Complexities of recapitulating polygenic effects in natural populations: replication of genetic effects on wing shape in artificially selected and wild-caught populations of Drosophila melanogaster

Abstract

Identifying the genetic architecture of complex traits is important to many geneticists, including those interested in human disease, plant and animal breeding, and evolutionary genetics. Advances in sequencing technology and statistical methods for genome-wide association studies (GWAS) have allowed for the identification of more variants with smaller effect sizes, however, many of these identified polymorphisms fail to be replicated in subsequent studies. In addition to sampling variation, this failure to replicate reflects the complexities introduced by factors including environmental variation, genetic background, and differences in allele frequencies among populations. Using Drosophila melanogaster wing shape, we ask if we can replicate allelic effects of polymorphisms first identified in a GWAS (Pitchers et al. 2019) in three genes: dachsous (ds), extra-macrochaete (emc) and neuralized (neur), using artificial selection in the lab, and bulk segregant mapping in natural populations. We demonstrate that multivariate wing shape changes associated with these genes are aligned with major axes of phenotypic and genetic variation in natural populations. Following seven generations of artificial selection along the ds shape change vector, we observe genetic differentiation of variants in ds and genomic regions containing other genes in the hippo signaling pathway. This suggests a shared direction of effects within a developmental network. We also performed artificial selection with the emc shape change vector, which is not a part of the hippo signaling network, but showed a largely shared direction of effects. The response to selection along the emc vector was similar to that of ds, suggesting that the available genetic diversity of a population, summarized by the genetic (co)variance matrix (G), influenced alleles captured by selection. Despite the success with artificial selection, bulk segregant analysis using natural populations did not detect these same variants, likely due to the contribution of environmental variation and low minor allele frequencies, coupled with small effect sizes of the contributing variants.

Polygenic architecture of adaptation to a high-altitude environment forDrosophila melanogasterwing shape and size

“…Alternatively, it is possible that these effect vectors do not estimate directions of effects well, and further titrating the strength of knockdowns may help to obtain better estimates. It is also possible that the RNAi knockdown does not correlate with the segregating allelic effect of the candidate genes, although previous studies have demonstrated correlation between segregating polymorphisms and genetic knockdown effects for wing shape (Pelletier et al, 2023; Pitchers et al, 2019). Quantitative complementation mapping experiments identified two regions that may be related to shape change in the same direction as the altitudinal effect vector (Figure 7).…”

“…For example, the Hippo developmental network is best known for its role in regulation of organ size, including the size of Drosophila wings. Variants in genes in the hippo signaling pathway influence wing shape variation, with correlated phenotypic effects (Pelletier et al, 2023; Pitchers et al, 2019). Interestingly, allele frequency changes across multiple hippo signaling loci following artificial selection for wing shape changes did not result in substantial wing size change (Pelletier et al, 2023).…”

“…Variants in genes in the hippo signaling pathway influence wing shape variation, with correlated phenotypic effects (Pelletier et al, 2023; Pitchers et al, 2019). Interestingly, allele frequency changes across multiple hippo signaling loci following artificial selection for wing shape changes did not result in substantial wing size change (Pelletier et al, 2023). In this study, we also see evidence for independent genetic bases of wing size and wing shape change (Figures 3,4).…”

Utilizing developmental dynamics for evolutionary prediction and control

“…This redundancy can explain why genetic changes underlying parallel evolution often fail to be replicated (e.g., ref. 41 ), since multiple changes at the genetic level can explain the same phenotypic adaptations.…”