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Joint Estimation of Relatedness Coefficients and Allele Frequencies from Ancient Samples.

ABSTRACT: Here, we develop and test a method to address whether DNA samples sequenced from a group of fossil hominin bone or tooth fragments originate from the same individual or from closely related individuals. Our method assumes low amounts of retrievable DNA, significant levels of sequencing error, and contamination from one or more present-day humans. We develop and implement a maximum likelihood method that estimates levels of contamination, sequencing error rates, and pairwise relatedness coefficients in a set of individuals. We assume that there is no reference panel for the ancient population to provide allele and haplotype frequencies. Our approach makes use of single nucleotide polymorphisms (SNPs) and does not make assumptions about the underlying demographic model. By artificially mating genomes from the 1000 Genomes Project, we determine the numbers of individuals at a given genomic coverage that are required to detect different levels of genetic relatedness with confidence.

SUBMITTER: Theunert C

PROVIDER: S-EPMC5499161 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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Joint Estimation of Relatedness Coefficients and Allele Frequencies from Ancient Samples.

Theunert Christoph C Racimo Fernando F Slatkin Montgomery M

Genetics 20170410 2

Here, we develop and test a method to address whether DNA samples sequenced from a group of fossil hominin bone or tooth fragments originate from the same individual or from closely related individuals. Our method assumes low amounts of retrievable DNA, significant levels of sequencing error, and contamination from one or more present-day humans. We develop and implement a maximum likelihood method that estimates levels of contamination, sequencing error rates, and pairwise relatedness coefficie ...[more]

PMID: 28396504

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Project description:BackgroundIn addition to heterogeneity and artificial selection, natural selection is one of the forces used to combat climate change and improve agrobiodiversity in evolutionary plant breeding. Accurate identification of the specific genomic effects of natural selection will likely accelerate transfer between populations. Thus, insights into changes in allele frequency, adequate population size, gene flow and drift are essential. However, observing such effects often involves a trade-off between costs and resolution when a large sample of genotypes for many loci is analysed. Pool genotyping approaches achieve high resolution and precision in estimating allele frequency when sequence coverage is high. Nevertheless, high-coverage pool sequencing of large genomes is expensive.ResultsThree pool samples (n = 300, 300, 288) from a barley backcross population were generated to assess the population's allele frequency. The tested population (BC2F21) has undergone 18 generations of natural adaption to conventional farming practice. The accuracies of estimated pool-based allele frequencies and genome coverage yields were compared using three next-generation sequencing genotyping methods. To achieve accurate allele frequency estimates with low sequence coverage, we employed a haplotyping approach. Low coverage allele frequencies of closely located single polymorphisms were aggregated into a single haplotype allele frequency, yielding 2-to-271-times higher depth and increased precision. When we combined different haplotyping tactics, we found that gene and chip marker-based haplotype analyses performed equivalently or better compared with simple contig haplotype windows. Comparing multiple pool samples and referencing against an individual sequencing approach revealed that whole-genome pool re-sequencing (WGS) achieved the highest correlation with individual genotyping (≥ 0.97). In contrast, transcriptome-based genotyping (MACE) and genotyping by sequencing (GBS) pool replicates were significantly associated with higher error rates and lower correlations, but are still valuable to detect large allele frequency variations.ConclusionsThe proposed strategy identified the allele frequency of populations with high accuracy at low cost. This is particularly relevant to evolutionary plant breeding of crops with very large genomes, such as barley. Whole-genome low coverage re-sequencing at 0.03 × coverage per genotype accurately estimated the allele frequency when a loci-based haplotyping approach was applied. The implementation of annotated haplotypes capitalises on the biological background and statistical robustness.

Dataset Information

Joint Estimation of Relatedness Coefficients and Allele Frequencies from Ancient Samples.

Publications

Joint Estimation of Relatedness Coefficients and Allele Frequencies from Ancient Samples.

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