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The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. We observe that: 1) Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia. 2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this “Great Divide”, including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP; 4) The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia; 5) Extensive regional differences in the ancestry components involved in these early events remain visible to this day, even within countries. Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall (this research has been conducted using the UK Biobank resource); 6) Shifts in diet, lifestyle and environment introduced new selection pressures involving at least 21 genomic regions. Most such variants were not universally selected across populations but were only advantageous in particular ancestral backgrounds. Contrary to previous claims, we find that selection on the FADS regions, associated with fatty acid metabolism, began before the Neolithisation of Europe. Similarly, the lactase persistence allele started increasing in frequency before the expansion of Steppe-related groups into Europe and has continued to increase up to the present. Along the genetic cline separating Mesolithic hunter-gatherers from Neolithic farmers, we find significant correlations with trait associations related to skin disorders, diet and lifestyle and mental health status, suggesting marked phenotypic differences between these groups with very different lifestyles. This work provides new insights into major transformations in recent human evolution, elucidating the complex interplay between selection and admixture that shaped patterns of genetic variation in modern populations.Competing Interest StatementThe authors have declared no competing interest.

Oikopleura dioica (Appendicularia) is a model organism to understand the evolution of chordates. Although its nuclear genome has been sequenced, its mitochondrial (mt) genome has not been determined, probably because of their fast evolutionary rate and extensive RNA editing. We sequenced cDNA of the cox1 gene and nuclear genomes (using Illumina) from O. dioica and Fritillaria pellucida. Mapping the resulting DNA reads onto the cox1 cDNA sequences, we confirmed the previously-published observation that, at DNA level, long poly-T stretches interrupt the mt ORFs, hampering their identification. In addition, we noticed that mitogenomic poly-T correspond at RNA level to TTTTTT (6T) regions in O. dioica but to shorter TTTT (4T) regions in F. pellucida, leading to hypothesize species-specific RNA editings by deletion. Remarkably, different editing sites were observed between Mediterranean and Japanese populations of O. dioica suggesting a rapid evolution of these sites.While tRNAs usually punctuate the protein-coding genes in chordate mt genome, only one tRNA, tRNAmet, was identified among O. dioica mt contigs assembled from published cDNA reads. To test if mt tRNAs could have been lost, we searched the genomic assembly for the presence of mt aminoacyl tRNA synthetase (aaRS) genes, which encode the proteins responsible for the aminoacylation of its cognate tRNA. No specific mt aaRS genes were found in the nuclear genome assembly of O. dioica except for mt-MetRS, which catalyzes the mt-tRNAMet aminoacylation. This suggests that the mt genome of O. dioica encodes only the single tRNAMet.

Fil: Raia, Pasquale. Università degli Studi di Napoli Federico II; Italia Fil: Passaro, Federico. Università degli Studi di Napoli Federico II; Italia Fil: Carotenuto, Francesco. Università degli Studi di Napoli Federico II; Italia Fil: Maiorino, Leonardo. Università degli Studi Roma Tre; Italia Fil: Piras, Paolo. Università degli Studi Roma Tre; Italia Fil: Teresi, Luciano. Università degli Studi Roma Tre; Italia Fil: Meiri, Shai. Tel Aviv University; Israel Fil: Itescu, Yuval. Tel Aviv University; Israel Fil: Novosolov, Maria. Tel Aviv University; Israel Fil: Baiano, Mattia A. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Fil: Baiano, Mattia A. Instituto Catalán de Paleontología Miquel Crusafont; España Fil: Baiano, Mattia A. Universidad Nacional de Río Negro; Argentina Fil: Martínez, Ricard. Universitat Autònoma de Barcelona; España Fil: Fortelius, Mikael. University Of Helsinski; Finlandia Luxuriant, bushy antlers, bizarre crests, and huge, twisting horns and tusks are conventionally understood as products of sexual selection. This view stems from both direct observation and from the empirical finding that the size of these structures grows faster than body size (i.e., ornament size shows positive allometry).We contend that the familiar evolutionary increase in the complexity of ornaments over time in many animal clades is decoupled from ornament size evolution. Increased body size comes with extended growth. Since growth scales to the quarter power of body size, we predicted that ornament complexity should scale according to the quarter power law as well, irrespective of the role of sexual selection in the evolution and function of the ornament. To test this hypothesis, we selected three clades (ammonites, deer, and ceratopsian dinosaurs) whose species bore ornaments that differ in terms of the importance of sexual selection to their evolution.We found that the exponent of the regression of ornament complexity to body size is the same for the three groups and is statistically indistinguishable from0.25.We suggest that the evolution of ornament complexity is a by-product of Cope’s rule. We argue that although sexual selection may control size in most ornaments, it does not influence their shape.