The genomic journey of modern and archaic humans may be older than we thought

Research conducted at the Department of Biology, University of Padova, has identified critical genomic milestones in the evolution of Homo sapiens, including key chromosomal rearrangements and specific gene variants that contributed to the development of current modern human traits.

Findings challenge traditional models that attribute certain genetic innovations exclusively to modern Homo sapiens. Similarities observed in both modern and archaic human genomes suggest many hallmarks of the Homo sapiens genetic landscape arose before the lineages split.

Homo sapiens evolved through a series of significant genetic events. A population bottleneck approximately 900,000 years ago is thought to coincide with genomic rearrangements, the fusion of chromosome 2 and the translocation of the pseudoautosomal region 2 (PAR2).

About 650,000 years ago, modern humans diverged from Neanderthals and Denisovans. Interbreeding events have occurred more than once, providing opportunities for shared genetic traits. At least one modern human-Neanderthal event occurred as early as 350,000 years ago.

In the study, “Partitioning the Genomic Journey to Becoming Homo sapiens,” published Dec. 9 on the bioRxiv preprint server, genomic sequences from modern humans, Neanderthals, and Denisovans were analyzed for genetic divergences and pinpointing human-specific genomic regions.

The researchers employed coalescence analyses, mutation rate estimates, and examination of archaic admixture signatures to partition the human genome and trace the emergence of these key variants. Molecular clock assessments provided a minimum age estimate for the PAR2 translocation, while phylogenetic methods tracked the timing and frequency changes of shared variants among modern and archaic populations.

Researchers focused on three key events: a bottleneck 900,000 years ago (Event 1), the divergence of modern and archaic humans 650,000 years ago (Event 2), and interbreeding between Homo sapiens and Neanderthals 350,000 years ago (Event 3).

Event 1 marked a critical reduction in ancestral human populations. This event is thought to coincide with significant chromosomal rearrangements, including the fusion of chromosome 2 and the translocation of the pseudoautosomal region 2 (PAR2) from chromosome X to Y.

Analysis of male Denisovan and Neanderthal genomes demonstrated that PAR2 was present on both X and Y as in modern humans. Rearrangement had to occur before the split between archaic and modern lineages, which the researchers estimate to be around 856,000 to 1.3 million years ago, potentially pushing back the estimated age of a shared PAR2 ancestor by 400,000 years.

During their analysis, the team identified 11 single nucleotide variants (SNVs) in the PAR2 regions of male chromosome X, which were mostly absent in females. The gender-specific distribution suggests that these mutations were likely male-specific and may have been incorrectly mapped in previous analyses. Importantly, these SNVs appeared to have arisen after the common ancestor of all Y-PAR2 sequences had diverged from the X-PAR2 gene pool.

By applying a Y chromosome mutation rate of 3 x 10^-8 mutations per base pair per generation, they calculated that the ancestor of all Y-PAR2 sequences diverged from the X-PAR2 gene pool approximately 518,000 years ago. This timeframe represents the period between the translocation event (856,000 to 1.3 million years ago) and the most recent common ancestor of all modern human Y chromosomes, dating to around 338,000 years ago.

For Event 2, when modern humans diverged from Neanderthals and Denisovans, scientists examined the genetic history of “Human650 regions” through coalescence events and variants appearing exclusively in modern humans.

They identified recent functional variants in 56 genes in modern humans, 24 of which are associated with brain functions and skull morphology. These genetic changes emerged soon after the divergence and are believed to underpin key aspects of modern human biology and behavior.

Researchers observed that the Altai Neanderthal genome exhibited more regions with coalescence events occurring within the last 650,000 years compared to the Denisova genome. Variants uniquely associated with the modern human lineage were not widely found in Neanderthal populations during Event 3.

This suggests that when Homo sapiens and Neanderthals interbred in Event 3, approximately 350,000 years ago, certain ancestral variants were reintroduced, potentially enhancing their Neanderthal genetic diversity.

Specific gene variants have a tendency to drop out of small population sizes, with inbreeding over long timeframes leading to less genetically diverse populations. Due to this drifting, certain genetic variants previously present in Neanderthal populations were lost.

When modern humans first intermingled with Neanderthal genomes, the effect was not so much an introduction to novel genes as a reintroduction of previously lost genetic variants finding their way back into the Neanderthal gene pool.

The study offers great new insights into the rich tapestry of archaic and modern human genome history. They would meet yet again around 50,000 to 65,000 years ago, continuing the braided stream of human genetic and cultural collaborations.

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