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Nuclear Genomic Analysis of 430,000-Year-Old Hominins Reveals Close Ties to Neanderthals

NEW YORK (GenomeWeb) – Sequencing and analysis of nuclear DNA from 430,000-year-old hominins uncovered in a cave in Spain has indicated that they are most closely related to Neanderthals, overturning previous mitochondrial DNA-based evidence that they were more like the archaic Denisovans from eastern Eurasia.

Using a specialized approach to handle samples of such age, researchers led by the Max Planck Institute for Evolutionary Anthropology's Svante Pääbo sequenced nuclear DNA from five samples from the Sima de los Huesos hominins. As reported today in Nature, this suggested that the hominins were more closely related to Neanderthals than to Denisovans and that the population divergence between Neanderthals and Denisovans could be traced back further than 430,000 years.

"These results provide important anchor points in the timeline of human evolution," Pääbo said in a statement. "They are consistent with a rather early divergence of 550,000 to 750,000 years ago of the modern human lineage from archaic humans."

While the Sima de los Huesos hominins share derived dental and cranial morphological features with Neanderthals, Pääbo and his team reported in 2013 in Nature that their mitochondrial genomes were more like those found among Denisovans. At the time, they noted that this finding was unexpected not only because of those shared features between the Sima de los Huesos hominins and Neanderthals, but also because of Denisovans' more easterly range.

This led them to speculate that the Sima de los Huesos hominins might have shared ancestral ties with an ancestor common to both Neanderthals and Denisovans, or that gene flow from another group brought this mitochondrial DNA genome to both the Denisovan and Sima de los Huesos hominin populations.

To further examine the relationships among these ancient hominins, the researchers extracted nuclear DNA from five bone samples from the Spanish cave: an incisor, a part of a femur, a molar, a scapula, and the femur from which mitochondrial DNA had previously been obtained.

Due to the extreme age of the samples, the researchers generated between 600 million and 2.6 billion sequence reads, but then focused on the ones generated from libraries with the high number of terminal C-to-T substitutions and short fragments, both of which are hallmarks of ancient DNA. They also isolated mitochondrial DNA from the four new samples using hybridization capture.

To account for contamination from microbial and human sources, the researchers estimated the number of reads with C-to-T substitutions as well as the number of reads that contained genetic patterns diagnostic for humans.

They estimated that their samples contained between 76 percent and 98 percent contamination, but when they limited their analysis to fragments that contained evidence of deamination that level of contamination fell for all samples but the scapula.

Pääbo and his colleagues then compared these sequences to those from the Altai Neanderthal, the Denisovan finger bone, and a modern human from Africa to find spots in their genomes where they differed from chimpanzees and other primates. They then estimated the percentage of positions where the Sima de los Huesos hominins shared the derived state with Neanderthal, Denisovan, or human samples.

Based on this, the researchers found that the incisor and one of the femur samples shared between 68 percent and 87 percent of the derived alleles belonging to both Neanderthals and Denisovans, but between 39 percent and 43 percent of the derived alleles specific to Neanderthals and only between 7 percent and 9 percent of the ones specific to Denisovans.

This, they added, indicates that the Sima de los Huesos hominins are early Neanderthals or are closely related to the ancestors of Neanderthals, after they diverged from the ancestors of Denisovans.

Still, the mitochondrial DNA the researchers analyzed from the Sima de los Huesos hominins was more similar to Denisovan mitochondrial DNA

While the researchers noted that this discrepancy could be due to Sima de los Huesos hominins harboring divergent mitochondrial genomes or to a separate hominin group contributing it to both Denisovans and Sima de los Huesos hominins, they added that it could also be due to Neanderthals later acquiring a new mitochondrial genome through gene flow, possibly from Africa. 

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