A genome‐wide investigation of adaptive signatures in protein‐coding genes related to tool behaviour in New Caledonian and Hawaiian crows

Dussex, Nicolás; Kutschera, Verena E.; Wiberg, R. Axel W.; Parker, Darren J.; Hunt, Gavin R.; Gray, Russell D.; Rutherford, Kim; Abe, Hideaki; Fleischer, Robert C.; Ritchie, Michael G.; Rutz, Christian; Wolf, Jochen B. W.; Gemmell, Neil J.

doi:10.1111/mec.15775

Cited by 5 publications

(3 citation statements)

References 105 publications

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“…Parallel adaptation for traits through different candidate genes has been reported across vertebrates (Langin et al., 2015; Milner et al., 1999; Walsh et al., 2019). Overall, our findings add to growing evidence of immunity and head/bill and body size as ecologically important traits for adaptive divergence and speciation (immune; Davies et al., 2021; Hughes & Yeager, 1998; Jarvi et al., 2001, and bill, Badyaev et al., 2008; Bosse et al., 2017; Dussex et al., 2021; Grant, 1968; Lundregan et al., 2018). Small numbers of individuals sampled per population, as used here, may lead to unrepresentative calculation of population‐based statistics, especially between the Tawny pipit and Berthelot's pipit.…”

Section: Discussionsupporting

confidence: 76%

Genomic landscapes of divergence among island bird populations: Evidence of parallel adaptation but at different loci?

Martin,

Sheppard,

Ali

et al. 2024

Molecular Ecology

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When populations colonise new environments, they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole‐genome resequencing (>22× coverage) in Berthelot's pipit (Anthus berthelotii), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. First, we quantify how genomic divergence accumulates across the speciation continuum, that is, among Berthelot's pipit populations, between sub species across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (Anthus campestris). Across these colonisation timeframes (2.1 million–ca. 8000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non‐neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism and immune defence.

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Section: Discussionsupporting

confidence: 76%

Genomic landscapes of divergence among island bird populations: Evidence of parallel adaptation but at different loci?

Martin,

Sheppard,

Ali

et al. 2024

Molecular Ecology

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“…Understanding heritability and genomic evolution across organisms [188] to investigate genes related to tool use in corvids [189] Transcriptomics Study of all ribonucleic acid RNA in a cell Detecting genes and defining regulatory pathways underpinning trait expression [190] aggressive host responses to cowbirds [177,191,192] Epigenomics Study of epigenetic processes in the genome, such as methylation and altered expression rates.…”

Section: Comparisons Of the Genomic Features Of Organismsmentioning

confidence: 99%

Beyond genes-for-behaviour: the potential for genomics to resolve questions in avian brood parasitism

Rönkä¹,

Eroukhmanoff²,

Kulmuni³

et al. 2022

Preprint

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Brood parasite-host interactions are among the most easily observable and amenable natural laboratories of antagonistic coevolution, and as such have intrigued evolutionary biologists for decades. It is therefore surprising they have not been at the forefront of genomic studies on evolutionary adaptation. Here we review state-of-the-art molecular methods in studying avian brood parasitism, a model system in behavioural ecology. We highlight outstanding questions to bring examples of how genomic tools are not merely about ‘finding a gene for behaviour’, but can be used to study the causes and mechanisms of (co)evolutionary adaptation. In doing so, we promote behavioural and molecular ecologists to integrate Tinbergen’s questions into a collaborative, coherent science aiming to solve the mysteries of nature and apply current methodology into other model systems in behavioural ecology.

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“…As a final example of the use of corvids as animal models, behavioral and cellular correlates of aging have been examined in the context of telomere length (Salomons et al, 2009 ; Grasman et al, 2011 ; Boonekamp et al, 2014 ). All of these categories of study are further enabled by the advances in the genomics and transcriptomics of corvids (Poelstra et al, 2015 ; Morinha et al, 2017 ; Dussex et al, 2021 ).…”

Section: Alternative Avian Models For Research In Developmentmentioning

confidence: 99%

Beyond the Chicken: Alternative Avian Models for Developmental Physiological Research

Flores-Santin

Burggren

2021

Front. Physiol.

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Biomedical research focusing on physiological, morphological, behavioral, and other aspects of development has long depended upon the chicken (Gallus gallus domesticus) as a key animal model that is presumed to be typical of birds and generally applicable to mammals. Yet, the modern chicken in its many forms is the result of artificial selection more intense than almost any other domesticated animal. A consequence of great variation in genotype and phenotype is that some breeds have inherent aberrant physiological and morphological traits that may show up relatively early in development (e.g., hypertension, hyperglycemia, and limb defects in the broiler chickens). While such traits can be useful as models of specific diseases, this high degree of specialization can color general experimental results and affect their translational value. Against this background, in this review we first consider the characteristics that make an animal model attractive for developmental research (e.g., accessibility, ease of rearing, size, fecundity, development rates, genetic variation, etc.). We then explore opportunities presented by the embryo to adult continuum of alternative bird models, including quail, ratites, songbirds, birds of prey, and corvids. We conclude by indicating that expanding developmental studies beyond the chicken model to include additional avian groups will both validate the chicken model as well as potentially identify even more suitable avian models for answering questions applicable to both basic biology and the human condition.

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A genome‐wide investigation of adaptive signatures in protein‐coding genes related to tool behaviour in New Caledonian and Hawaiian crows

Cited by 5 publications

References 105 publications

Genomic landscapes of divergence among island bird populations: Evidence of parallel adaptation but at different loci?

Genomic landscapes of divergence among island bird populations: Evidence of parallel adaptation but at different loci?

Beyond genes-for-behaviour: the potential for genomics to resolve questions in avian brood parasitism

Beyond the Chicken: Alternative Avian Models for Developmental Physiological Research

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