Whole-genome resequencing reveals diversity and selective signals in the Wuxue goat

Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline in the genetic diversity of livestock has occurred worldwide. This decline is pronounced in developing countries, where the management of these resources is insufficient. In the current study, we performed whole genome sequencing for 20 Wuxue (WX) and five Guizhou White (GW) goats. Additionally, we utilized the published genomes of 131 samples representing five different goat breeds from various regions in China. We investigated and compared the genetic diversity and selection signatures of WX goats. Whole genome sequencing analysis of the WX and GW populations yielded 120 425 063 SNPs, which resided primarily in intergenic and intron regions. Population genetic structure revealed that WX exhibited genetic resemblance to GW, Chengdu Brown, and Jintang Black and significant differentiation from the other goat breeds. In addition, three methods (nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity) showed moderate genetic diversity in WX goats. We used nucleotide diversity and composite likelihood ratio methods to identify within-breed signatures of positive selection in WX goats. A total of 369 genes were identified using both detection methods, including genes related to reproduction (GRID2, ZNF276, TCF25, and SPIRE2), growth (HMGA2 and GJA3), and immunity (IRF3 and SRSF3). Overall, this study explored the adaptability of WX goats, shedding light on their genetic richness and potential to thrive in challenges posed by climatic changes and diseases. Further investigations are warranted to harness these insights to enhance more efficient and sustainable goat breeding initiatives.

Weaving social networks from cultural similarities on the neolithisation process in the Western Mediterranean: Evolutionary trajectories using projectile tools

In this paper, we concentrate on the neolithisation process in Mediterranean Iberia through a diachronic view (from 8600-6800 cal. BP), focusing on social interaction as a factor in articulating new cultural ties. To do this, we apply techniques centred on similarities in material culture by applying Social Network Analysis (SNA). For the first time, we point to the geometric projectiles, taking into account their recurrence in both Mesolithic and Neolithic groups as part of their characteristic hunting equipment. We hypothesise that patterns of cultural variability would express the changing flow of information between communities according to their mobility strategies (last hunter-gatherer groups), including economic and social behaviour, and that these relationships will be restructured with the arrival of the newcomer farmers and herders and their new spatial and social arrangement. The results obtained allow us to describe a connected and homogeneous Late Mesolithic network dramatically structured by the Neolithic arrival. Since then, a heterogenous pattern emerged, involving connected periods, network ruptures, and small-world phenomena. The emergence of this characteristic could support the flow of information when the network presents a clustered structure, the last probably due to regionalisation events. These diachronic dynamics fit well with demographic and socioecological trends observed from regional literature.

Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection

West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22's West Asian origin, associated population movements, and possible linguistic impacts.

The Genetic Selection of HSPD1 and HSPE1 Reduce Inflammation of Liver and Spleen While Restraining the Growth and Development of Skeletal Muscle in Wuzhishan Pigs

Wuzhishan (WZS) pigs, which are minipigs native to Hainan Province in China, are characterized by strong resistance to extreme hot temperatures and humidity. The relationship between their immune response and growth still needs to be clarified. In this study, we used whole genome sequencing (WGS) to detect variations within 37 WZS pigs, 32 Large White (LW) pigs, and 22 Xiangxi black (XXB) pigs, and ~2.49 GB of SNPs were obtained. These data were combined with those of two other pig breeds, and it was found that most of the genes detected (354) were located within the distinct genetic regions between WZS pigs and LW pigs. The network that was constructed using these genes represented a center including 12 hub genes, five of which had structural variations (SVs) within their regulatory regions. Furthermore, RNA-seq and RT-qPCR data for 12 genes were primarily consistent in liver, spleen, and LDM tissues. Notably, the expression of HSPs (HSPD1 and HSPE1) was higher while that of most genes involved in the JAK3-STAT pathway were lower in liver tissue of WZS pigs, compared with LW pigs. This likely not only reduced inflammation-related immune response but also impaired their growth. Our findings demonstrated the role of HSPs in the connection between inflammation and growth rate, while also providing the fundamental genetic selection of the adaptability of WZS pigs.

Characteristic processes of human evolution caused the Anthropocene and may obstruct its global solutions

We propose that the global environmental crises of the Anthropocene are the outcome of a ratcheting process in long-term human evolution which has favoured groups of increased size and greater environmental exploitation. To explore this hypothesis, we review the changes in the human ecological niche. Evidence indicates the growth of the human niche has been facilitated by group-level cultural traits for environmental control. Following this logic, sustaining the biosphere under intense human use will probably require global cultural traits, including legal and technical systems. We investigate the conditions for the evolution of global cultural traits. We estimate that our species does not exhibit adequate population structure to evolve these traits. Our analysis suggests that characteristic patterns of human group-level cultural evolution created the Anthropocene and will work against global collective solutions to the environmental challenges it poses. We illustrate the implications of this theory with alternative evolutionary paths for humanity. We conclude that our species must alter longstanding patterns of cultural evolution to avoid environmental disaster and escalating between-group competition. We propose an applied research and policy programme with the goal of avoiding these outcomes. This article is part of the theme issue 'Evolution and sustainability: gathering the strands for an Anthropocene synthesis'.

Reconstructing patterns of domestication in reindeer using 3D muscle attachment areas

The use of reindeer has been a crucial element in the subsistence strategies of past Arctic and Subarctic populations. However, the spatiotemporal occurrence of systematic herding practices has been difficult to identify in the bioarchaeological record. To address this research gap, this study proposes a new virtual anthropological approach for reconstructing habitual physical activity in reindeer, relying on the protocols of the "Validated Entheses based Reconstruction of Activity" (VERA) method. Following blind analytical procedures, we focused on eight muscle attachment sites ("entheses") in 36 reindeer free ranging in the wild, 21 specimens in captivity (zoo), and eight racing reindeer (habitual runners). Importantly, our analyses accounted for the effects of variation by subspecies, sex, age, and estimated body size. Our results showed clear differences across activity groups, leading to the development of discriminant function equations with cross-validated accuracies ranging from approximately 88 to 100%. The reliability of our functions was additionally confirmed using a blind test involving six zoo individuals not included in the initial dataset. Our findings support the use of the proposed approach for identifying domestication-related activities in zooarchaeological contexts, introducing a valuable tool for locating suspected domestication hotspots and elucidating the nature of past human-reindeer interactions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12520-023-01910-5.

The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa

We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or 'unidentifiable bovid' from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments.

Parallel worlds and mixed economies: multi-proxy analysis reveals complex subsistence systems at the dawn of early farming in the northeast Baltic

The transition from foraging to farming was a key turning point in ancient socio-economies. Yet, the complexities and regional variations of this transformation are still poorly understood. This multi-proxy study provides a new understanding of the introduction and spread of early farming, challenging the notions of hierarchical economies. The most extensive biological and biomolecular dietary overview, combining zooarchaeological, archaeobotanical, dietary stable isotope and pottery lipid residue analyses is presented, to unravel the nature and extent of early farming in the 3rd millennium cal BCE in the northeast Baltic. Farming was introduced by incoming Corded Ware cultural groups (CWC), but some dietary segregation existed within these communities, with some having more access to domesticates, others incorporating more wild resources into their diet. The CWC groups coexisted in parallel with local hunter-fisher-gatherers (HFG) without any indication of the adoption of domesticates. There was no transition from foraging to farming in the 3rd millennium cal BCE in the NE Baltic. Instead, we see a complex system of parallel worlds with local HFGs continuing forager lifeways, and incoming farmers practising mixed economies, with the continuation of these subsistence strategies for at least a millennium after the first encounter with domesticated animals.

Isotopic and proteomic evidence for communal stability at Pre-Pottery Neolithic Jericho in the Southern Levant

As one of the key, long-term occupied sites in the Southern Levant, Jericho was one of the most important early Neolithic centres to witness social and economic changes associated with the domestication of plants and animals. This study applies strontium (87Sr/86Sr), oxygen (δ18O) and carbon (δ13C) isotope analyses to the enamel of 52 human teeth from Pre-Pottery Neolithic (PPN) layers of Jericho to directly study human diet and mobility and investigate the degree of consolidation and the flexibility of social organization of Jericho society in the PPN period. The results indicate only two non-local individuals out of the 44 sampled inhabitants identified by strontium isotope analysis and are consistent with the presence of a largely sedentary community at PPN Jericho with no evidence for large-scale migration. We also construct strontium spatial baselines (87Sr/86Sr map) with local 87Sr/86Sr signatures for the sites across the Southern Levant based on systematic compilation and analysis of available data. In addition, we apply proteomic analysis of sex-specific amelogenin peptides in tooth enamel for sex estimation of the sampled individuals (n = 44), the results of which showed a sex-biased ratio (more male than female detected in this sample pool) in Jericho society during the PPN period, which may be due to the limited sample size or selective ritual practices like particular burial zones used for specific groups. We also pretreated a batch of human bone samples recovered from PPNB Jericho for stable carbon and nitrogen isotope analyses for dietary investigations. However, the extracted collagen showed poor preservation and no valid δ13C or δ15N data were obtained.

Harvesting cereals at Tappeh Sang-e Chakhmaq and the introduction of farming in Northeastern Iran during the Neolithic

Tappeh Sang-e Chakhmaq is the only Neolithic site in Northeastern Iran, characterised by aceramic and ceramic levels corresponding to an occupation of 1500 years from the eighth to the end of the sixth millennium BCE. The Western and Eastern Mounds represent the oldest and longest occupation among the sites identified East of the Zagros, providing a unique context to explore the origin and spread of farming outside the core area of the Eastern Fertile Crescent. We present data about the first harvesting activities in the Northeastern Iranian Central Plateau by applying usewear and microtexture analysis through confocal microscopy on sickle gloss blades. Our results indicate a community of pioneer farmers who settled down in the area carrying with them both domestic cereals as well as advanced techniques of cereal cultivation. We demonstrate that most of the tools were used for harvesting cereals in a fully ripened state collected near the ground, indicating a well-established cereal cultivation strategy. The use of straight shafts with parallel inserts in Tappeh Sang-e Chakhmaq, as known in some sites in the Zagros, suggests the dispersal of farming practices and technologies from the Eastern Fertile Crescent north-eastward across Iran. We observe an evolution in the degree of ripeness of harvested cereals along the first four levels of occupation of the Western Mound, where semi-ripe harvesting is relatively important, suggesting that domestic cereals to be harvested before full maturity were introduced into the village. From the topmost of the Western Mound and along the occupation of the Eastern Mound, ripe harvesting is dominant, showing a well-established cultivation strategy of fully mature cereal. This shift could indicate an in-situ evolution towards a better-established agricultural technology, including harvesting riper crops, that would have resulted in higher yields, as cereals were collected when the grain was fully formed.

Earth Systems to Anthropocene Systems: An Evolutionary, System-of-Systems, Convergence Paradigm for Interdependent Societal Challenges

Humans have made profound changes to the Earth. The resulting societal challenges of the Anthropocene (e.g., climate change and impacts, renewable energy, adaptive infrastructure, disasters, pandemics, food insecurity, and biodiversity loss) are complex and systemic, with causes, interactions, and consequences that cascade across a globally connected system of systems. In this Critical Review, we turn to our "origin story" for insight, briefly tracing the formation of the Universe and the Earth, the emergence of life, the evolution of multicellular organisms, mammals, primates, and humans, as well as the more recent societal transitions involving agriculture, urbanization, industrialization, and computerization. Focusing on the evolution of the Earth, genetic evolution, the evolution of the brain, and cultural evolution, which includes technological evolution, we identify a nested evolutionary sequence of geophysical, biophysical, sociocultural, and sociotechnical systems, emphasizing the causal mechanisms that first formed, and then transformed, Earth systems into Anthropocene systems. Describing how the Anthropocene systems coevolved, and briefly illustrating how the ensuing societal challenges became tightly integrated across multiple spatial, temporal, and organizational scales, we conclude by proposing an evolutionary, system-of-systems, convergence paradigm for the entire family of interdependent societal challenges of the Anthropocene.

Coupled and decoupled legumes and cereals in prehistoric northern and southern China

Legumes and cereals, which provide different nutrients, are cultivated as coupled crops in most centers of plant domestication worldwide. However, as the only legume domesticated in China, the spatio-temporal distribution of soybeans and its status in the millet- and rice-based agricultural system of the Neolithic and Bronze Ages remains elusive. Here, archaeobotanical evidence of soybeans (n=254), millet (n=462), rice (n=482), and zooarchaeological evidence of fish (n=138) were synthesized to elucidate the phenomenon of coupled or decoupled cereals and legumes in prehistoric China. During the Neolithic and Bronze Ages, soybeans was mostly confined to northern China and rarely found in southern China, serving as a companion to millet. In contrast, fish remains have been widely found in southern China, indicating a continuous reliance on fish as a staple food besides rice. Thus, an antipodal pattern of millet-soybeans and rice-fish agricultural systems may have been established in northern and southern China since the late Yangshao period (6000-5000 cal BP) respectively. These two agricultural systems were not only complementary in terms of diet, but they also exhibited positive interactions and feedback in the coculture system. Consequently, these two systems enabled the sustainable intensification of agriculture and served as the basis for the emergence of complex societies and early states in the Yellow and Yangtze Rivers.

Epipalaeolithic animal tending to Neolithic herding at Abu Hureyra, Syria (12,800–7,800 calBP): Deciphering dung spherulites

Excavations at Abu Hureyra, Syria, during the 1970s exposed a long sequence of occupation spanning the transition from hunting-and-gathering to agriculture. Dung spherulites preserved within curated flotation samples from Epipalaeolithic (ca. 13,300–11,400 calBP) and Neolithic (ca. 10,600–7,800 calBP) occupations are examined here alongside archaeological, archaeobotanical, and zooarchaeological data to consider animal management, fuel selection, and various uses of dung. Spherulites were present throughout the entire sequence in varying concentrations. Using a new method to quantify spherulites, exclusion criteria were developed to eliminate samples possibly contaminated with modern dung, strengthening observations of ancient human behavior. Darkened spherulites within an Epipalaeolithic 1B firepit (12,800–12,300 calBP) indicate burning between 500–700°C, documenting early use of dung fuel by hunter-gatherers as a supplement to wood, coeval with a dramatic shift to rectilinear architecture, increasing proportions of wild sheep and aurochsen, reduced emphasis on small game, and elevated dung concentrations immediately outside the 1B dwelling. Combined, these observations suggest that small numbers of live animals (possibly wild sheep) were tended on-site by Epipalaeolithic hunter-gatherers to supplement gazelle hunting, raising the question of whether early experiments in animal management emerged contemporaneously with, or pre-date, cultivation. Dung was used to prepare plaster floors during the Neolithic and continued to be burned as a supplemental fuel, indicating that spherulites were deposited via multiple human- and animal-related pathways. This has important implications for interpretations of archaeobotanical assemblages across the region. Spherulite concentrations dropped abruptly during Neolithic 2B (9,300–8,000 calBP) and 2C (8,000–7,800 calBP), when sheep/goat herding surpassed gazelle hunting, possibly corresponding with movement of animals away from the site as herd sizes increased. As hunter-gatherers at Abu Hureyra began interacting with wild taxa in different ways, they set in motion a remarkable transformation in the ways people interacted with animals, plants, and their environment.

Towards a science of archaeoecology

We propose defining a field of research called 'archaeoecology' that examines the past ~60 000 years of interactions between humans and ecosystems to better understand the human place within them. Archaeoecology explicitly integrates questions, data, and approaches from archaeology and ecology, and coalesces recent and future studies that demonstrate the usefulness of integrating archaeological, environmental, and ecological data for understanding the past. Defining a subfield of archaeoecology, much as the related fields of environmental archaeology and palaeoecology have emerged as distinct areas of research, provides a clear intellectual context for helping us to understand the trajectory of human-ecosystem interactions in the past, during the present, and into the future.

Historical Westward Migration Phases of Ovis aries Inferred from the Population Structure and the Phylogeography of Occidental Mediterranean Native Sheep Breeds

In this study, the genetic relationship and the population structure of western Mediterranean basin native sheep breeds are investigated, analyzing Maghrebian, Central Italian, and Venetian sheep with a highly informative microsatellite markers panel. The phylogeographical analysis, between breeds’ differentiation level (Wright’s fixation index), gene flow, ancestral relatedness measured by molecular coancestry, genetic distances, divergence times estimates and structure analyses, were revealed based on the assessment of 975 genotyped animals. The results unveiled the past introduction and migration history of sheep in the occidental Mediterranean basin since the early Neolithic. Our findings provided a scenario of three westward sheep migration phases fitting properly to the westward Neolithic expansion argued by zooarcheological, historical and human genetic studies.

Evolution and origin of bread wheat

Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated free-threshing tetraploid progenitor, genome BBAA, and Aegilops tauschii, the diploid donor of the D subgenome. Very soon after its formation, it spread globally from its cradle in the fertile crescent into new habitats and climates, to become a staple food of humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty through the acquisition of new traits, new intergenomic interactions, and buffering of mutations, and by the attractiveness of bread wheat's large, tasty, and nutritious grain with high baking quality. New genome sequences suggest that the elusive donor of the B subgenome is a distinct (unknown or extinct) species rather than a mosaic genome. We discuss the origin of the diploid and tetraploid progenitors of bread wheat and the conflicting genetic and archaeological evidence on where it was formed and which species was its free-threshing tetraploid progenitor. Wheat experienced many environmental changes throughout its evolution, therefore, while it might adapt to current climatic changes, efforts are needed to better use and conserve the vast gene pool of wheat biodiversity on which our food security depends.

When Scent Becomes a Weapon—Plant Essential Oils as Potent Bioinsecticides

Crop protection still mostly relies on synthetic pesticides for crop pest control. However, the rationale for their continued use is shaded by the revealed adverse effects, such as relatively long environmental persistence that leads to water and soil contamination and retention of residues in food that brings high risks to human and animal health. As part of integrated pest management, biopesticides may provide crop protection, being eco-friendly and safe for humans and non-target organisms. Essential oils, complex mixtures of low-molecular-weight, highly volatile compounds, have been highlighted as major candidates for plant-derived bioinsecticides that are up to the sustainable biological standard. In this review, we screened the insecticidal activity of essential oils or their purified compounds, with focus given to their modes of action, along with the analyzed advantages and problems associated with their wider usage as plant-derived insecticides in agriculture.

Whole-genome resequencing of the wheat A subgenome progenitor Triticum urartu provides insights into its demographic history and geographic adaptation

Triticum urartu is the progenitor of the A subgenome in tetraploid and hexaploid wheat. Uncovering the landscape of genetic variations in T. urartu will help us understand the evolutionary and polyploid characteristics of wheat. Here, we investigated the population genomics of T. urartu by genome-wide sequencing of 59 representative accessions collected around the world. A total of 42.2 million high-quality single-nucleotide polymorphisms and 3 million insertions and deletions were obtained by mapping reads to the reference genome. The ancient T. urartu population experienced a significant reduction in effective population size (Ne) from ∼3 000 000 to ∼140 000 and subsequently split into eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations during the Younger Dryas period. A map of allelic drift paths displayed splits and mixtures between different geographic groups, and a strong genetic drift towards hexaploid wheat was also observed, indicating that the direct donor of the A subgenome originated from northwestern Syria. Genetic changes were revealed between the eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations in genes orthologous to those regulating plant development and stress responses. A genome-wide association study identified two single-nucleotide polymorphisms in the exonic regions of the SEMI-DWARF 37 ortholog that corresponded to the different T. urartu ecotype groups. Our study provides novel insights into the origin and genetic legacy of the A subgenome in polyploid wheat and contributes a gene repertoire for genomics-enabled improvements in wheat breeding.

Population Genetics and Signatures of Selection in Early Neolithic European Farmers

Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA research in the last 10 years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation. Here, we present high quality genome-wide data from the Linear Pottery Culture site Derenburg-Meerenstieg II (DER) (N = 32 individuals) in Central Germany. Population genetic analyses show that the DER individuals carried predominantly Anatolian Neolithic-like ancestry and a very limited degree of local hunter-gatherer admixture, similar to other early European farmers. Increasing the Linear Pottery culture cohort size to ∼100 individuals allowed us to perform various frequency- and haplotype-based analyses to investigate signatures of selection associated with changes following the adoption of the Neolithic lifestyle. In addition, we developed a new method called Admixture-informed Maximum-likelihood Estimation for Selection Scans that allowed us test for selection signatures in an admixture-aware fashion. Focusing on the intersection of results from these selection scans, we identified various loci associated with immune function (JAK1, HLA-DQB1) and metabolism (LMF1, LEPR, SORBS1), as well as skin color (SLC24A5, CD82) and folate synthesis (MTHFR, NBPF3). Our findings shed light on the evolutionary pressures, such as infectious disease and changing diet, that were faced by the early farmers of Western Eurasia.

The Feeding Landscape: Bird and Human Use of Food Resources across a Biocultural Landscape of the Colombian Andes

Agriculture impacts both human welfare and biodiversity at the same time. Still, social and ecological assessments have commonly analyzed the relevance of agroecosystems separately. We evaluated the human and avian feeding use of the biocultural landscape in Jardín, Colombia, using a socioecological approach. Together with farmers, we identified the main socioecological units of the landscape (i.e., fincas, grazing lands, town, forests) and determined the use of each unit in terms of food foraging from forests, crop cultivation, cattle grazing, food commercialization, and food industrialization. We compared the richness of the food resources produced among finca sections (i.e., gardens, coffee–banana plantations, grazing lands). Then, we surveyed avian behavior to contrast the richness of bird species, feeding use and intensity, and food types consumed by birds among the units. Fincas were shown to play a pivotal role in feeding both humans and birds. Gardens provide food for people as well as nectarivore and frugivore birds. Coffee–banana plantations are economically relevant, but their food provision is limited and could be enhanced by increasing the diversity of the food crops within them. The town supports commerce and granivorous birds, whereas grazing lands have limited feeding importance. Forests are used by birds to capture invertebrates but do not supply much food for the people. Our approach fosters the identification of key socioecological units, demonstrating that studying both humans and wildlife enhances the comprehension of biocultural landscapes.

An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers

Human culture, biology, and health were shaped dramatically by the onset of agriculture ∼12,000 y B.P. This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared “predicted” genetic contributions to height from paleogenomic data and “achieved” adult osteological height estimated from long bone measurements for 167 individuals across Europe spanning the Upper Paleolithic to Iron Age (∼38,000 to 2,400 B.P.). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of −3.82 cm relative to individuals from the Upper Paleolithic and Mesolithic (P = 0.040) and −2.21 cm shorter relative to post-Neolithic individuals (P = 0.068), with osteological vs. expected stature steadily increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when we additionally accounted for genome-wide genetic ancestry variation: for example, with Neolithic individuals −2.82 cm shorter than expected on average relative to pre-Neolithic individuals (P = 0.120). We also incorporated observations of paleopathological indicators of nonspecific stress that can persist from childhood to adulthood in skeletal remains into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.

Domestication reprogrammed the budding yeast life cycle

Domestication of plants and animals is the foundation for feeding the world human population but can profoundly alter the biology of the domesticated species. Here we investigated the effect of domestication on one of our prime model organisms, the yeast Saccharomyces cerevisiae, at a species-wide level. We tracked the capacity for sexual and asexual reproduction and the chronological life span across a global collection of 1,011 genome-sequenced yeast isolates and found a remarkable dichotomy between domesticated and wild strains. Domestication had systematically enhanced fermentative and reduced respiratory asexual growth, altered the tolerance to many stresses and abolished or impaired the sexual life cycle. The chronological life span remained largely unaffected by domestication and was instead dictated by clade-specific evolution. We traced the genetic origins of the yeast domestication syndrome using genome-wide association analysis and genetic engineering and disclosed causative effects of aneuploidy, gene presence/absence variations, copy number variations and single-nucleotide polymorphisms. Overall, we propose domestication to be the most dramatic event in budding yeast evolution, raising questions about how much domestication has distorted our understanding of the natural biology of this key model species.

Broad maternal geographic origin of domestic sheep in Anatolia and the Zagros

We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome-b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large-scale process that captured diverse maternal lineages (haplogroups).

Coproduction of Food, Cultural Heritage and Biodiversity by Livestock Grazing in Swedish Semi-natural Grasslands

Livestock has been a backbone of people's livelihood as long as agriculture has existed in Scandinavia, c. 6,000 years. In the early Iron Age, c. 2,000 years ago, a land management system began to form, composed of infields (enclosed hay-meadows and crop fields) and outlying land used for livestock grazing. Despite many later innovations and societal changes affecting agricultural technology and practices, this way of organizing land use was a template for how landscapes were managed and structured until the modernization of agriculture and forestry during the last centuries. There are legacies of this historic land-use, mainly as “semi-natural grasslands” managed by livestock grazing (open or semi-open; long continuity of management; not much influenced by commercial fertilizers, plowing etc.). These semi-natural grasslands harbor an exceptional small-scale biodiversity, particularly plants and insects. Landscapes with semi-natural grasslands represent cultural heritage, and are appreciated for their beauty. The total area of semi-natural grasslands has declined considerably during the past 100 years, and the current trend suggest that further declines are expected. A large fraction of threatened biodiversity in Sweden thrives in these grasslands. Livestock grazing in semi-natural grasslands makes an important contribution to food production, and there is an increasing interest in consumption of products, mainly meat, from these grasslands. This implies that there is a positive feedback between food production, maintenance of biological diversity, and cultural heritage. This paper gives an overview of semi-natural grasslands, focusing on Sweden, from a historic, cultural and ecological perspective, and aims at discussing challenges and prospects for developing and maintaining positive associations between producing food, biodiversity, and cultural heritage, in the future.

Estimations of Fe0/−1–N2 interaction energies of iron(0)-dicarbene and its reduced analogue by EDA-NOCV analyses: crucial steps in dinitrogen activation under mild conditions

Metal complexes containing low valence iron atoms are often experimentally observed to bind with the dinitrogen (N₂) molecule. This phenomenon has attracted the attention of industrialists, chemists and bio-chemists since these N₂-bonded iron complexes can produce ammonia under suitable chemical or electrochemical conditions. The higher binding affinity of the Fe-atom towards N₂ is a bit ‘mysterious’ compared to that of the other first row transition metal atoms. Fine powders of α-Fe⁰ are even part of industrial ammonia production (Haber–Bosch process) which operates at high temperature and high pressure. Herein, we report the EDA-NOCV analyses of the previously reported dinitrogen-bonded neutral molecular complex (cAAC^R)₂Fe⁰–N₂ (1) and mono-anionic complex (cAAC^R)₂Fe⁻¹–N₂ (2) to give deeper insight of the Fe–N₂ interacting orbitals and corresponding pairwise intrinsic interaction energies (cAAC^R = cyclic alkyl(amino) carbene; R = Dipp or Me). The Fe⁰ atom of 1 prefers to accept electron densities from N₂via σ-donation while the comparatively electron rich Fe⁻¹ centre of 2 donates electron densities to N₂via π-backdonation. However, major stability due to the formation of an Fe–N₂ bond arises due to Fe → N₂ π-backdonation in both 1 and 2. The cAAC^R ligands act as a charge reservoir around the Fe centre. The electron densities drift away from cAAC ligands during the binding of N₂ molecules mostly via π-backdonation. EDA-NOCV analysis suggests that N₂ is a stronger π-acceptor rather than a σ-donor.

The stable Fe–N₂ bond of stable complex should have a sufficiently high interaction energy.

Ancient DNA reveals the maternal genetic history of East Asian domestic pigs

Zoo-archaeological and genetic evidence suggest that pigs were domesticated independently in Central China and Eastern Anatolia along with the development of agricultural communities and civilizations. However, the genetic history of domestic pigs, especially in China, has not been fully explored. In this study, we generated 42 complete mitochondrial DNA sequences from ∼7500- to 2750-year-old individuals from the Yellow River basin. Our results show that the maternal genetic continuity of East Asian domestic pigs dates back to at least the Early to Middle Neolithic. In contrast, the Near Eastern ancestry in European domestic pigs saw a near-complete genomic replacement by the European wild boar. The majority of East Asian domestic pigs share close haplotypes, and the most recent common ancestor of most branches dates back to less than 20,000 years before present, inferred using new substitution rates of whole mitogenomes or combined protein-coding regions. Two major population expansion events of East Asian domestic pigs coincided with changes in climate, widespread adoption of introduced crops, and the development of agrarian societies. These findings add to our understanding of the maternal genetic composition and help to complete the picture of domestic pig evolutionary history in East Asia.

The role of soil in the contribution of food and feed

Soils play a critical role in the production of food and feed for a growing global population. Here, we review global patterns in soil characteristics, agricultural production and the fate of embedded soil nutrients. Nitrogen- and organic-rich soils supported the highest crop yields, yet the efficiency of nutrient utilization was concentrated in regions with lower crop productivity and lower rates of chemical fertilizer inputs. Globally, soil resources were concentrated in animal feed, resulting in large inefficiencies in nutrient utilization and losses from the food system. Intercontinental transport of soil-derived nutrients displaced millions of tonnes of nitrogen and phosphorus annually, much of which was ultimately concentrated in urban waste streams. Approximately 40% of the global agricultural land area was in small farms providing over 50% of the world's food and feed needs but yield gaps and economic constraints limit the ability to intensify production on these lands. To better use and protect soil resources in the global food system, policies and actions should encourage shifts to more nutrient-efficient diets, strategic intensification and technological improvement, restoration and maintenance of soil fertility and stability, and enhanced resilience in the face of global change. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

New insights into the spatial organization, stratigraphy and human occupations of the Aceramic Neolithic at Ganj Dareh, Iran

The Aceramic Neolithic site of Ganj Dareh (Kermanshah, Iran) is arguably one of the most significant sites for enhancing our understanding of goat domestication and the onset of sedentism. Despite its central importance, it has proven difficult to obtain contextually reliable data from it and integrate the site in regional syntheses because it was never published in full after excavations ceased in 1974. This paper presents the Ganj Dareh archive at Université de Montréal and shows how the documentation and artifacts it comprises still offer a great deal of useful information about the site. In particular, we 1) present the first stratigraphic profile for the site, which reveals a more complex depositional history than Smith's five-level sequence; 2) reveal the presence of two possible pre-agricultural levels (H-01 and P-01); 3) explore the spatial organization of different levels; 4) explain possible discrepancies in the radiocarbon dates from the site; 5) show some differences in lithic technological organization in levels H-01 and P-01 suggestive of higher degrees of residential mobility than subsequent phases of occupation at the site; and 6) reanalyze the burial data to broaden our understanding of Aceramic Neolithic mortuary practices in the Zagros. These data help refine our understanding of Ganj Dareh's depositional and occupational history and recenter it as a key site to improve our understanding the Neolithization process in the Middle East.

Let's go fishing: A quantitative analysis of subsistence choices with a special focus on mixed economies among small-scale societies

The transition to agriculture is regarded as a major turning point in human history. In the present contribution we propose to look at it through the lens of ethnographic data by means of a machine learning approach. More specifically, we analyse both the subsistence economies and the socioecological context of 1290 societies documented in the Ethnographic Atlas with a threefold purpose: (i) to better understand the variability and success of human economic choices; (ii) to assess the role of environmental settings in the configuration of the different subsistence economies; and (iii) to examine the relevance of fishing in the development of viable alternatives to cultivation. All data were extracted from the publicly available cross-cultural database D-PLACE. Our results suggest that not all subsistence combinations are viable, existing just a subset of successful economic choices that appear recurrently in specific ecological systems. The subsistence economies identified are classified as either primary or mixed economies in accordance with an information-entropy-based quantitative criterion that determines their degree of diversification. Remarkably, according to our results, mixed economies are not a marginal choice, as they constitute 25% of the cases in our data sample. In addition, fishing seems to be a key element in the configuration of mixed economies, as it is present across all of them.

Localized management of non-indigenous animal domesticates in Northwestern China during the Bronze Age

The movements of ancient crop and animal domesticates across prehistoric Eurasia are well-documented in the archaeological record. What is less well understood are the precise mechanisms that farmers and herders employed to incorporate newly introduced domesticates into their long-standing husbandry and culinary traditions. This paper presents stable isotope values (δ¹³C, δ¹⁵N) of humans, animals, and a small number of plants from the Hexi Corridor, a key region that facilitated the movement of ancient crops between Central and East Asia. The data show that the role of animal products in human diets was more significant than previously thought. In addition, the diets of domestic herbivores (sheep/goat, and cattle) suggest that these two groups of domesticates were managed in distinct ways in the two main ecozones of the Hexi Corridor: the drier Northwestern region and the wetter Southeastern region. Whereas sheep and goat diets are consistent with consumption of naturally available vegetation, cattle exhibit a higher input of C₄ plants in places where these plants contributed little to the natural vegetation. This suggests that cattle consumed diets that were more influenced by human provisioning, and may therefore have been reared closer to the human settlements, than sheep and goats.

Foragers and Their Tools: Risk, Technology and Complexity

The subsistence technology of forager communities has varied greatly over space and time. This paper (i) reviews briefly the main causal factors the literature identifies as responsible for this variation; (ii) analyzes in some detail the most prominent idea in the literature on spatial variation:Complex technology is an adaptive response to elevated risks of subsistence failure; (iii) it argues that the alleged empirical support for this hypothesis depends on dubious proxies of risk; (iv) it argues that it fails to explain the subsistence technologies of desert foragers, who generally live with simple technologies in high-risk environments; (v) it offers an alternative analysis, based on the reduced opportunity costs of complex technologies in highly seasonal environments, on the high value of typical forager targets in those environments and their relatively predictable location in space and time; and (v) the paper concludes with a conjecture about the role of environmental variation in toolkit change over deep time.

Large-scale genomic analysis reveals the genetic cost of chicken domestication

BACKGROUND

Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication.

RESULTS

We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes.

CONCLUSION

This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.

Herded and hunted goat genomes from the dawn of domestication in the Zagros Mountains

The Aceramic Neolithic (∼9600 to 7000 cal BC) period in the Zagros Mountains, western Iran, provides some of the earliest archaeological evidence of goat (Capra hircus) management and husbandry by circa 8200 cal BC, with detectable morphological change appearing ∼1,000 y later. To examine the genomic imprint of initial management and its implications for the goat domestication process, we analyzed 14 novel nuclear genomes (mean coverage 1.13X) and 32 mitochondrial (mtDNA) genomes (mean coverage 143X) from two such sites, Ganj Dareh and Tepe Abdul Hosein. These genomes show two distinct clusters: those with domestic affinity and a minority group with stronger wild affinity, indicating that managed goats were genetically distinct from wild goats at this early horizon. This genetic duality, the presence of long runs of homozygosity, shared ancestry with later Neolithic populations, a sex bias in archaeozoological remains, and demographic profiles from across all layers of Ganj Dareh support management of genetically domestic goat by circa 8200 cal BC, and represent the oldest to-this-date reported livestock genomes. In these sites a combination of high autosomal and mtDNA diversity, contrasting limited Y chromosomal lineage diversity, an absence of reported selection signatures for pigmentation, and the wild morphology of bone remains illustrates domestication as an extended process lacking a strong initial bottleneck, beginning with spatial control, demographic manipulation via biased male culling, captive breeding, and subsequently phenotypic and genomic selection.

Multi-isotope evidence of population aggregation in the Natufian and scant migration during the early Neolithic of the Southern Levant

Human mobility and migration are thought to have played essential roles in the consolidation and expansion of sedentary villages, long-distance exchanges and transmission of ideas and practices during the Neolithic transition of the Near East. Few isotopic studies of human remains dating to this early complex transition offer direct evidence of mobility and migration. The aim of this study is to identify first-generation non-local individuals from Natufian to Pre-Pottery Neolithic C periods to explore the scope of human mobility and migration during the Neolithic transition in the Southern Levant, an area that is central to this historical process. The study adopted a multi-approach resorting to strontium (⁸⁷Sr/⁸⁶Sr), oxygen (δ18O_VSMOW) and carbon (δ¹³C) isotope ratio analyses of tooth enamel of 67 human individuals from five sites in Jordan, Syria, and Israel. The isotope ratios point both to a significant level of human migration and/or mobility in the Final Natufian which is compatible with early sedentarism and seasonal mobility and with population aggregation in early sedentary hamlets. The current findings, in turn, offer evidence that most individuals dating to the Pre-Pottery Neolithic were local to their respective settlements despite certain evidence of non-locals. Interestingly, isotopic data suggest that two possible non-local individuals benefitted from particular burial practices. The results underscore a decrease in human mobility and migration as farming became increasingly dominant among the subsistence strategies throughout the Neolithic transition of the Southern Levant.

The genomes of ancient date palms germinated from 2,000 y old seeds

Resurrection genomics is an alternative to ancient DNA approaches in studying the genetics and evolution of past and possibly extinct populations. By reviving biological material such as germinating ancient seeds from archaeological and paleontological sites, or historical collections, one can study genomes of lost populations. We applied this approach by sequencing the genomes of seven Judean date palms (Phoenix dactylifera) that were germinated from ∼2,000 y old seeds recovered in the Southern Levant. Using this genomic data, we were able to document that introgressive hybridization of the wild Cretan palm Phoenix theophrasti into date palms had occurred in the Eastern Mediterranean by ∼2,200 y ago and examine the evolution of date palm populations in this pivotal region two millennia ago.

Seven date palm seeds (Phoenix dactylifera L.), radiocarbon dated from the fourth century BCE to the second century CE, were recovered from archaeological sites in the Southern Levant and germinated to yield viable plants. We conducted whole-genome sequencing of these germinated ancient samples and used single-nucleotide polymorphism data to examine the genetics of these previously extinct Judean date palms. We find that the oldest seeds from the fourth to first century BCE are related to modern West Asian date varieties, but later material from the second century BCE to second century CE showed increasing genetic affinities to present-day North African date palms. Population genomic analysis reveals that by ∼2,400 to 2,000 y ago, the P. dactylifera gene pool in the Eastern Mediterranean already contained introgressed segments from the Cretan palm Phoenix theophrasti, a crucial genetic feature of the modern North African date palm populations. The P. theophrasti introgression fraction content is generally higher in the later samples, while introgression tracts are longer in these ancient germinated date palms compared to modern North African varieties. These results provide insights into crop evolution arising from an analysis of plants originating from ancient germinated seeds and demonstrate what can be accomplished with the application of a resurrection genomics approach.

Stable isotope analysis of human bone from Ganj Dareh, Iran, ca. 10,100 calBP

We report here on stable carbon, nitrogen, and sulfur isotope values from bone collagen of human (n = 20) and faunal (n = 11) remains from the Early Neolithic site of Ganj Dareh, Iran, dating to ca. 10,100 cal. BP. Our focus explores how isotope values of human bone vary by age and sex, and evaluates dietary practices at this site. It also provides a baseline for future studies of subsistence in the early Holocene Central Zagros Mountains, from the site with the first evidence for human ovicaprid management in the Near East. Human remains include individuals of all age groups for dietary reconstruction, as well two Ottoman intrusive burials for temporal and cultural comparison. All analyzed individuals exhibited δ13C and δ15N values consistent with a diet based heavily on C3 terrestrial sources. There is no statistically significant difference between the isotopic compositions of the two sexes, though males appear to show larger variations compared to females. Interesting patterns in the isotopic compositions of the subadults suggested weaning children may be fed with supplements with distinctive δ13C values. Significant difference in sulfur isotope values between humans and fauna could be the earliest evidence of transhumance and could identify one older adult male as a possible transhumant shepherd. Both Ottoman individuals had distinctively different δ13C, δ15N, and δ34S values compared to the Neolithic individuals. This is the first large scale analysis of human stable isotopes from the eastern end of the early Holocene Fertile Crescent. It provides a baseline for future intersite exploration of stable isotopes and insight into the lifeways, health, and processes of neolithisation associated with the origins of goat domestication at Ganj Dareh and the surrounding Central Zagros.

The prehistoric roots of Chinese cuisines: Mapping staple food systems of China, 6000 BC-220 AD

We conducted a meta-analysis of published carbon and nitrogen isotope data from archaeological human skeletal remains (n = 2448) from 128 sites cross China in order to investigate broad spatial and temporal patterns in the formation of staple cuisines. Between 6000-5000 cal BC we found evidence for an already distinct north versus south divide in the use of main crop staples (namely millet vs. a broad spectrum of C3 plant based diet including rice) that became more pronounced between 5000-2000 cal BC. We infer that this pattern can be understood as a difference in the spectrum of subsistence activities employed in the Loess Plateau and the Yangtze-Huai regions, which can be partly explained by differences in environmental conditions. We argue that regional differentiation in dietary tradition are not driven by differences in the conventional "stages" of shifting modes of subsistence (hunting-foraging-pastoralism-farming), but rather by myriad subsistence choices that combined and discarded modes in a number of innovative ways over thousands of years. The introduction of wheat and barley from southwestern Asia after 2000 cal BC resulted in the development of an additional east to west gradient in the degree of incorporation of the different staple products into human diets. Wheat and barley were rapidly adopted as staple foods in the Continental Interior contra the very gradual pace of adoption of these western crops in the Loess Plateau. While environmental and social factors likely contributed to their slow adoption, we explored local cooking practice as a third explanation; wheat and barley may have been more readily folded into grinding-and-baking cooking traditions than into steaming-and-boiling traditions. Changes in these culinary practices may have begun in the female sector of society.

Living off the land: Terrestrial-based diet and dairying in the farming communities of the Neolithic Balkans

The application of biomolecular techniques to archaeological materials from the Balkans is providing valuable new information on the prehistory of the region. This is especially relevant for the study of the neolithisation process in SE Europe, which gradually affected the rest of the continent. Here, to answer questions regarding diet and subsistence practices in early farming societies in the central Balkans, we combine organic residue analyses of archaeological pottery, taxonomic and isotopic study of domestic animal remains and biomolecular analyses of human dental calculus. The results from the analyses of the lipid residues from pottery suggest that milk was processed in ceramic vessels. Dairy products were shown to be part of the subsistence strategies of the earliest Neolithic communities in the region but were of varying importance in different areas of the Balkan. Conversely, milk proteins were not detected within the dental calculus. The molecular and isotopic identification of meat, dairy, plants and beeswax in the pottery lipids also provided insights into the diversity of diet in these early Neolithic communities, mainly based on terrestrial resources. We also present the first compound-specific radiocarbon dates for the region, obtained directly from absorbed organic residues extracted from pottery, identified as dairy lipids.

Reconstructing breastfeeding and weaning practices in the Bronze Age Near East using stable nitrogen isotopes

Objectives

Breastfeeding and childhood diet have significant impact on morbidity and mortality within a population, and in the ancient Near East, it is possible to compare bioarchaeological reconstruction of breastfeeding and weaning practices with the scant textual evidence.

Materials and Methods

Nitrogen stable isotopes (δ¹⁵N) are analyzed here for dietary reconstruction in skeletal collections from five Bronze Age (ca. 2,800–1,200 BCE) sites in modern Lebanon and Syria. We employed Bayesian computational modeling on cross‐sectional stable isotope data of collagen samples (n = 176) mainly from previous studies to test whether the bioarchaeological evidence aligns with the textual evidence of breastfeeding and weaning practices in the region, as well as compare the estimated weaning times to the global findings using the WARN (weaning age reconstruction with nitrogen isotope analysis) Bayesian model.

Results

Though the Near East sites in this study had different ecological settings and economic strategies, we found that weaning was introduced to the five sites at 0.5 ± 0.2 years of age and complete weaning occurred around 2.6 ± 0.3 years of age on using the WARN computational model. These weaning processes are within the time suggested by historical texts, though average estimated weaning age on the Mediterranean coast is later than inland sites.

Discussion

Compared globally, these Near Eastern populations initiated the weaning process earlier but completed weaning within the global average. Early initial weaning may have created short spacing between pregnancies and a high impact on demographic growth within these agricultural populations, with some variation in subsistence practices accounting for the inland/coastal discrepancies.

Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.

Bioarchaeology of Neolithic Çatalhöyük reveals fundamental transitions in health, mobility, and lifestyle in early farmers

The transition from a human diet based exclusively on wild plants and animals to one involving dependence on domesticated plants and animals beginning 10,000 to 11,000 y ago in Southwest Asia set into motion a series of profound health, lifestyle, social, and economic changes affecting human populations throughout most of the world. However, the social, cultural, behavioral, and other factors surrounding health and lifestyle associated with the foraging-to-farming transition are vague, owing to an incomplete or poorly understood contextual archaeological record of living conditions. Bioarchaeological investigation of the extraordinary record of human remains and their context from Neolithic Çatalhöyük (7100-5950 cal BCE), a massive archaeological site in south-central Anatolia (Turkey), provides important perspectives on population dynamics, health outcomes, behavioral adaptations, interpersonal conflict, and a record of community resilience over the life of this single early farming settlement having the attributes of a protocity. Study of Çatalhöyük human biology reveals increasing costs to members of the settlement, including elevated exposure to disease and labor demands in response to community dependence on and production of domesticated plant carbohydrates, growing population size and density fueled by elevated fertility, and increasing stresses due to heightened workload and greater mobility required for caprine herding and other resource acquisition activities over the nearly 12 centuries of settlement occupation. These changes in life conditions foreshadow developments that would take place worldwide over the millennia following the abandonment of Neolithic Çatalhöyük, including health challenges, adaptive patterns, physical activity, and emerging social behaviors involving interpersonal violence.

Cereal processing at Early Neolithic Göbekli Tepe, southeastern Turkey

We analyze the processing of cereals and its role at Early Neolithic Göbekli Tepe, southeastern Anatolia (10th / 9th millennium BC), a site that has aroused much debate in archaeological discourse. To date, only zooarchaeological evidence has been discussed in regard to the subsistence of its builders. Göbekli Tepe consists of monumental round to oval buildings, erected in an earlier phase, and smaller rectangular buildings, built around them in a partially contemporaneous and later phase. The monumental buildings are best known as they were in the focus of research. They are around 20 m in diameter and have stone pillars that are up to 5.5 m high and often richly decorated. The rectangular buildings are smaller and–in some cases–have up to 2 m high, mostly undecorated, pillars. Especially striking is the number of tools related to food processing, including grinding slabs/bowls, handstones, pestles, and mortars, which have not been studied before. We analyzed more than 7000 artifacts for the present contribution. The high frequency of artifacts is unusual for contemporary sites in the region. Using an integrated approach of formal, experimental, and macro- / microscopical use-wear analyses we show that Neolithic people at Göbekli Tepe have produced standardized and efficient grinding tools, most of which have been used for the processing of cereals. Additional phytolith analysis confirms the massive presence of cereals at the site, filling the gap left by the weakly preserved charred macro-rests. The organization of work and food supply has always been a central question of research into Göbekli Tepe, as the construction and maintenance of the monumental architecture would have necessitated a considerable work force. Contextual analyses of the distribution of the elements of the grinding kit on site highlight a clear link between plant food preparation and the rectangular buildings and indicate clear delimitations of working areas for food production on the terraces the structures lie on, surrounding the circular buildings. There is evidence for extensive plant food processing and archaeozoological data hint at large-scale hunting of gazelle between midsummer and autumn. As no large storage facilities have been identified, we argue for a production of food for immediate use and interpret these seasonal peaks in activity at the site as evidence for the organization of large work feasts.

Dental microwear texture analysis of Homo sapiens sapiens: Foragers, farmers, and pastoralists

OBJECTIVES

The current study seeks to determine if a sample of foragers, farmers, and pastoralists are distinguishable based on their dental microwear texture signatures.

MATERIALS AND METHODS

The study included a sample of 719 individuals from 51 archeological sites (450 farmers, 192 foragers, 77 pastoralists). All were over age 12 and sexes were pooled. Using a Sensofar® white-light confocal profiler we collected dental microwear texture analysis (DMTA) data from a single first or second molar from each individual. We leveled and cleaned data clouds following standard procedures and analyzed the data with Sfrax® and Toothfrax® software. The DMTA variables were complexity and anisotropy. Statistics included ANOVA with partial eta squared and Hedges's g. We also performed a follow-up K-means cluster analysis.

RESULTS

We found significant differences between foragers and farmers and pastoralists for complexity and anisotropy, with foragers having greater complexity than either the farmers or the pastoralists. The farmers and pastoralists had greater anisotropy than the foragers. The Old World foragers had significantly higher anisotropy values than New World foragers. Old and New World farmers did not differ. Among the Old World farmers, those dating from the Neolithic through the Late Bronze Age had higher complexity values than those from the Iron Age through the medieval period. The cluster analysis discerned foragers and farmers but also indicated similarity between hard food foragers and hard food farmers.

DISCUSSION

Our findings reaffirm that DMTA is capable of distinguishing human diets. We found that foragers and farmers, in particular, differ in their microwear signatures across the globe. There are some exceptions, but nothing that would be unexpected given the range of human diets and food preparation techniques. This study indicates that in general DMTA is an efficacious means of paleodietary reconstruction in humans.

Detecting selection signatures in three Iranian sheep breeds

The objective of genome mapping is to achieve valuable insight into the connection between gene variants (genotype) and observed traits (phenotype). Part of that objective is to understand the selective forces that have operated on a population. Finding links between genotype-phenotype changes makes it possible to identify selective sweeps by patterns of genetic variation and linkage disequilibrium. Based on Illumina 50KSNP chip data, two approaches, XP-EHH (cross-population extend haplotype homozygosity) and F_ST (fixation index), were carried out in this research to identify selective sweeps in the genome of three Iranian local sheep breeds: Baluchi (n = 86), Lori-Bakhtiari (n = 45) and Zel (n = 45). Using both methods, 93 candidate genomic regions were identified as harboring putative selective sweeps. Bioinformatics analysis of the genomic regions showed that signatures of selection related to multiple candidate genes, such as HOXB9, HOXB13, ACAN, NPR2, TRIL, AOX1, CSF2, GHR, TNS2, SPAG8, HINT2, ALS2, AAAS, RARG, SYCP2, CAV1, PPP1R3D, PLA2G7, TTLL7 and C20orf10, that play a role in skeletal system and tail, sugar and energy metabolisms, growth, reproduction, immune and nervous system traits. Our findings indicated diverse genomic selection during the domestication of Iranian sheep breeds.

Discontinuities in quinoa biodiversity in the dry Andes: An 18-century perspective based on allelic genotyping

History and environment shape crop biodiversity, particularly in areas with vulnerable human communities and ecosystems. Tracing crop biodiversity over time helps understand how rural societies cope with anthropogenic or climatic changes. Exceptionally well preserved ancient DNA of quinoa (Chenopodium quinoa Willd.) from the cold and arid Andes of Argentina has allowed us to track changes and continuities in quinoa diversity over 18 centuries, by coupling genotyping of 157 ancient and modern seeds by 24 SSR markers with cluster and coalescence analyses. Cluster analyses revealed clear population patterns separating modern and ancient quinoas. Coalescence-based analyses revealed that genetic drift within a single population cannot explain genetic differentiation among ancient and modern quinoas. The hypothesis of a genetic bottleneck related to the Spanish Conquest also does not seem to apply at a local scale. Instead, the most likely scenario is the replacement of preexisting quinoa gene pools with new ones of lower genetic diversity. This process occurred at least twice in the last 18 centuries: first, between the 6th and 12th centuries—a time of agricultural intensification well before the Inka and Spanish conquests—and then between the 13th century and today—a period marked by farming marginalization in the late 19th century likely due to a severe multidecadal drought. While these processes of local gene pool replacement do not imply losses of genetic diversity at the metapopulation scale, they support the view that gene pool replacement linked to social and environmental changes can result from opposite agricultural trajectories.