A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition

Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and foodways. We present thirteen ancient genomes (c.8500-7500 calBCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying a mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organised along biological family lines. We document bodily interventions such as head-shaping and cauterization among the individuals examined, reflecting Çayönü's cultural ingenuity. Finally, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesise that Upper Mesopotamia's cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean

We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term “the expanding mobility model.” Interestingly, this increase in inter-regional divergence can be captured by outgroup-f$_3$-based genetic distances, but not by the commonly used F$_{ST}$ statistic, due to the sensitivity of F$_{ST}$, but not outgroup-f$_3$, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene

Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

Yurtman, ozer, Yuncu et al. provide an ancient DNA data set to demonstrate the impact of human activity on the demographic history of domestic sheep. The authors demonstrate that there may have been multiple domestication events with notable changes to the gene pool of European and Anatolian sheep since the Neolithic. Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic

Determinants and inverses of circulant matrices with complex Fibonacci numbers

Let ℱn = circ (︀F*1 , F*2, . . . , F*n︀ be the n×n circulant matrix associated with complex Fibonacci numbers F*1, F*2, . . . , F*n. In the present paper we calculate the determinant of ℱn in terms of complex Fibonacci numbers. Furthermore, we show that ℱn is invertible and obtain the entries of the inverse of ℱn in terms of complex Fibonacci numbers

Indian genetic heritage in Southeast Asian populations.

The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, a cultural influence that is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA populations, we generated genome-wide SNP data (using the Affymetrix Human Origins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data using PCA, ADMIXTURE, and methods relying on f-statistics and on autosomal haplotypes. We found low levels of South Asian admixture in various MSEA populations for whom there is evidence of historical connections with the ancient Indian-influenced states but failed to find this genetic component in present-day hunter-gatherer groups and relatively isolated groups from the highlands of Northern Thailand. The results suggest that migration of Indian populations to MSEA may have been responsible for the spread of Indian culture in the region. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families

Benchmarking kinship estimation tools for ancient genomes using pedigree simulations

There is growing interest in identifying genetic kinship levels among ancient individuals buried in physical proximity, from graveyards to archaeological crime scenes. Ancient genome data produced using massively parallel sequencing allow such estimation, albeit with significant limitations owing to the extremely low coverage of ancient genomes, frequently ranging between 0.2x - 0.01x. Estimating the kinship coefficient reliably using such sparse data is a challenge. Both likelihood-based and non-parametric tools have been recently developed to address this question, but their efficiency has not yet been systematically and comparatively studied. Here we present work where we compared the accuracy of three most commonly employed tools, using ancient genome data produced from simulated pedigrees. We studied accuracy with respect to both kinship coefficient estimation, and also Cotterman coefficients. Our results show that genotype data that include >5,000 SNPs allow close kinship coefficients to be relatively reliably estimated, although accuracy falls dramatically beyond the 3rd degree. In addition, we confirm that pedigree relationship estimation (e.g. distinguishing between parent-child pairs vs. siblings) using Cotterman coefficients is a noteworthy problem, and will require alternative, and holistic approaches to address

Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America

Much of the American Arctic was first settled 5,000 years ago, by groups of people known as Palaeo-Eskimos. They were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yup’ik. The genetic relationship between Palaeo-Eskimos and Native American, Inuit, Yup’ik and Aleut populations remains uncertain. Here we present genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyse these data with data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Using methods based on rare-allele and haplotype sharing, as well as established techniques, we show that Palaeo-Eskimo-related ancestry is ubiquitous among people who speak Na-Dene and Eskimo–Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that Na-Dene-speaking peoples, people of the Aleutian Islands, and Yup’ik and Inuit across the Arctic region all share ancestry from a single Palaeo-Eskimo-related Siberian source