We undertook a functional dissection of chromatin remodeler BAZ1B in neural crest (NC) stem cells (NCSCs) from a uniquely informative cohort of typical and atypical patients harboring 7q11.23 copy number variants. Our results reveal a key contribution of BAZ1B to NCSC in vitro induction and migration, coupled with a crucial involvement in NC-specific transcriptional circuits and distal regulation. By intersecting our experimental data with new paleogenetic analyses comparing modern and archaic humans, we found a modern-specific enrichment for regulatory changes both in BAZ1B and its experimentally defined downstream targets, thereby providing the first empirical validation of the human self-domestication hypothesis and positioning BAZ1B as a master regulator of the modern human face. In so doing, we provide experimental evidence that the craniofacial and cognitive/behavioral phenotypes caused by alterations of the Williams-Beuren syndrome critical region can serve as a powerful entry point into the evolution of the modern human face and prosociality.

Analyses of ancient DNA from extinct hominins have provided unique insights into the complex evolutionary history of Homo sapiens, intricately related to that of the Neanderthals and the Denisovans as revealed by several instances of admixture events. These analyses have also allowed the identification of introgression deserts: genomic regions in our species that are depleted of “archaic” haplotypes. The presence of genes like FOXP2 in these deserts has been taken to be suggestive of brain-related functional differences between Homo species. Here, we seek a deeper characterization of these regions and the specific expression trajectories of genes within them, taking into account signals of positive selection in our lineage. Analyzing publicly available transcriptomic data from the human brain at different developmental stages, we found that structures outside the cerebral neocortex, in particular the cerebellum, the striatum and the mediodorsal nucleus of the thalamus show the most divergent transcriptomic profiles when considering genes within large introgression deserts and under positive selection.

10Modern humans' lifestyle strongly depends on complex social skills like empathy, tolerance and cooperation. Variation in the oxytocin receptor (OXTR) and the arginine-vasopressin receptors (AVPR1A, AVPR1B genes) has been widely associated with diverse facets of social cognition, but the extent to which these variants may have contributed to the evolution of human prosociality remains to be elucidated. In this study, we compared the OXTR, AVPR1A and AVPR1B DNA sequences of modern humans to those of our closest extinct and extant relatives, and then clustered the variants we identified based on their distribution in the species studied. This clustering, along with the functional importance retrieved for each variant and their frequency in different modern-human populations, is then used to determine if any of the OXTR, AVPR1A and AVPR1B-variants might have had an impact at different evolutionary stages. We report a total of 29 SNPs, associated with phenotypic effects ranging from clearly pro-social to mixed or antisocial. Regarding modern human-specific alleles that could correlate with a shift towards prosociality in modern-humans, we highlight one allele in AVPR1A (rs11174811), found at high frequency and linked to prosocial phenotypes in modern humans, while the ancestral allele is associated with antisocial phenotypes. We also report three sites of putatively convergent changes between modern humans and bonobos (rs237897(A), rs2228485(G) and rs1042615(A)), and note the absence of such a convergent pattern between modern humans and chimpanzees. Finally, we observe the high concentration of 'modern human specific' alleles in vasopressin receptors not paralleled in the oxytocin receptor. 11 1 Introduction 12 Oxytocin (OXT) and vasopressin (AVP) are important neurotransmitters that function through their respective receptors to 13 regulate a diverse set of biological processes, such as pregnancy and uterine contractions, milk-ejection, copulation and orgasm, 14 attachment between mothers and their young, bond formation, suppression of stress, thermoregulation, olfactory processing, 15 eye-contact and recognition of familiar individuals 1 . OXT and AVP are closely related structurally and evolutionarily: they 16 have been argued to be the product of a local duplication event that took place before the origin of vertebrates 2 , and they only 17 differ in two (of the nine) amino acids, although they display differences at a functional level 1 . Each binds to their respective 18 receptor(s) (OXTR in the case of oxytocin, and AVPR1A, AVPR1B, and AVPR2 in the case of vasopressin), but their molecular 19 similarities allow for crosstalk in the brain and peripheral organs 3 . 20Variation in the genes that code for OXT and AVP receptors (OXTR and mainly AVPR1A and AVPR1B) have long been 21 associated with different social behaviors 4 . Single Nucleotide Polymorphisms (SNPs) in these genes in modern humans have 22 been claimed to be implicated in altruism, face recognition, stress levels and empathy, but also in socioco...

No abstract

Large-scale estimations of the time of emergence of variants are essential to examine hypotheses concerning human evolution with precision. Using an open repository of genetic variant age estimations, we offer here a temporal evaluation of various evolutionarily relevant datasets, such as Homo 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 specific to various brain regions. We find a recurrent bimodal distribution of high-frequency variants, but also evidence for specific enrichments of gene categories in distinct time windows, pointing to different periods of phenotypic changes, resulting in a mosaic. With a temporal classification of genetic mutations in hand, we then applied a machine learning tool to predict what genes have changed more in certain time windows, and which tissues these genes may have impacted more. Overall, we provide a fine-grained temporal mapping of derived variants in Homo sapiens that helps to illuminate the intricate evolutionary history of our species.

Analyses of ancient DNA from extinct hominins have provided unique insights into the complex evolutionary history of Homo sapiens, intricately related to that of the Neanderthals and the Denisovans as revealed by several instances of admixture events. These analyses have also allowed the identification of introgression deserts: genomic regions in our species that are depleted of `archaic' haplotypes. The presence of genes like FOXP2 in these deserts has been taken to be suggestive of brain-related functional differences between Homo species. Here, we seek a deeper characterization of these regions, taking into account signals of positive selection in our lineage. Analyzing publicly available transcriptomic data from the human brain at different developmental stages, we found that structures outside the cerebral neocortex, and especially the cerebellum and the striatum at prenatal stages, show the most divergent transcriptomic profiles when considering genes under positive selection within introgression deserts.

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.

The availability of high-coverage genomes of our extinct relatives, the Neanderthals and Denisovans, and the emergence of large, tissue-specific databases of modern human genetic variation, offer the possibility of probing the effects of modern-derived alleles in specific tissues, such as the brain, and its specific regions. While previous research has explored the effects of introgressed variants in gene expression, the effects of Homo sapiens-specific gene expression variability are still understudied. Here we identify derived, Homo sapiens-specific high-frequency (≥90%) alleles that are associated with differential gene expression across 15 brain structures derived from the GTEx database. We show that regulation by these derived variants targets regions under positive selection more often than expected by chance, and that high-frequency derived alleles lie in functional categories related to transcriptional regulation. Our results highlight the role of these variants in gene regulation in specific regions like the cerebellum and pituitary.