The biocultural origins and dispersal of domestic chickens

SignificanceChickens are the world's most numerous domestic animal. In order to understand when, where, and how they first became associated with human societies, we critically assessed the domestic status of chicken remains described in >600 sites in 89 countries, and evaluated zoogeographic, morphological, osteometric, stratigraphic, contextual, iconographic, and textual data. Although previous studies have made claims for an early origin of chickens, our results suggest that unambiguous chickens were not present until ∼1650 to 1250 BCE in central Thailand. A correlation between early chickens and the first appearance of rice and millet cultivation suggests that the production and storage of these cereals may have acted as a magnet, thus initiating the chicken domestication process

Origins and genetic legacy of prehistoric dogs

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Archaeological evidence indicates that pig domestication had begun by ~10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ~8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local Euro-pean wild boars, although it is also possible that European wild boars were domesticated independently without any genetic con-tribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process

Quantitative Human Paleogenetics:What can Ancient DNA Tell us About Complex Trait Evolution?

Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human archaeological remains are now easier than ever to obtain, and provide a direct window into changes in frequencies of trait-associated alleles in the past. This has generated a new wave of studies aiming to analyse the genetic component of traits in historic and prehistoric times using ancient DNA, and to determine whether any such traits were subject to natural selection. In humans, however, issues about the portability and robustness of complex trait inference across different populations are particularly concerning when predictions are extended to individuals that died thousands of years ago, and for which little, if any, phenotypic validation is possible. In this review, we discuss the advantages of incorporating ancient genomes into studies of trait-associated variants, the need for models that can better accommodate ancient genomes into quantitative genetic frameworks, and the existing limits to inferences about complex trait evolution, particularly with respect to past populations

The selection landscape and genetic legacy of ancient Eurasians

The Holocene (beginning ~12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical, and mental health of present-day populations. Using a dataset of >1600 imputed ancient genomes, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify major selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported, and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in >400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic, and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, while risk alleles for diabetes and Alzheimer’s disease are enriched for Western Hunter-gatherer ancestry. Our results suggest that ancient selection and migration were major contributors to the distribution of phenotypic diversity in present-day Europeans

Accuracy of HAYSTAC and other methods for an oral microbiome simulation.

Bar plot showing the mean count of false positives (red), false negatives (orange), and true detected species (blue) for two versions of the oral microbiome dataset, each with six replicates: (A) modern simulation, with fixed read lengths (n = 6); and (B) ancient simulation, with variable read lengths and post-mortem damage (n = 6). The dotted line shows the average number of simulated species in each set of samples (i.e., the maximum true positive; n = 178), and numbers above the error bars indicate the mean species count in each category. For the modern simulation, HAYSTAC substantially outperforms Kraken2/Bracken, KrakenUniq and MALT with respect to false positives, and performs equivalently with Sigma. For the ancient simulation, HAYSTAC outperforms all four other methods with respect to false positives. The overall high rates of false negative identifications are due to the absence of many simulated species from the reference database for all four methods. HAYSTAC also outperforms all the other four methods in both the modern and ancient Oral Microbiome datasets by identifying the highest number of true positive species.</p