ABSTRACT
Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel's rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.
Subject(s)
Genome, Human , Genotyping Techniques , Humans , Genotyping Techniques/methods , Genome, Human/genetics , DNA, Ancient , Genotype , Genome-Wide Association Study/methods , Polymorphism, Single NucleotideABSTRACT
OBJECTIVE: This study provides a baseline of pathological and sub-pathological changes in the lower-limb bones of a semi-feral herd of domestic cattle. The purpose is to refine an existing method for identifying the use of cattle for traction using zooarchaeological evidence. METHODS: A published recording system for identifying draught cattle was applied to a sample of 15 individuals from Chillingham Park, Northumberland. Correlations were explored between individual pathological index values, the scores obtained for individual pathological/sub-pathological changes, and three biological variables: age, sex and body size. RESULTS: Pathological index values in the Chillingham cattle were low. Positive correlations between individual pathological index values and age, sex and body size were identified. Broadening of the distal metacarpal, proximal and distal exostoses in the metatarsal, distal exostoses of the proximal phalanx, and proximal lipping and exostoses of the distal phalanx, were strongly correlated with age. CONCLUSIONS: Pathological index scores demonstrate that adaptive remodeling of the autopodia is low in a free-ranging population of cattle, supporting the view that more pronounced changes provide useful identifiers of traction use. Application of modified pathological index formulae to nine archaeological sites from England indicated that cattle were only intensively used for traction in the Roman and later medieval periods. SIGNIFICANCE: This study refines the methods used to identify traction in the archaeological record through the consideration of cows and a wider range of ages than has been considered previously. LIMITATIONS: Only 15 individuals from the Chillingham herd were available for analysis. SUGGESTIONS FOR FURTHER RESEARCH: The refined formulae should be applied to additional archaeological datasets from different regions and time periods to explore the changing exploitation of cattle for traction.
Subject(s)
Metatarsal Bones , Animals , Archaeology , Cattle , England , FemaleABSTRACT
The Gjerrild burial provides the largest and best-preserved assemblage of human skeletal material presently known from the Single Grave Culture (SGC) in Denmark. For generations it has been debated among archaeologists if the appearance of this archaeological complex represents a continuation of the previous Neolithic communities, or was facilitated by incoming migrants. We sampled and analysed five skeletons from the Gjerrild cist, buried over a period of c. 300 years, 2600/2500-2200 cal BCE. Despite poor DNA preservation, we managed to sequence the genome (>1X) of one individual and the partial genomes (0.007X and 0.02X) of another two individuals. Our genetic data document a female (Gjerrild 1) and two males (Gjerrild 5 + 8), harbouring typical Neolithic K2a and HV0 mtDNA haplogroups, but also a rare basal variant of the R1b1 Y-chromosomal haplogroup. Genome-wide analyses demonstrate that these people had a significant Yamnaya-derived (i.e. steppe) ancestry component and a close genetic resemblance to the Corded Ware (and related) groups that were present in large parts of Northern and Central Europe at the time. Assuming that the Gjerrild skeletons are genetically representative of the population of the SGC in broader terms, the transition from the local Neolithic Funnel Beaker Culture (TRB) to SGC is not characterized by demographic continuity. Rather, the emergence of SGC in Denmark was part of the Late Neolithic and Early Bronze Age population expansion that swept across the European continent in the 3rd millennium BCE, resulting in various degrees of genetic replacement and admixture processes with previous Neolithic populations.
Subject(s)
Archaeology , Genomics , Skeleton/metabolism , DNA, Ancient , Denmark , Female , Haplotypes , History, Ancient , Human Migration , Humans , Male , Sex Determination AnalysisABSTRACT
Cultural evolutionary theory conceptualises culture as an information-transmission system whose dynamics take on evolutionary properties. Within this framework, however, innovation has been likened to random mutations, reducing its occurrence to chance or fortuitous transmission error. In introducing the special collection on children and innovation, we here place object play and play objects - especially functional miniatures - from carefully chosen archaeological contexts in a niche construction perspective. Given that play, including object play, is ubiquitous in human societies, we suggest that plaything construction, provisioning and use have, over evolutionary timescales, paid substantial selective dividends via ontogenetic niche modification. Combining findings from cognitive science, ethology and ethnography with insights into hominin early developmental life-history, we show how play objects and object play probably had decisive roles in the emergence of innovative capabilities. Importantly, we argue that closer attention to play objects can go some way towards addressing changes in innovation rates that occurred throughout human biocultural evolution and why innovations are observable within certain technological domains but not others.
ABSTRACT
How did human symbolic behavior evolve? Dating up to about 100,000 y ago, the engraved ochre and ostrich eggshell fragments from the South African Blombos Cave and Diepkloof Rock Shelter provide a unique window into presumed early symbolic traditions of Homo sapiens and how they evolved over a period of more than 30,000 y. Using the engravings as stimuli, we report five experiments which suggest that the engravings evolved adaptively, becoming better-suited for human perception and cognition. More specifically, they became more salient, memorable, reproducible, and expressive of style and human intent. However, they did not become more discriminable over time between or within the two archeological sites. Our observations provide support for an account of the Blombos and Diepkloof engravings as decorations and as socially transmitted cultural traditions. By contrast, there was no clear indication that they served as denotational symbolic signs. Our findings have broad implications for our understanding of early symbolic communication and cognition in H. sapiens.
Subject(s)
Biological Evolution , Engraving and Engravings/history , Social Behavior , Symbolism , History, Ancient , HumansABSTRACT
The third millennium BCE was a period of major cultural and demographic changes in Europe that signaled the beginning of the Bronze Age. People from the Pontic steppe expanded westward, leading to the formation of the Corded Ware complex and transforming the genetic landscape of Europe. At the time, the Globular Amphora culture (3300-2700 BCE) existed over large parts of Central and Eastern Europe, but little is known about their interaction with neighboring Corded Ware groups and steppe societies. Here we present a detailed study of a Late Neolithic mass grave from southern Poland belonging to the Globular Amphora culture and containing the remains of 15 men, women, and children, all killed by blows to the head. We sequenced their genomes to between 1.1- and 3.9-fold coverage and performed kinship analyses that demonstrate that the individuals belonged to a large extended family. The bodies had been carefully laid out according to kin relationships by someone who evidently knew the deceased. From a population genetic viewpoint, the people from Koszyce are clearly distinct from neighboring Corded Ware groups because of their lack of steppe-related ancestry. Although the reason for the massacre is unknown, it is possible that it was connected with the expansion of Corded Ware groups, which may have resulted in competition for resources and violent conflict. Together with the archaeological evidence, these analyses provide an unprecedented level of insight into the kinship structure and social behavior of a Late Neolithic community.
Subject(s)
Burial/history , DNA, Ancient/analysis , Violence/history , Adolescent , Adult , Archaeology , Child , Child, Preschool , Female , History, Ancient , Human Migration , Humans , Infant , Male , Middle Aged , Pedigree , Poland , Young AdultABSTRACT
In this contribution, we address a major puzzle in the evolution of human material culture: If maturing individuals just learn their parental generation's material culture, then what is the origin of key innovations as documented in the archeological record? We approach this question by coupling a life-history model of the costs and benefits of experimentation with a niche-construction perspective. Niche-construction theory suggests that the behavior of organisms and their modification of the world around them have important evolutionary ramifications by altering developmental settings and selection pressures. Part of Homo sapiens' niche is the active provisioning of children with play objects - sometimes functional miniatures of adult tools - and the encouragement of object play, such as playful knapping with stones. Our model suggests that salient material culture innovation may occur or be primed in a late childhood or adolescence sweet spot when cognitive and physical abilities are sufficiently mature but before the full onset of the concerns and costs associated with reproduction. We evaluate the model against a series of archeological cases and make suggestions for future research.