Abstract
Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide.
Highlights
Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past
ROH has been identified in ancient DNA11–18, that is, genetic material extracted from ancient human remains
We developed a Hidden Markov Model (HMM) with hidden copying states, one for each reference haplotype, to model copying long stretches from the panel [similar to the copying model of ref. 22], and an additional single non-ROH state as in ref
Summary
Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. ROH has been identified in ancient DNA (aDNA), that is, genetic material extracted from ancient human remains. This advance is especially promising, as large datasets of aDNA have been generated in the last decade. Recent methodological advances enable identifying ROH in data with at least 5 × coverage, but this threshold precludes analysis on all but a small fraction of the currently available aDNA record
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