Using genomic prediction to detect microevolutionary change of a quantitative trait

Abstract

Detecting microevolutionary responses to natural selection by observing temporal changes in individual breeding values is challenging. The collection of suitable datasets can take many years and disentangling the contributions of the environment and genetics to phenotypic change is not trivial. Furthermore, pedigree-based methods of obtaining individual breeding values have known biases. Here, we apply a genomic prediction approach to estimate breeding values of adult weight in a 35-year dataset of Soay sheep ( Ovis aries) . Comparisons are made with a traditional pedigree-based approach. During the study period, adult body weight decreased, but the underlying genetic component of body weight increased, at a rate that is unlikely to be attributable to genetic drift. Thus cryptic microevolution of greater adult body weight has probably occurred. Genomic and pedigree-based approaches gave largely consistent results. Thus, using genomic prediction to study microevolution in wild populations can remove the requirement for pedigree data, potentially opening up new study systems for similar research.

Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic

“…Few other studies have thus far sought evidence for micro-evolutionary change via shifts in GEBVs ( 16), though several studies in animals have examined shifts in predicted breeding values based on pedigrees (37). A recent study showed an increase in GEBVs calculated using genomic prediction algorithms for adult weight in a 35 year data set for Soay sheep which aligned with changes in predicted breeding values (from pedigree based studies), though phenotypic body weight decreased over this time span (15). In the present study, by contrast, we used the difference between predicted GEBV (based on relatedness) and observed GEBV (based on loci associated with the trait of interest) to infer that changes in allele frequency could be attributed to selection.…”

“…Few other studies have thus far sought evidence for micro-evolutionary change via shifts in GEBVs, though several studies in animals have examined shifts in predicted breeding values based on pedigrees 19 . A recent study showed a shift in GEBVs for adult weight in a 35 year data set for Soay sheep, though phenotypic body weight decreased over this time span 20 . Genomic prediction approaches have a wide future applicability in evolutionary studies 21 .…”

“…Few other studies have thus far sought evidence for micro-evolutionary change via shifts in GEBVs, though several studies in animals have examined shifts in predicted breeding values based on pedigrees 19 . A recent study showed a shift in GEBVs for adult weight in a 35 year data set for Soay sheep, though phenotypic body weight decreased over this time span 20 . Genomic prediction approaches have a wide future applicability in evolutionary studies 21 The action of natural selection in the wild for increased health of European ash under ash dieback is good news, but whether the rate of change will be sufficient for evolutionary rescue to occur 15 , and whether its end point will be a fully resistant tree, is as yet unknown.…”

“…While the methods of quantitative genetics can show, by statistical comparison of related individuals, that additive genetic variance exists for complex traits under selection, it has often not been possible to show by these methods that response to selection is occurring (11–14). This situation has led to something of a disconnect between population genetics and quantitative genetics, which may be bridged by genome-wide molecular studies that allow the contribution to genetic variance in complex traits to be estimated across thousands of loci (5, 15, 16) – something that has only now become possible due to the reduction in cost of genome sequencing.…”

“…Consequently, much more convincing evidence for the genetic basis of evolutionary responses has been shown empirically for one or a few newly arisen loci of large effect 12,13 than for responses involving many loci of small effect.Population-level whole genome re-sequencing can be used in a strategy to detect the potentially more widespread polygenic responses to selection if two requirements are met: (1) many single nucleotide polymorphisms (SNP) are identified associated with a trait, and (2) temporal change in their frequencies under selective pressure for the trait can be shown. Genomic prediction approaches, developed for agricultural breeding, using genome-wide SNP data to predict individuals' genetic merit for a quantitative trait of interest, could enable us to meet the first requirement 14,15 . To meet the second requirement we must know genome-wide allele frequencies before and after the arrival of a new selective pressure 16 or in different age classes at a single time point 8,[17][18][19][20][21] .…”