Detecting adaptive convergent amino acid evolution

Abstract

In evolutionary genomics, researchers have taken an interest in identifying substitutions that subtend convergent phenotypic adaptations. This is a difficult question that requires distinguishing foreground convergent substitutions that are involved in the convergent phenotype from background convergent substitutions. Those may be linked to other adaptations, may be neutral or may be the consequence of mutational biases. Furthermore, there is no generally accepted definition of convergent substitutions. Various methods that use different definitions have been proposed in the literature, resulting in different sets of candidate foreground convergent substitutions. In this article, we first describe the processes that can generate foreground convergent substitutions in coding sequences, separating adaptive from non-adaptive processes. Second, we review methods that have been proposed to detect foreground convergent substitutions in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes—including in the presence of a change in the efficacy of selection—and on empirical alignments. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions'.

The perils of intralocus recombination for inferences of molecular convergence

“…Whole-genome comparisons have revealed high levels of molecular convergence in multiple clades [7][8][9][10][11][12][13][14][15][16]. Although a large fraction of this convergence is undoubtedly due to non-adaptive processes [17][18][19], patterns of molecular convergence hold the promise of revealing general mechanisms of protein evolution [20,21].…”

Convergent evolution in the genomics era: new insights and directions

“…R. Soc. B 374: 20190102 sites have been presented, another contribution from Rey et al [38] contrasts those methods on the basis of their theoretical bases and practical performances. They raise the concern that contrasting definitions of molecular convergence can be confusing to the field and that inferential results often cannot be compared when differing definitions were used.…”

Cytochrome c nitrite reductase from the bacterium Geobacter lovleyi represents a new NrfA subclass

“…Consistent with this, replacing the active-site arginine with a lysine (R277K) reduced the nitrite reductase activity of the G. lovleyi NrfA to levels comparable with a radical substitution (R277A). This suggests a higher fitness conferred by this substitution relative to Lys (51,52). This helps define diagnostic features of NrfA proteins of the Ca 21 -dependent and -independent subclasses.…”