomes Shatter Record for Oldest DNA Sequences Feb 23, 2021 20:43:06 GMT

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RESULTS AND DISCUSSION
Analyses of palaeogenomes have provided unparalleled insights
into the evolution of numerous vertebrate lineages. Assembling
these datasets represents a considerable technical challenge,
however, due to postmortem degradation and the loss of endogenous
DNA molecules over time.1 This is especially true for warm
temperate and tropical environments, where DNA degradation
proceeds more rapidly than in colder boreal or arctic environments.
1 As a consequence, comparatively few ancient DNA
studies have successfully retrieved genetic data from temperate
zone samples of Middle Pleistocene age (Chibanian age, 129–
774 ka2). Notable successes include high coverage genome
datasets from samples dating around the Middle to Late Pleistocene
boundary from Germany3,4 and from the Altai Mountains.5
Much older DNA sequences have been retrieved from samples
dating to 430 ka from Spain, but with a lower magnitude of
data recovery, comprising of mitochondrial genome sequences
6,7 and 1–2 megabases of nuclear DNA.8 Nonetheless,
these achievements suggest that the retrieval of genome-scale
datasets of this age is possible, provided samples of sufficient
quality can be found.

Middle Pleistocene cave bear genome
One recent and notable advance in palaeogenome sequencing
has been the discovery of the mammalian petrous bone as a
source of high purity ancient DNA.9 One group where this
approach has been successfully applied are extinct cave
bears,10,11 which form the sister lineage to the clade consisting
of the extant brown (Ursus arctos) and polar (Ursus maritimus)
bears. To investigate if petrous bones may provide a way of extending
both the time depth and magnitude of Middle Pleistocene
genome data retrieval, we investigated the petrous bone
of a Middle Pleistocene cave bear from Kudaro 1 cave located
in South Ossetia in the Southern Caucasus. The sedimentary
layer (5c) from which this sample was recovered has been dated
using radiothermoluminescence at 360,000 ± 90,000 years,12
and multiple additional sources of evidence support a Middle
Pleistocene age for the specimen (see STAR methods). The Kudaro
1 sample is assigned to the taxon Ursus kudarensis praekudarensis,
which is thought to be ancestral to the Late Pleistocene
Caucasian cave bear U. k. kudarensis based on morphological
evidence.13,14

We extracted DNA from the praekudarensis petrous bone and
sequenced it using Illumina technology. From a total of 2.6
billion sequenced molecules, we were able to map 2.1 Gb of
sequence with high confidence to the reference genome assembly
of the polar bear (Table S1). This represents a low coverage
genome dataset where the majority of sequenced positions are
covered by a single sequencing read (Figure S1). The estimated
proportion of endogenous DNA molecules in the praekudarensis
extract is 3.6% (Table S1), which is remarkable given the age of
the specimen, and exceeds the endogenous proportions of
some previously studied temperate-zone Middle Pleistocene extracts
8 by several orders of magnitude.

Last Edit: Feb 23, 2021 20:43:29 GMT by Admin