Avian phenotypic convergence is subject to low genetic constraints based on genomic evidence

Yu-Chi Chen,Wen-Sui Lo,Chih-Ming Hung,Hao-Chih Kuo

doi:10.1186/s12862-020-01711-7

Abstract

BackgroundPhenotypic convergence between distinct species provides an opportunity to examine the predictability of genetic evolution. Unrelated species sharing genetic underpinnings for phenotypic convergence suggests strong genetic constraints, and thus high predictability of evolution. However, there is no clear big picture of the genomic constraints on convergent evolution. Genome-based phylogenies have confirmed many cases of phenotypic convergence in birds, making them a good system for examining genetic constraints in phenotypic convergence. In this study, we used hierarchical genomic approaches to estimate genetic constraints in three convergent avian traits: nocturnality, raptorial behavior and foot-propelled diving.ResultsPhylogeny-based hypothesis tests and positive selection tests were applied to compare 16 avian genomes, representing 14 orders, and identify genes with strong convergence signals. We found 43 adaptively convergent genes (ACGs) associated with the three phenotypic convergence cases and assessed genetic constraints in all three cases, from (amino acid) site mutations to genetic pathways. We found that the avian orders shared few site mutations in the ACGs that contributed to the convergent phenotypes, and that these ACGs were not enriched in any genetic pathways. In addition, different pairs of orders with convergent foot-propelled diving or raptorial behaviors shared few ACGs. We also found that closely related orders that shared foot-propelled diving behavior did not share more ACGs than did distinct orders, suggesting that convergence among these orders could not be explained by their initial genomic backgrounds.ConclusionsOur analyses of three avian convergence events suggest low constraints for phenotypic convergence across multiple genetic levels, implying that genetic evolution is unpredictable at the phylogenetic level of avian order. Ours is one of first studies to apply hierarchical genomic examination to multiple avian convergent cases to assess the genetic constraints in life history trait evolution.

Highlights

Phenotypic convergence between distinct species provides an opportunity to examine the predict‐ ability of genetic evolution
We developed a two-step approach to identify “adaptively convergent genes (ACGs)” that might contribute to the convergent traits among the focal taxa
For the sequence-convergent genes, positive selection signals were detected in 24 genes for nocturnal birds, 13 for foot-propelled diving birds and 6 for diurnal raptors; we considered these ACGs contributing to the focal phenotypic convergence because they had convergent sequences and were under positive selection in the convergent taxa (Fig. 2 and Additional file 1: Table S1)

Summary

Introduction

Phenotypic convergence between distinct species provides an opportunity to examine the predict‐ ability of genetic evolution. Stephen Jay Gould argued that, if the tape of life could be replayed, the outcome would be different every time [1] This suggests that evolution is unrepeatable, but cases. Authors argue that different species may find the same genetic solutions in response to similar environmental pressures, causing adaptive convergence [10, 11]. If this is the case, another question is whether genetic convergence tends to occur at the level of (nucleotide or amino acid) site mutations, individual genes or genetic pathways

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