Biology subjects

Peter Ralph

Publications and source records attributed to Peter Ralph.

3 recordsLinked to original sources

bioRxiv2016

Local PCA shows how the effect of population structure differs along the genome

Population structure leads to systematic patterns in measures of mean relatedness between individuals in large genomic datasets, which are often discovered and visualized using dimension reduction techniques such as principal component analysis (PCA). Mean relatedness is an average of the relationships across locus-specific genealogical trees, which can be strongly affected on intermediate genomic scales by linked selection and other factors. We show how to use local principal components analysis to describe this meso-scale heterogeneity in patterns of relatedness, and apply the method to genomic data from three species, finding in each that the effect of population structure can vary substantially across only a few megabases. In a global human dataset, localized heterogeneity is likely explained by polymorphic chromosomal inversions. In a range-wide dataset of Medicago truncatula, factors that produce heterogeneity are shared between chromosomes, correlate with local gene density, and may be caused by linked selection, such as background selection or local adaptation. In a dataset of primarily African Drosophila melanogaster, large-scale heterogeneity across each chromosome arm is explained by known chromosomal inversions thought to be under recent selection, and after removing samples carrying inversions, remaining heterogeneity is correlated with recombination rate and gene density, again suggesting a role for linked selection. The visualization method provides a flexible new way to discover biological drivers of genetic variation, and its application to data highlights the strong effects that linked selection and chromosomal inversions can have on observed patterns of genetic variation.

Genomics↗

bioRxiv2016

Beyond clines: lineages and haplotype blocks in hybrid zones

Hybrid zones formed between recently diverged populations offer an opportunity to study the mechanisms underlying reproductive isolation and the process of speciation. Here, we use a combination of analytical theory and explicit forward simulations to show how selection against hybrid genotypes impacts patterns of introgression across genomic and geographic space. By understanding how lineages move across the hybrid zone, in a model without coalescence, we describe how clines form and how parental haplotypes are broken up during introgression. Clines form in about 1/s generations, where s is the strength of selection against hybrids, and linked clines persist over a physical scale of 1/T, where T is the age, in generations, of the hybrid zone. Locally disadvantageous alleles tend to exist as small families, whose lineages trace back to the side from which they originated at speed [Formula] dispersal distances per generation. The lengths of continuous tracts of ancestry provide an additional source of information: blocks of ancestry surrounding single-locus incompatibilities can be substantially longer than the genome-wide average block length at the same spatial location, an observation that might be used to characterize the age of hybrid zones and identify candidate targets of selection.

Genetics↗

bioRxiv2015

Independent molecular basis of convergent highland adaptation in maize

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection, and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation, and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.

Evolutionary Biology↗