The genomics of adaptation in birds

Campagna, Leonardo; Toews, David P. L.

doi:10.1016/j.cub.2022.07.076

Cited by 18 publications

(11 citation statements)

References 123 publications

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“…These results represent a striking deviation from a solely polygenic model involving many loci of small effect assumed to underlie most phenotypic traits (Rockman 2012; Barton 2022; Campagna and Toews 2022). However, in wild populations, an increasing number of studies show that large effect loci (Shapiro et al 2004; Chan et al 2010; Barrett et al 2019; Han et al 2020; Schluter and Rieseberg 2022) play a more important role in maintaining phenotypic variation in natural populations than anticipated from GWAS in humans (Manolio et al 2009) and artificial selection data (Goddard et al 2016).…”

Section: Discussionmentioning

confidence: 79%

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

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Sendell‐Price

Sprehn

et al. 2022

Preprint

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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.

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Section: Discussionmentioning

confidence: 79%

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

Enbody

Sendell‐Price

Sprehn

et al. 2022

Preprint

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“…Although genotype-phenotype associations have most commonly involved SNPs (Campagna & Toews, 2022), there are also examples of SVs which mediate traits in non-model birds. These studies show an improved understanding of the genetic bases of phenotypes when SVs, which involve a larger portion of the genome, are included (e.g.…”

Section: S Vs/phenot Ype a Sso Ciati On S In Non -Model B Irdsmentioning

confidence: 99%

How structural variants shape avian phenotypes: Lessons from model systems

Recuerda,

Campagna

2024

Molecular Ecology

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Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although recent advances in long‐read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify some general patterns in SV type, length and their associated traits. We found that most of the avian SVs so far identified are short indels in chickens, which are frequently associated with changes in body weight and plumage colouration. Overall, we found that relatively short SVs are more frequently detected, likely due to a combination of their prevalence compared to large SVs, and a detection bias, stemming primarily from the widespread use of short‐read sequencing and associated analytical methods. SVs most commonly involve non‐coding regions, especially introns, and when patterns of inheritance were reported, SVs associated primarily with dominant discrete traits. We summarise several examples of phenotypic convergence across different species, mediated by different SVs in the same or different genes and different types of changes in the same gene that can lead to various phenotypes. Complex rearrangements and supergenes, which can simultaneously affect and link several genes, tend to have pleiotropic phenotypic effects. Additionally, SVs commonly co‐occur with single‐nucleotide polymorphisms, highlighting the need to consider all types of genetic changes to understand the basis of phenotypic traits. We end by summarising expectations for when long‐read technologies become commonly implemented in non‐model birds, likely leading to an increase in SV discovery and characterisation. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years.

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“…Research on the mechanisms that shape and maintain biological diversity is one of the hot topics in evolutionary biology, with non-model organisms progressively improving our understanding of the molecular basis of phenotypic traits 1 . Among other systems 2 , 3 , research on birds has provided crucial insights into the mechanisms underlying phenotypic variation as well as the molecular basis of adaptation 4 . In particular, feather color has attracted much attention because of its importance in mate choice and speciation, with genes identified that function in melanin pigmentation 5 and in carotenoid conversion from yellow to red feather color among species 6 and between the sexes 7 .…”

Section: Introductionmentioning

confidence: 99%

A genomic basis of vocal rhythm in birds

Sebastianelli,

Lukhele,

Secomandi

et al. 2024

Nat Commun

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Vocal rhythm plays a fundamental role in sexual selection and species recognition in birds, but little is known of its genetic basis due to the confounding effect of vocal learning in model systems. Uncovering its genetic basis could facilitate identifying genes potentially important in speciation. Here we investigate the genomic underpinnings of rhythm in vocal non-learning Pogoniulus tinkerbirds using 135 individual whole genomes distributed across a southern African hybrid zone. We find rhythm speed is associated with two genes that are also known to affect human speech, Neurexin-1 and Coenzyme Q8A. Models leveraging ancestry reveal these candidate loci also impact rhythmic stability, a trait linked with motor performance which is an indicator of quality. Character displacement in rhythmic stability suggests possible reinforcement against hybridization, supported by evidence of asymmetric assortative mating in the species producing faster, more stable rhythms. Because rhythm is omnipresent in animal communication, candidate genes identified here may shape vocal rhythm across birds and other vertebrates.

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The genomics of adaptation in birds

Cited by 18 publications

References 123 publications

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

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

How structural variants shape avian phenotypes: Lessons from model systems

A genomic basis of vocal rhythm in birds

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