Ancient DNA and human history

Slatkin, Montgomery; Racimo, Fernando

doi:10.1073/pnas.1524306113

Cited by 181 publications

(110 citation statements)

References 82 publications

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“…A natural extension to the analyses we performed here would be to look at admixture graphs that include extinct populations or species, using ancient DNA (Slatkin and Racimo 2016). For example, present-day Europeans are known to have resulted from admixture processes involving at least 4 ancestral populations (Lazaridis et al 2014(Lazaridis et al , 2016, and so modeling them as a sister group to East Asians or as a 2-way mixture between a Native American-related component and a basal Eurasian component may be overly simplistic.…”

Section: Future Directionsmentioning

confidence: 99%

Detecting Polygenic Adaptation in Admixture Graphs

2018

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An open question in human evolution is the importance of polygenic adaptation: adaptive changes in the mean of a multifactorial trait due to shifts in allele frequencies across many loci. In recent years, several methods have been developed to detect polygenic adaptation using loci identified in genome-wide association studies (GWAS). Though powerful, these methods suffer from limited interpretability: they can detect which sets of populations have evidence for polygenic adaptation, but are unable to reveal where in the history of multiple populations these processes occurred. To address this, we created a method to detect polygenic adaptation in an admixture graph, which is a representation of the historical divergences and admixture events relating different populations through time. We developed a Markov chain Monte Carlo (MCMC) algorithm to infer branch-specific parameters reflecting the strength of selection in each branch of a graph. Additionally, we developed a set of summary statistics that are fast to compute and can indicate which branches are most likely to have experienced polygenic adaptation. We show via simulations that this method -which we call PolyGraph -has good power to detect polygenic adaptation, and applied it to human population genomic data from around the world. We also provide evidence that variants associated with several traits, including height, educational attainment, and self-reported unibrow, have been influenced by polygenic adaptation in different populations during human evolution.

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Section: Future Directionsmentioning

confidence: 99%

Detecting Polygenic Adaptation in Admixture Graphs

2018

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“…Next-generation sequencing (NGS) has led to significantly lower sequencing costs and improved sequencing output, opening doors to the massively parallel production of genetic data from ancient individuals (8). In the last 3 years, NGS has led to a 100-fold increase in the number of ancient human specimens analyzed as well as the magnitude and coverage of the genomic data obtained (9,10). Additional recent developments in aDNA analysis have focused on increasing DNA yields through optimized extraction protocols (11), improved library preparation (12,13), and the addition of enrichment techniques prior to sequencing (14,15).…”

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confidence: 99%

A Minimally-Invasive Method for Sampling Human Petrous Bones from the Cranial Base for Ancient DNA Analysis

et al. 2017

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Ancient DNA (aDNA) research involves invasive and destructive sampling procedures that are often incompatible with anthropological, anatomical, and bioarcheological analyses requiring intact skeletal remains. The osseous labyrinth inside the petrous bone has been shown to yield higher amounts of endogenous DNA than any other skeletal element; however, accessing this labyrinth in cases of a complete or reconstructed skull involves causing major structural damage to the cranial vault or base. Here, we describe a novel cranial base drilling method (CBDM) for accessing the osseous labyrinth from the cranial base that prevents damaging the surrounding cranial features, making it highly complementary to morphological analyses. We assessed this method by comparing the aDNA results from one petrous bone processed using our novel method to its pair, which was processed using established protocols for sampling disarticulated petrous bones. We show a decrease in endogenous DNA and molecular copy numbers when the drilling method is used; however, we also show that this method produces more endogenous DNA and higher copy numbers than any postcranial bone. Our results demonstrate that this minimally-invasive method reduces the loss of genetic data associated with the use of other skeletal elements and enables the combined craniometric and genetic study of individuals with archeological, cultural, and evolutionary value.

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“…As humans spread across the globe, they encountered new climates, geography, food sources, and pathogens, which presented novel selective pressures [8]. In addition, early humans migrating out of Africa encountered archaic populations including Neanderthals and Denisovans, resulting in low levels of admixture and introgression of archaic genomes into modern humans genomes (representing ~1 – 6% of non-African genomes) [12]. Plant and animal domestication led to substantial shifts in diet, as populations moved from a hunting and gathering lifestyle to an agricultural lifestyle rich in grains and carbohydrates or towards a pastoralist lifestyle rich in milk and protein within the past 10 ky.…”

Section: Recent Insights From Global Samplingmentioning

confidence: 99%

Global variation in gene expression and the value of diverse sampling

Kelly

Hansen

Tishkoff

2017

Current Opinion in Systems Biology

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The genomics era has accelerated our understanding of how genetic and epigenetic factors influence both normal variable traits and disease risk in humans. However, the majority of “omics” studies have focused on individuals living in urban centers, primarily from Europe and Asia, neglecting much of the genetic and environmental variation that exists across worldwide populations. Comparative studies of gene regulation in ethnically diverse populations are informing our understanding of how evolutionary forces have shaped the genetic and molecular mechanisms underlying complex traits, and studying gene expression in different environmental contexts is enabling the dissection of disease-related pathways such as immune response. Such approaches are vital to the equitable application of genomics and medicine.

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Ancient DNA and human history

Cited by 181 publications

References 82 publications

Detecting Polygenic Adaptation in Admixture Graphs

Detecting Polygenic Adaptation in Admixture Graphs

A Minimally-Invasive Method for Sampling Human Petrous Bones from the Cranial Base for Ancient DNA Analysis

Global variation in gene expression and the value of diverse sampling

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