Abstract
Migratory traits in birds have been shown to have a strong heritable component and several candidate genes have been suggested to control these migratory traits. To investigate if the genetic makeup of one or a set of these candidate genes can be used to identify a general pattern between migratory and non-migratory birds, we extracted genomic sequence data for 25 hypothesised candidate genes for migration from 70 available genomes across all orders of Aves and characterised sequence divergence between migratory and non-migratory phenotypes. When examining each gene separately across all species, we did not identify any genetic variants in candidate genes that distinguished migrants from non-migrants; any resulting pattern was driven by the phylogenetic signal. This was true for each gene analysed independently, but also for concatenated sequence alignments of all candidate genes combined. We also attempted to distinguish between migrant and non-migrants using structural features at four candidate genes that have previously been reported to show associated with migratory behaviour but did not pick up a signal for migratory phenotype here either. Finally, a screen for dN/dS ratio across all focal candidate genes to probe for putative features of selection did not uncover a pattern, though this might not be expected given the broad phylogenetic scale used here. Our study demonstrates the potential of public genomic data to test for general patterns of migratory gene candidates in a cross-species comparative context, and raise questions on the applicability of candidate gene approaches in a macro-evolutionary context to understand the genetic architecture of migratory behaviour.
Highlights
Bird migration is one of the most fascinating and well-studied behaviours among birds, including work on the physiological and morphological adaptations required for successful migration and ecological correlates of this behaviour
In order to make an attempt to see if variance within on candidate gene could be higher/lower in a specific migratory phenotype, we focused on CLOCK gene polymorphism, the only candidate gene with a sufficiently high number of individual sequence data available for several species (n = 10), including both migratory (n = 8) and resident (n = 2) species
The intra-specific analysis focusing on individual variability of CLOCK gene polymorphism shows a tendency for higher variability in migratory species (Fig. S4); given that only two non-migratory species were
Summary
Bird migration is one of the most fascinating and well-studied behaviours among birds, including work on the physiological and morphological adaptations required for successful migration and ecological correlates of this behaviour. Lockwood et al 1998; Fuchs et al 2014) Given this common set of features among migratory birds and demonstrations of both their heritability and potentially shared genetic basis (e.g. the aforementioned involvement of CLOCK and ADCYAP1 across species), it has been postulated that there may be a shared set of genes for migration among birds (Berthold 1999). We compare patterns of evolutionary divergence of each candidate gene using three different approaches: (1) comparing observed topologies for candidate genes to trees built using phylogenetic relationships with and without distinguishing migratory species from non-migratory species; (2) performing a gene-wide and branch-specific dN/dS analysis to identify if selective pressures on these candidate genes play a role related to migration; and (3) focussing on structural features that previous studies have shown to correlate with migratory behaviour Selective pressures on those candidate genes with a clear role in shaping the focal phenotype should be picked up in lineages with migratory species and linear models would show strong associations between genetic variation at structural features and predictors of migratory phenotype
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