Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time

Mendes, Fábio K.; Hahn, Yoonsoo; Hahn, Matthew W.

doi:10.1093/molbev/msw197

Cited by 63 publications

(73 citation statements)

References 63 publications

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“…Though we have not explored the effect of additional taxa on improving the underlying topology, this will clearly affect inferences of convergence. Incorrect topologies—either due to error in species tree inference or biological differences in the histories among different genes—can lead to truly convergent substitutions being missed, but can also lead to many incorrect inferences of convergence (Mendes and Hahn 2016; Mendes et al. 2016).…”

Section: Discussionmentioning

confidence: 99%

The effects of increasing the number of taxa on inferences of molecular convergence

Thomas

Hahn

2017

Genome Biol Evol

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Convergent evolution provides insight into the link between phenotype and genotype. Recently, large-scale comparative studies of convergent evolution have become possible, but researchers are still trying to determine the best way to design these types of analyses. One aspect of molecular convergence studies that has not yet been investigated is how taxonomic sample size affects inferences of molecular convergence. Here we show that increased sample size decreases the amount of inferred molecular convergence associated with the three convergent transitions to a marine environment in mammals. The sampling of more taxa—both with and without the convergent phenotype—reveals that alleles associated only with marine mammals in small datasets are actually more widespread, or are not shared by all marine species. The sampling of more taxa also allows finer resolution of ancestral substitutions, revealing that they are not in fact on lineages leading to solely marine species. We revisit a previous study on marine mammals and find that only 7 of the reported 43 genes with convergent substitutions still show signs of convergence with a larger number of background species. However, four of those seven genes also showed signs of positive selection in the original analysis and may still be good candidates for adaptive convergence. Though our study is framed around the convergence of marine mammals, we expect our conclusions on taxonomic sampling are generalizable to any study of molecular convergence.

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Section: Discussionmentioning

confidence: 99%

The effects of increasing the number of taxa on inferences of molecular convergence

Thomas

Hahn

2017

Genome Biol Evol

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“…Therefore, in these cases mapping characters onto a single species tree has an elevated risk of incorrectly inferring the number of times a trait has evolved and the timing of trait changes (Avise & Robinson, ; Hahn & Nakhleh, ; Storz, ). Hemiplasy also affects inferences about the specific loci inferred to underlie trait transitions because the substitutions underlying trait transitions may occur on gene trees that are discordant with the species tree, when ILS or introgression are common (Mendes, Hahn, & Hahn, ). Therefore, genome‐wide analyses must take into account the extent and distribution of ILS and introgression if they are to accurately infer the number and timing of evolutionary changes in specific traits, and the genes underlying these changes.…”

Section: Introductionmentioning

confidence: 99%

Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance

Kostyun

Hahn

et al. 2018

Molecular Ecology

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Phylogenetic analyses of trait evolution can provide insight into the evolutionary processes that initiate and drive phenotypic diversification. However, recent phylogenomic studies have revealed extensive gene tree-species tree discordance, which can lead to incorrect inferences of trait evolution if only a single species tree is used for analysis. This phenomenon-dubbed "hemiplasy"-is particularly important to consider during analyses of character evolution in rapidly radiating groups, where discordance is widespread. Here, we generate whole-transcriptome data for a phylogenetic analysis of 14 species in the plant genus Jaltomata (the sister clade to Solanum), which has experienced rapid, recent trait evolution, including in fruit and nectar colour, and flower size and shape. Consistent with other radiations, we find evidence for rampant gene tree discordance due to incomplete lineage sorting (ILS) and to introgression events among the well-supported subclades. As both ILS and introgression increase the probability of hemiplasy, we perform several analyses that take discordance into account while identifying genes that might contribute to phenotypic evolution. Despite discordance, the history of fruit colour evolution in Jaltomata can be inferred with high confidence, and we find evidence of de novo adaptive evolution at individual genes associated with fruit colour variation. In contrast, hemiplasy appears to strongly affect inferences about floral character transitions in Jaltomata, and we identify candidate loci that could arise either from multiple lineage-specific substitutions or standing ancestral polymorphisms. Our analysis provides a generalizable example of how to manage discordance when identifying loci associated with trait evolution in a radiating lineage.

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“…Indeed, if a clade is erroneously split on a phylogeny, synapomorphies (shared derived character states) may be mistaken for parallel substitutions, and this is more likely for closely related species (Mendes et al 2016). We tested the contribution of such artefacts by performing our analyses only on high-confidence pairs of substitutions (see “Materials and Methods” section).…”

Section: Resultsmentioning

confidence: 99%

Parallel Evolution of Metazoan Mitochondrial Proteins

Klink

Bazykin

2017

Genome Biology and Evolution

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Amino acid propensities at amino acid sites change with time due to epistatic interactions or changing environment, affecting the probabilities of fixation of different amino acids. Such changes should lead to an increased rate of homoplasies (reversals, parallelisms, and convergences) at closely related species. Here, we reconstruct the phylogeny of twelve mitochondrial proteins from several thousand metazoan species, and measure the phylogenetic distances between branches at which either the same allele originated repeatedly due to homoplasies, or different alleles originated due to divergent substitutions. The mean phylogenetic distance between parallel substitutions is ∼20% lower than the mean phylogenetic distance between divergent substitutions, indicating that a variant fixed in a species is more likely to be deleterious in a more phylogenetically remote species, compared with a more closely related species. These findings are robust to artefacts of phylogenetic reconstruction or of pooling of sites from different conservation classes or functional groups, and imply that single-position fitness landscapes change at rates similar to rates of amino acid changes.

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Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time

Cited by 63 publications

References 63 publications

The effects of increasing the number of taxa on inferences of molecular convergence

The effects of increasing the number of taxa on inferences of molecular convergence

Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance

Parallel Evolution of Metazoan Mitochondrial Proteins

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