Large effect loci have a prominent role in Darwin’s finch evolution

Abstract

A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits and its evolutionary relevance. Using whole-genome data of 3,958 Darwin's finches on the Galápagos Island of Daphne Major we identify six loci of large effect that explain 46% of the variation in beak size of Geospiza fortis, a key ecological trait. Allele frequency changes across 30 years at these loci affected beak morphology in two ways. An abrupt change in beak size occurred in Geospiza fortis as a result of natural selection associated with a drought, and a more gradual change occurred in G. scandens as a result of introgressive hybridization. This study demonstrates how large effect loci are a major contributor to the genetic architecture of rapid diversification during adaptive radiations.

Where and when local adaptation happens: lessons from the European barn owl (Tyto alba)

“…These alleles were then sorted through space by local adaptation, with different environments (biotic and abiotic) acting as a filter on deleterious and/or less advantageous alleles. This whole process has been reported in species as diverse as Arabidopsis thaliana and Drosophila melanogaster (Barrett and Schluter 2008), birds (Enbody et al 2022) or in humans, following the ‘Out-of-Africa’ migration (50’000 - 70’000 years ago) (Haber et al 2019; Rees et al 2020). The latter example has been corroborated by de Filippo et al (2016) as they highlighted that a change in selective regime following the ‘Out-of-Africa’ migration and consequently positive selection of standing variation in some populations was the most likely process explaining the observed genetic diversity.…”

A single nucleotide variant in the PPARγ-homologEip75Baffects fecundity inDrosophila

“…How individual nucleotide variants contribute to complex, quantitative traits is a largely unresolved question in evolutionary genetics. While it is clear that quantitative traits are highly polygenic, with many loci of small effect contributing to trait variation (the ‘infinitesimal model’; Rockman 2012; Yang et al 2015; Boyle et al 2017; Yengo et al 2022; Barton 2022), surprisingly little is known about the effect sizes and properties of individual variants (Orr and Coyne 1992; Seehausen et al 2014; Enbody et al 2022). A small, but growing number of functional studies are beginning to reveal that natural variants can make large contributions to variation in fitness-related traits (Schmidt et al 2008; Durmaz et al 2019; Mokashi et al 2021; Schluter et al 2021; Enbody et al 2022).…”

“…While it is clear that quantitative traits are highly polygenic, with many loci of small effect contributing to trait variation (the ‘infinitesimal model’; Rockman 2012; Yang et al 2015; Boyle et al 2017; Yengo et al 2022; Barton 2022), surprisingly little is known about the effect sizes and properties of individual variants (Orr and Coyne 1992; Seehausen et al 2014; Enbody et al 2022). A small, but growing number of functional studies are beginning to reveal that natural variants can make large contributions to variation in fitness-related traits (Schmidt et al 2008; Durmaz et al 2019; Mokashi et al 2021; Schluter et al 2021; Enbody et al 2022). Our study provides a rare example of functional characterization of an individual naturally segregating SNP, and demonstrates that it has causal pleiotropic effects on two complex fitness traits, viability and fecundity.…”

A Single Nucleotide Variant in the PPARγ-homolog Eip75B Affects Fecundity in Drosophila

“…How individual nucleotide variants contribute to complex, quantitative traits is a largely unresolved question in evolutionary genetics. While it is clear that quantitative traits are highly polygenic, with many loci of small effect contributing to trait variation (the “infinitesimal model”; Rockman 2012 ; Yang et al 2015 ; Boyle et al 2017 ; Barton 2022 ; Yengo et al 2022 ), surprisingly little is known about the effect sizes and properties of individual variants ( Orr and Coyne 1992 ; Seehausen et al 2014 ; Enbody et al 2022 ). A small, but growing number of studies are beginning to reveal that natural variants can make large contributions to variation in fitness-related traits ( Schmidt et al 2008 ; Durmaz et al 2019 ; Mokashi et al 2021 ; Schluter et al 2021 ; Enbody et al 2022 ).…”

“…While it is clear that quantitative traits are highly polygenic, with many loci of small effect contributing to trait variation (the “infinitesimal model”; Rockman 2012 ; Yang et al 2015 ; Boyle et al 2017 ; Barton 2022 ; Yengo et al 2022 ), surprisingly little is known about the effect sizes and properties of individual variants ( Orr and Coyne 1992 ; Seehausen et al 2014 ; Enbody et al 2022 ). A small, but growing number of studies are beginning to reveal that natural variants can make large contributions to variation in fitness-related traits ( Schmidt et al 2008 ; Durmaz et al 2019 ; Mokashi et al 2021 ; Schluter et al 2021 ; Enbody et al 2022 ). For example, functional tests of two closely linked SNPs in foxo , a transcription factor of the insulin/insulin-like growth factor pathway, revealed that this haplotype affects viability, several size-related traits and starvation resistance in the fruit fly; notably, polymorphism at this SNP explained 14% of the total latitudinal cline for wing area ( Durmaz et al 2019 ; Betancourt et al 2021 ).…”