Fine-grained temporal mapping of derived high-frequency variants supports the mosaic nature of the evolution of Homo sapiens

Abstract

As our knowledge about the history of the sapiens lineage becomes increasingly complex, large-scale estimations of the time of emergence of derived variants become essential to be able to offer more precise answers to time-sensitive hypotheses concerning human evolution. Using an open repository of genetic variant age estimations recently made available, we offer here a temporal evaluation of various evolutionarily relevant datasets, such as sapiens-specific variants, high-frequency variants found in genetic windows under positive selection, introgressed variants from extinct human species, as well as putative regulatory variants in various brain regions. We find a recurrent bimodal distribution of high-frequency variants, but also evidence for specific enrichments of gene categories in various time windows, which brings into prominence the 300-500k time slice. We also find evidence for very early mutations impacting the facial phenotype, and much more recent molecular events linked to specific brain regions such as the cerebellum or the precuneus. Additionally, we present a case study of an evolutionarily relevant gene, BAZ1B, and its targets, to emphasize the importance of applying temporal data to specific evolutionary questions. Overall, we present a unique resource that informs and complements our previous knowledge of sapiens evolution using publicly available data, and reinforce the case for the mosaic, temporally very extended nature of the evolutionary trajectory of our species.

Self-Domestication: From Analogy to Homology via Genomics

“…The emerging picture, then, is one of stratification or stepped cline (Figure 2), with separate 'domestication' events or stages distributed in time and possibly space, much like what has been hypothesized for plants like maize 117 (see 118 in this context). Accordingly, we expect signals of domestication in the genome to be distributed in time, as discussed in 119,120 (this is also consistent with the conclusion in 103 , who note that in the case of the NPS precursor, the selection has already started in Neandertals, as they detect an instance of introgression preserved in modern humans.) If our argument is on the right track, we expect different 'disease' models (schizophrenia and other stress-related disorders, neurocristopathies, autism, etc.)…”

Genetic variations within human gained enhancer elements affect human brain sulcal morphology

“…We limited our study to genetic annotations over a selection of broadly defined periods of primate evolutionary history. Other approaches could be used with better temporal resolution and more comprehensive temporal distribution along lineages that led to emergence of Homo sapiens (Albers & McVean, 2020;Andirkó et al, 2021). Moreover, with our methodology we assessed only genetic variations that are polymorphic in current human populations.…”