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Convergent evolution and predictability of gene copy numbers associated with diets in mammals

Kitano, Jun1

Published Dec 06, 2023; Updated Oct 17, 2024 on Dryad. https://doi.org/10.5061/dryad.q2bvq83r2

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Dec 06, 2023 version files 2.75 MB
Oct 17, 2024 version files 2.76 MB

Abstract

Convergent evolution, the evolution of the same or similar phenotypes in phylogenetically independent lineages, is a widespread phenomenon in nature. If the genetic basis for convergent evolution is predictable to some extent, it may be possible to infer organismic phenotypes and adaptability based on genome sequence data. While repeated amino acid changes have been studied in association with convergent evolution, relatively little is known about the potential contribution of repeated gene copy number changes. In this study, we explore whether certain gene copy number changes are linked to diet shifts in mammals and assess if trophic ecology can be inferred from the copy numbers of a specific set of genes. Using 86 mammalian genome sequences, we identified several genes with higher copy numbers in herbivores, carnivores, and omnivores, even after phylogenetic corrections. We were able to confirm previous findings on genes such as amylase, olfactory receptor, and xenobiotic metabolism genes, and identify novel genes whose copy numbers correlate with dietary patterns. For example, omnivores exhibited higher copy numbers of genes encoding gene expression regulators. We also established a discriminant function based on the copy numbers of 13 genes that can help predict trophic ecology based on genome sequence data. These findings highlight a possible association between convergent evolution and repeated copy number changes in specific genes, suggesting the potential to develop a method for predicting animal ecology and adaptability from genome sequence data.