Early Domestication Research Articles

Multiple lines of evidence of early goose domestication in a 7,000-y-old rice cultivation village in the lower Yangtze River, China

Poultry are farmed globally, with chicken (Gallus gallus domesticus) being the leading domesticated species. Although domestic chicken bones have been reported from some Early Holocene sites, their origin is controversial and there is no reliable domestic chicken bone older than the Middle Holocene. Here, we studied goose bones from Tianluoshan—a 7,000-y-old rice cultivation village in the lower Yangtze River valley, China—using histological, geochemical, biochemical, and morphological approaches. Histological analysis revealed that one of the bones was derived from a locally bred chick, although no wild goose species breed in southern China. The analysis of oxygen-stable isotope composition supported this observation and further revealed that some of the mature bones were also derived from locally bred individuals. The nitrogen-stable isotope composition showed that locally bred mature birds fed on foods different from those eaten by migrant individuals. Morphological analysis revealed that the locally bred mature birds were homogenous in size, whereas radiocarbon dating clearly demonstrated that the samples from locally bred individuals were ∼7,000 y old. The histological, geochemical, biochemical, morphological, and contextual evidence suggest that geese at Tianluoshan village were at an early stage of domestication. The goose population appears to have been maintained for several generations without the introduction of individuals from other populations and may have been fed cultivated paddy rice. These findings indicate that goose domestication dates back 7,000 y, making geese the oldest domesticated poultry species in history.

Sequencing Reveals Population Structure and Selection Signatures for Reproductive Traits in Yunnan Semi-Fine Wool Sheep (Ovis aries).

Yunnan semi-fine wool sheep are among the most important cultivated sheep breeds in China. However, their population structure, genetic characteristics and traits of interest are poorly studied. In this study, we systematically studied the population characteristics and selection signatures of 40 Yunnan semi-fine wool sheep using SNPs obtained from whole-genome resequencing data. A total of 1393 Gb of clean data were acquired. The mapping rate against the reference genome was 91.23% on average (86.01%–92.26%), and the average sequence depth was 9.51X. After filtering, 28,593,198 SNPs and 4,725,259 indels with high quality were obtained. The heterozygosity rate, inbreeding coefficient and effective population size of the sheep were calculated to preliminarily explore their genetic characteristics. The average heterozygosity rate was 0.264, the average inbreeding coefficient was 0.0099, and the effective population size estimated from the heterozygote excess (HE) was 242.9. Based on the Tajima’s D and integrated haplotype score (iHS) approaches, 562 windows and 11,356 core SNPs showed selection signatures in the Yunnan semi-fine wool sheep population. After genome annotation and gene enrichment analysis, we found traces of early domestication in sensory organs, behavioural activity and the nervous system as well as adaptive changes in reproductive and wool traits under selection in this population. Some selected genes related to litter size, including FSHR, BMPR1B and OXT, were identified as being under selection. Specific missense mutations of the FSHR gene that differed from the reference genome were also identified in the population, and we found some SNP variations that may affect litter size. Our findings provide a theoretical basis for the conservation and utilization of Yunnan semi-fine wool sheep. Furthermore, our results reveal some changes common to sheep after domestication and provide a new opportunity to investigate the genetic variation influencing fecundity within a population evolving under artificial selection.

Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies

BackgroundAsian rice (Oryza sativa L.) has been a model plant but its cultivation history is inadequately understood, and its origin still under debate. Several enigmas remain, including how this annual crop shifted its growth habit from its perennial ancestor, O. rufipogon, why genetic divergence between indica and japonica appears older than the history of human domestication, and why some domestication genes do not show signals of introgression between subgroups. Addressing these issues may benefit both basic research and rice breeding.ResultsGene genealogy-based mutation (GGM) analysis shows that history of Asian rice is divided into two phases (Phase I and II) of about equal lengths. Mutations occurred earlier than the partition of indica and japonica to Os genome mark Phase-I period. We diagnosed 91 such mutations among 101 genes sampled across 12 chromosomes of Asian rice and its wild relatives. Positive selection, detected more at 5′ regions than at coding regions of some of the genes, involved 22 loci (e.g., An-1, SH4, Rc, Hd3a, GL3.2, OsMYB3, OsDFR, and OsMYB15), which affected traits from easy harvesting, grain color, flowering time, productivity, to likely taste and tolerance. Phase-I mutations of OsMYB3, OsHd3a and OsDFR were experimentally tested and all caused enhanced functions of the genes in vivo. Phase-II period features separate cultivations, lineage-specific selection, and expanded domestication to more genes. Further genomic analysis, along with phenotypic comparisons, indicates that O. sativa is hybrid progeny of O. rufipogon and O. nivara, inherited slightly more genes of O. rufipogon. Congruently, modern alleles of the sampled genes are approximately 6% ancient, 38% uni-specific, 40% bi-specific (mixed), and 15% new after accumulating significant mutations. Results of sequencing surveys across modern cultivars/landraces indicate locus-specific usages of various alleles while confirming the associated mutations.ConclusionsAsian rice was initially domesticated as one crop and later separate selection mediated by human resulted in its major subgroups. This history and the hybrid origin well explain previous puzzles. Positive selection, particularly in 5′ regions, was the major force underlying trait domestication. Locus-specific domestication can be characterized and the result may facilitate breeders in developing better rice varieties in future.

Early fish domestication affects methylation of key genes involved in the rapid onset of the farmed phenotype

ABSTRACT Animal domestication is a process of environmental modulation and artificial selection leading to permanent phenotypic modifications. Recent studies showed that phenotypic changes occur very early in domestication, i.e., within the first generation in captivity, which raises the hypothesis that epigenetic mechanisms may play a critical role on the early onset of the domestic phenotype. In this context, we applied reduced representation bisulphite sequencing to compare methylation profiles between wild Nile tilapia females and their offspring reared under farmed conditions. Approximately 700 differentially methylated CpG sites were found, many of them associated not only with genes involved in muscle growth, immunity, autophagy and diet response but also related to epigenetic mechanisms, such as RNA methylation and histone modifications. This bottom-up approach showed that the phenotypic traits often related to domestic animals (e.g., higher growth rate and different immune status) may be regulated epigenetically and prior to artificial selection on gene sequences. Moreover, it revealed the importance of diet in this process, as reflected by differential methylation patterns in genes critical to fat metabolism. Finally, our study highlighted that the TGF-β1 signalling pathway may regulate and be regulated by several differentially methylated CpG-associated genes. This could be an important and multifunctional component in promoting adaptation of fish to a domestic environment while modulating growth and immunity-related traits.

No disruption of rhizobial symbiosis during early stages of cowpea domestication.

Modern agriculture intensely selects aboveground plant structures, while often neglecting belowground features, and evolutionary tradeoffs between these traits are predicted to disrupt host control over microbiota. Moreover, drift, inbreeding, and relaxed selection for symbiosis in crops might degrade plant mechanisms that support beneficial microbes. We studied the impact of domestication on the nitrogen-fixing symbiosis between cowpea and root-nodulating Bradyrhizobium. We combined genome-wide analyses with a greenhouse inoculation study to investigate genomic diversity, heritability, and symbiosis trait variation among wild and early-domesticated cowpea genotypes. Cowpeas experienced modest decreases in genome-wide diversity during early domestication. Nonetheless, domesticated cowpeas responded efficiently to variation in symbiotic effectiveness, by forming more root nodules with nitrogen-fixing rhizobia and sanctioning nonfixing strains. Domesticated populations invested a larger proportion of host tissues into root nodules than wild cowpeas. Unlike soybean and wheat, cowpea showed no compelling evidence for degradation of symbiosis during domestication. Domesticated cowpeas experienced a less severe bottleneck than these crops and the low nutrient conditions in Africa where cowpea landraces were developed likely favored plant genotypes that gain substantial benefits from symbiosis. Breeders have largely neglected symbiosis traits, but artificial selection for improved plant responses to microbiota could increase plant performance and sustainability.

Genomic footprints of sorghum domestication and breeding selection for multiple end uses

Domestication and diversification have had profound effects on crop genomes. Originating in Africa and subsequently spreading to different continents, sorghum (Sorghum bicolor) has experienced multiple onsets of domestication and intensive breeding selection for various end uses. However, how these processes have shaped sorghum genomes is not fully understood. In the present study, population genomics analyses were performed on a worldwide collection of 445 sorghum accessions, covering wild sorghum and four end-use subpopulations with diverse agronomic traits. Frequent genetic exchanges were found among various subpopulations, and strong selective sweeps affected 14.68% (∼107.5 Mb) of the sorghum genome, including 3649, 4287, and 3888 genes during sorghum domestication, improvement of grain sorghum, and improvement of sweet sorghum, respectively. Eight different models of haplotype changes in domestication genes from wild sorghum to landraces and improved sorghum were observed, and Sh1- and SbTB1-type genes were representative of two prominent models, one of soft selection or multiple origins and one of hard selection or an early single domestication event. We also demonstrated that the Dry gene, which regulates stem juiciness, was unconsciously selected during the improvement of grain sorghum. Taken together, these findings provide new genomic insights into sorghum domestication and breeding selection, and will facilitate further dissection of the domestication and molecular breeding of sorghum.

Oxytocin effects on the behavior in historical and experimental domesticated animals

Domestication is one of the important evolutionary and genetic problems of biology. It addresses fundamental evolution aspects as well as allows us to study mechanisms of aggression, pro-social behavior and anthropogenesis. One of the potential key mechanisms of domestication may be associated with the central oxytocin (OT) system. OT has been repeatedly shown to exhibit pro-social and anxiolytic eff ects rodents, dogs, humans and other species [1]. In our study, we used intranasal OT administration on Siberian tame foxes and non-selected one. It is well-known experimental domestication model of. Th e OT eff ect on behavior had been investigated in intermale interactions (triple cage aft er adaptation) and human contact (new enclosure). OT administration increased patterns of playful (crouches on paws), affi liative (friendly) behavior, motor (fast move) and mixed activity in male-to-male interactions in tame foxes, whereas in case of unselected foxes, OT administration increased behavior patterns associated with anxiety (latent time for home cage exit, freezing, total time in home cage). In fox-human interactions, OT administration had the greatest eff ect on increasing the time tamed fox stayed at less than a meter away from a human. It is this parameter that is the defi ning one in similar tests on dogs. Th e results allow to suggest that OT has a context-dependent eff ect rather than explicitly pro-social eff ect in the tests, therefore amplifying the perception of social conditions according to the social salience hypothesis of OT. OT eff ect is associated with emotional positive and negative animal behaviors toward human that could be related to the genotype. Such OT eff ect might separate animals into more or less tolerant to humans under the same early domestication conditions.

APLICACIÓN DE DIFERENTES METODOLOGÍAS EN EL MEJORAMIENTO DE LENTEJA (Lens culinaris MEDIK)

Lentil (Lens culinaris Medik.) is a self-pollinating diploid (2n=2x=14) species belonging to the Fabaceae family. It is one of the oldest crops known, with 8,000 to 9,000 years of history and it is among the earliest domesticates from the Near East Fertile Crescent. The seeds have high nutritional value. This crop is an interesting substitute to wheat in cereal rotations but its importance is low due to a lack of suitable varieties with local adaptation. Some of the major problems that Argentinian lentil breeders face are the narrow genetic base of the current cultivated germplasm and its low yield potential. A lentil breeding program was initiated in 2004 to develop new varieties with adaptation to prevalent conditions in growing areas of Argentina. Germplasm was obtained from ICARDA (International Center for Agricultural Research in the Dry Areas) and local producers. Conventional breeding methods using hybridization and selection are being carried out to develop improved varieties, broad the genetic base, and isolate superior recombinant inbred lines. Two new varieties have been obtained, one of the macrosperm type (Boyerito FCA) and the other of the microsperm type (Tacuarita FCA) through the application of mass selection in F2 populations from the cross of selected materials. This program complements traditional breeding methods with biotechnological techniques such as transgenesis, use of molecular markers, in vitro embryo culture combined with the SSD method to shorten the breeding time, and digital phenotyping. Key words: Lentil, conventional methodologies, in vitro embryo culture, biotechnology techniques, digital phenotyping.

PALEOPROTEOMICS STUDIES OF ANCIENT CAPRINAE: A REVIEW

In the Neolithic era, people began to graze sheep and goats primarily due to easier access to meat, milk, and fleeces. Thus, in ancient times, Caprinae were the key animals in the development of early domestication and agriculture. The analysis of ancient proteins of Caprinae from paleontological and archeological materials reveals new data on their migration, complements research on the diet of ancient people, their culture, and habits. Here, we discuss paleoproteomics methods, such as matrix-assisted laser desorption/ionization with time-of-flight mass analyzer (MALDI-TOF MS) and liquid chromatography with tandem mass spectrometry (LC-MS / MS). We will also consider the most important discoveries in the field of the study of ancient sheep and in which direction the paleoproteomics of Caprinae will develop in the near future. In addition, general recommendations for analyzing data from ancient proteins are considered, for example, programs and requirements for databases. We will consider the main search algorithms in proteomics, as well as identify effective ones for identifying peptides and proteins. It also describes the commonly used ancient protein targets, and the basic principles of working with ancient samples. In addition, this review describes the main research conducted on ancient Caprinae of ancient proteins such as collagen, keratin, and milk proteins.

Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication.

Domestication of animals can lead to profound phenotypic modifications within short evolutionary time periods, and for many species behavioral selection is likely at the forefront of this process. Animal studies have strongly implicated that the gut microbiome plays a major role in host behavior and cognition through the microbiome-gut-brain axis. Consequently, herein, it is hypothesized that host gut microbiota may be one of the earliest phenotypes to change as wild animals were domesticated. Here, the gut microbiome community in two selected lines of red junglefowl that are selected for either high or low fear of humans up to eight generations is examined. Microbiota profiles reveal taxonomic differences in gut bacteria known to produce neuroactive compounds between the two selection lines. Gut-brain module analysis by means of genome-resolved metagenomics identifies enrichment in the microbial synthesis and degradation potential of metabolites associated with fear extinction and reduces anxiety-like behaviors in low fear fowls. In contrast, high fear fowls are enriched in gut-brain modules from the butyrate and glutamate pathways, metabolites associated with fear conditioning. Overall, the results identify differences in the composition and functional potential of the gut microbiota across selection lines that may provide insights into the mechanistic explanations of the domestication process.

Ornamental potential of the coastal plant Lapiedra martinezii Lag. (Amaryllidaceae): the role of its revalorization in xero-gardening and ex-situ conservation

Lapiedra martinezii Lag. (Amaryllidaceae) is an autumn-flowering geophyte that grows in coastal and sublittoral environments. The interests on this species has come out during the last decades due to its content in bioactive alkaloids and its conservational status. The aim of this work was to review the available information on L. martinezii and to assess whether it could be introduced as ornamental plant in xero-gardening. Therefore, the aesthetic traits were analyzed and compared to other cultivated and wild plants. Also, information on its ecological and propagation requirements were checked to discern whether it could be adapted under different production systems and culture conditions. In addition, other aspects were also analyzed to identify strengths and limitations of this species for its further revalorization as ornamental plant. The results obtained suggest that L. martinezii could be a good choice as foliage plant to grow it on gardens as an alpine bulb or pot plant. Moreover, it might be quite well adapted under different production and culture conditions in dry and semi-arid regions. The horticultural traits related to its germination and in vitro multiplication are interesting strengths to bear in mind for its industrial propagation and early domestication. Finally considered, the introduction in xero-gardening could also help in its ex-situ conservation. However, a more-in-depth research would be needed to finally introduce it in the ornamental plants’ market.

A conserved genetic architecture among populations of the maize progenitor, teosinte, was radically altered by domestication

Very little is known about how domestication was constrained by the quantitative genetic architecture of crop progenitors and how quantitative genetic architecture was altered by domestication. Yang et al. [C. J. Yang et al., Proc. Natl. Acad. Sci. U.S.A. 116, 5643-5652 (2019)] drew multiple conclusions about how genetic architecture influenced and was altered by maize domestication based on one sympatric pair of teosinte and maize populations. To test the generality of their conclusions, we assayed the structure of genetic variances, genetic correlations among traits, strength of selection during domestication, and diversity in genetic architecture within teosinte and maize. Our results confirm that additive genetic variance is decreased, while dominance genetic variance is increased, during maize domestication. The genetic correlations are moderately conserved among traits between teosinte and maize, while the genetic variance-covariance matrices (G-matrices) of teosinte and maize are quite different, primarily due to changes in the submatrix for reproductive traits. The inferred long-term selection intensities during domestication were weak, and the neutral hypothesis was rejected for reproductive and environmental response traits, suggesting that they were targets of selection during domestication. The G-matrix of teosinte imposed considerable constraint on selection during the early domestication process, and constraint increased further along the domestication trajectory. Finally, we assayed variation among populations and observed that genetic architecture is generally conserved among populations within teosinte and maize but is radically different between teosinte and maize. While selection drove changes in essentially all traits between teosinte and maize, selection explains little of the difference in domestication traits among populations within teosinte or maize.

Parallel selection of distinct Tof5 alleles drove the adaptation of cultivated and wild soybean to high latitudes

Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor. In particular, the genetic basis of the adaptation in wild soybean remains poorly understood. In this study, by combining whole-genome resequencing and genome-wide association studies we identified a novel locus, Time of Flowering 5 (Tof5), which promotes flowering and enhances adaptation to high latitudes in both wild and cultivated soybean. By genomic, genetic and transgenic analyses we showed that Tof5 encodes a homolog of Arabidopsis thaliana FRUITFULL (FUL). Importantly, further analyses suggested that different alleles of Tof5 have undergone parallel selection. The Tof5H1 allele was strongly selected by humans after the early domestication of cultivated soybean, while Tof5H2 allele was naturally selected in wild soybean, and in each case facilitating adaptation to high latitudes. Moreover, we found that the key flowering repressor E1 suppresses the transcription of Tof5 by binding to its promoter. In turn, Tof5 physically associates with the promoters of two important FLOWERING LOCUS T (FT), FT2a and FT5a, to upregulate their transcription and promote flowering under long photoperiods. Collectively, our findings provide insights into how wild soybean adapted to high latitudes through natural selection and indicate that cultivated soybean underwent changes in the same gene but evolved a distinct allele that was artificially selected after domestication.

Ancient Mitogenomes Provide New Insights into the Origin and Early Introduction of Chinese Domestic Donkeys.

Both molecular data and archaeological evidence strongly support an African origin for the domestic donkey. Recent genetic studies further suggest that there were two distinct maternal lineages involved in its initial domestication. However, the exact introduction time and the dispersal process of domestic donkeys into ancient China are still unresolved. To address these questions, we retrieved three near-complete mitochondrial genomes from donkey specimens excavated from Gaoling County, Shaanxi Province, and Linxia Basin, Gansu Province, China, dated at 2,349-2,301, 469-311, and 2,160-2,004 cal. BP, respectively. Maximum-likelihood and Bayesian phylogenetic analyses reveal that the two older samples fall into the two different main lineages (i.e., clade Ⅰ and clade Ⅱ) of the domestic donkey, suggesting that the two donkey maternal lineages had been introduced into Midwestern China at least at the opening of Silk Road (approximately the first century BC). Bayesian analysis shows that the split of the two donkey maternal lineages is dated at 0.323 Ma (95% CI: 0.583–0.191 Ma) using root-tip dating calibrations based on near-complete mitogenomes, supporting the hypothesis that modern domestic donkeys go back to at least two independent domestication events. Moreover, Bayesian skyline plot analyses indicate an apparent female population increase between 5,000 and 2,500 years ago for clade I followed by a stable population size to the present day. In contrast, clade II keeps a relatively stable population size over the past 5,000 years. Overall, our study provides new insights into the early domestication history of Chinese domestic donkeys.

Genomic insights into the origin, domestication and diversification of Brassica juncea

Despite early domestication around 3000 BC, the evolutionary history of the ancient allotetraploid species Brassica juncea (L.) Czern & Coss remains uncertain. Here, we report a chromosome-scale de novo assembly of a yellow-seeded B. juncea genome by integrating long-read and short-read sequencing, optical mapping and Hi-C technologies. Nuclear and organelle phylogenies of 480 accessions worldwide supported that B. juncea is most likely a single origin in West Asia, 8,000–14,000 years ago, via natural interspecific hybridization. Subsequently, new crop types evolved through spontaneous gene mutations and introgressions along three independent routes of eastward expansion. Selective sweeps, genome-wide trait associations and tissue-specific RNA-sequencing analysis shed light on the domestication history of flowering time and seed weight, and on human selection for morphological diversification in this versatile species. Our data provide a comprehensive insight into the origin and domestication and a foundation for genomics-based breeding of B. juncea.

Impact of selection and domestication on hindlimb bones of modern reindeer populations: Archaeological implications for early reindeer management by Sámi in Fennoscandia

ABSTRACT For centuries, reindeer herding has been an integral part of the subsistence and culture among the Sámi of northern Fennoscandia. Despite the importance of this husbandry in their history, the timing and details of early reindeer domestication are still highly debated. Indeed, identifying domesticated individuals in the archaeological record remains complicated because reindeer are still considered to be in the early phases of the domestication process. In this work, we propose solutions for identifying domestic individuals using 3D geometric morphometrics on isolated elements from the long bones of the hindlimb in modern reindeer populations. These bones are important for understanding both the mobility of reindeer and the effect of load carrying or draught. A good level of distinction between the size and shape variables of these bones was found among subspecies, sex and lifestyles. This demonstrates that the long bones of the hindlimb can provide information on changes in locomotor behaviour induced by the domestication process, such as control and reduction of reindeer mobility by humans. This also demonstrates that analysis in geometric morphometrics is useful for exploring the use of draught reindeer in early Sámi reindeer herding and the implications for understanding reindeer domestication and early reindeer herding strategies.

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

BackgroundSpecies 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.ResultsWe 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.ConclusionThis 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.

Spatial and temporal pattern of rice domestication during the early Holocene in the lower Yangtze region, China

Rice is among the world’s most important and ancient domesticated crops. However, the spatial and temporal pattern of the early rice domestication process remains unclear due to the lack of systematic study of wild/domesticated rice remains and corresponding dates during the early Holocene. Here, we collected 248 samples from five typical Shangshan cultural sites in the lower Yangtze region where is the most likely origin place of rice for phytolith analysis. The results showed the following. (1) Rice bulliform phytoliths from the five sites all present domestication traits, suggesting that the rice domestication process had begun across the region by the early stage of the Holocene. (2) The relative domestication rates reflected by the rice bulliform phytoliths were different between sites, the sites with higher domestication rates were distributed closer to the mainstream river. (3) The rice domestication process revealed by bulliform phytoliths can be divided into three periods during the early Holocene: from 10 to 9 ka, rice domestication began and stayed at a low level under 35%; from 9 to 8.5 ka, rice domestication level increased to 50%; and from 8.5 to 8 ka, rice domestication level was in a fluctuating state. (4) By 9 ka BP, rice double-peaked phytoliths from glume cells are present in most of the studied sites, which imply the presence of crop dehusking processing. This study reconstructed the spatial and temporal patterns of rice domestication during the early Holocene, which will improve our knowledge of early crop domestication and enhance our understanding of changes in rice status.

Neolithic avifaunal resource utilisation in the lower Yangtze River: A case study of the Tianluoshan site

The lower Yangtze River region in China was a centre of early Neolithic rice cultivation and animal domestication. It is also an important habitat for wintering birds; however, our current understanding of prehistoric avifaunal resource utilisation by human populations in this region is limited. To clarify the use of birds by early Neolithic rice-cultivating societies further, we analysed bird remains from one excavation grid at the Tianluoshan site, which dates to between 7000 and 6100 cal BP. Ducks (Anatinae), rails (Rallidae), and geese (Anserinae) were dominant in every layer, suggesting that birds wintering in inland waters were the primary avifaunal taxa exploited at the Tianluoshan site. The taxonomic composition, bone modification rate, and skeletal part representation of these dominant taxa differed between layers. Overall, there was an abundance of duck and goose wing elements and both the wing and leg elements of rails, suggesting that exploitation patterns differed among these primary taxa. There is no evidence of domestic exploitation of ducks and/or chickens (Gallus gallus domesticus), but the appearance of immature goose bones may suggest the existence of domestic geese.

Rethinking the evidence for early horse domestication at Botai

Despite its transformative impact on human history, the early domestication of the horse (Equus caballus) remains exceedingly difficult to trace in the archaeological record. In recent years, a scientific consensus emerged linking the Botai culture of northern Kazakhstan with the first domestication of horses, based on compelling but largely indirect archaeological evidence. A cornerstone of the archaeological case for domestication at Botai is damage to the dentition commonly linked with the use of bridle mouthpieces, or “bit wear.” Recent archaeogenetic analyses reveal, however, that horse remains from Botai are not modern domesticates but instead the Przewalski’s horse, E. przewalskii—warranting reevaluation of evidence for domestication. Here, we compare osteological traits hypothesized to have been caused by horse transport at Botai with wild Pleistocene equids in North America. Our results suggest that damage observed in Botai horse teeth is likely generated by natural disturbances in dental development and wear, rather than through contact with bridle equipment. In light of a careful reconsideration of the mid-Holocene archaeological record of northern Eurasia, we suggest that archaeological materials from Botai are most effectively explained through the regularized mass harvesting of wild Przewalski’s’ horses—meaning that the origins of horse domestication may lie elsewhere.