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Recent Neanderthal Diversity Reveals Population History, Human Interactions

NEW YORK (GenomeWeb) – A team from Germany, China, and elsewhere has documented the genetic diversity and apparent population relationships between Neanderthals that lived relatively recently in Europe or the Caucasus, dubbed "late Neanderthals."

As they reported online today in Nature, the researchers did low-coverage whole-genome sequencing on remains from five Neanderthals, dated at roughly 39,000 to 47,000 years old. In these Neanderthals, they saw genetic clustering that coincided with location, while their broader analyses provided clues to historical Neanderthal population splits, replacements, and interactions with modern humans.

"Our work demonstrates that the generation of genome sequences from a large number of archaic human individuals is now technically feasible, and opens up the possibility to study Neanderthal populations across their temporal and geographical range," senior authors Janet Kelso and Svante Pääbo, evolutionary genetics researchers at the Max Planck Institute for Evolutionary Anthropology, and their colleagues wrote.

Using an approach that relied on a hypochlorite chemical solution to get rid of contaminating DNA from microbes or present-day humans, the team analyzed DNA extracted from Neanderthal bone or tooth samples at sites in Belgium, France, Croatia, and the Russian Caucasus, spanning a time period from roughly 37,880 years to more than 45,000 years ago.

"Hypochlorite treatment increased the proportion of DNA fragments mapping to the human reference genome between" nearly sixfold and one hundred sixty onefold, the authors explained, "and reduced present-day human contamination in four of the specimens" between twofold and eighteenfold.

After preliminary genome library sequencing with Illumina MiSeq or HiSeq 2500 instruments, the researchers used the HiSeq 2500 to sequence nearly two-dozen libraries from the five late Neanderthals selected. In the process, they generated between onefold and nearly threefold average coverage of each ancient genome.

To further weed out contaminating sequences, the team focused on nuclear and mitochondrial genome sequences containing deaminated cytosine bases characteristic of ancient DNA.

When they compared the late Neanderthal genomes with previously reported human and Neanderthal sequences — including a 120,000-year-old Neanderthal from Siberia's Altai Mountains and a 45,000-year-old Neanderthal from Vindija in Croatia — the researchers teased apart relationships between Neanderthals from different locations over time.

One of the newly sequenced Neanderthal samples appeared to belong to the same Vindija Neanderthal sequenced in the past, the researchers noted. Consequently, it was not included in their other follow-up analyses.

The team detected clustering by location, although all of the late Neanderthals appeared to be more closely related to one another than to the more ancient Altai Neanderthal. The results also pointed to potential turnover in the Russian Caucasus, with an uptick in derived alleles appearing in more recent Neanderthal individuals.

Based on their data, the researchers estimated that the newly sequenced late Neanderthals likely split from the lineage leading to much older Altai Neanderthal roughly 150,000 years ago. They put a more recent split between the Vindija Neanderthal lineage and younger Neanderthals from other locations at around 70,000 years ago.

By scrutinizing introgressed Neanderthal sequences in hundreds of present-day human genomes, the authors concluded that the "majority of gene flow into early modern humans appears to have originated from one or more Neanderthal populations that diverge from other late Neanderthals after their split from the Altai Neanderthal," about 150,000 years ago. On the other hand, they did not detect signs of recent gene flow from modern humans into Neanderthal populations, despite testing Neanderthals that lived after humans arrived in Europe.

"It may be that gene flow was mostly unidirectional, from Neanderthals into modern humans," Max Planck's Pääbo said in a statement.

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