Quantifying the risk of hemiplasy in phylogenetic inference

Guerrero, Rafael F.; Hahn, Matthew W.

doi:10.1073/pnas.1811268115

Cited by 57 publications

(87 citation statements)

References 56 publications

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“…While both datasets contain very closely related species -with very low levels of nucleotide divergence -there is still a possibility that homoplasy has occurred. In order to estimate the proportion of incongruent sites due to homoplasy in any dataset, we have developed a population genetic model of both hemiplasy and homoplasy (Guerrero and Hahn, 2018). Using estimates of the speciation times, mutation rate, and effective population sizes of the primates studied here, this model predicts that 84% of sites incongruent with the species tree are due to hemiplasy, with the other 16% due to homoplasy.…”

Section: Discussionmentioning

confidence: 99%

The perils of intralocus recombination for inferences of molecular convergence

Mendes

Livera

Hahn

2018

Preprint

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Accurate inferences of convergence require that the appropriate tree topology be used. If there is a mismatch between the tree a trait has evolved along and the tree used for analysis, then false inferences of convergence ("hemiplasy") can occur. To avoid problems of hemiplasy when there are high levels of gene tree discordance with the species tree, researchers have begun to construct tree topologies from individual loci. However, due to intralocus recombination even locus-specific trees may contain multiple topologies within them. This implies that the use of individual tree topologies discordant with the species tree can still lead to incorrect inferences about molecular convergence. Here we examine the frequency with which single exons and single protein-coding genes contain multiple underlying tree topologies, in primates and Drosophila, and quantify the effects of hemiplasy when using trees inferred from individual loci. In both clades we find that there are most often multiple diagnosable topologies within single exons and whole genes, with 91% of Drosophila protein-coding genes containing multiple topologies. Because of this underlying topological heterogeneity, even using trees inferred from individual protein-coding genes results in 25% and 38% of substitutions falsely labeled as convergent in primates and Drosophila, respectively. While constructing local trees can reduce the problem of hemiplasy, our results suggest that it will be difficult to completely avoid false inferences of convergence. We conclude by suggesting several ways forward in the analysis of convergent evolution, for both molecular and morphological characters.

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Section: Discussionmentioning

confidence: 99%

The perils of intralocus recombination for inferences of molecular convergence

Mendes

Livera

Hahn

2018

Preprint

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“…Methods that estimate phenotype-genotype associations incorporating heterogeneity across gene trees or that at least take into account differential state probabilities stemming from gene tree discordance (e.g., Guerrero & Hahn, 2018). Similarly, extensions of the MSC for quantitative traits that take into account genealogical heterogeneity represent a promising avenue for research and implementation (e.g., Mendes et al, 2018).…”

Section: Phylogenetic Inference Models and Methodsmentioning

confidence: 99%

Peer Review #2 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.1)"

Morgan¹

2019

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Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by highthroughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression.Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We Manuscript to be reviewed discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.

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“…ILS shown in Figure 1A) has been termed hemiplasy (to contrast it with homoplasy Avise and Robinson, 2008;Wake et al, 2011). This term has also been more generally applied to alleles shared by gene flow and with some authors seeing it as an alternative explanation to convergence (Hahn and Nakhleh, 2016;Mendes et al, 2018;Guerrero and Hahn, 2018). While these approaches to assess discordance between gene trees and species trees that lead to spurious inference of convergence are important, we argue that the sharing of an allele due to ILS or introgression does not invalidate the case for convergent adaptation.…”

Section: Establishing Independencementioning

confidence: 99%

“…This is conceptually similar to how a species phylogeny specifies the shared branch lengths for pairs of species back to their common ancestors and hence the degree of shared ancestry relative to the most recent common ancestor of all the samples. However, using the relatedness matrix is a somewhat different statement from the importance of species phylogeny in judging trait similarity since introgression and ILS increase the chance that alleles and traits can be discordant with a species phylogeny (Hahn and Nakhleh, 2016;Mendes et al, 2018;Guerrero and Hahn, 2018). This issue is well accommodated for by using the relatedness matrix which naturally accounts for allele sharing that is discordant with the species tree.…”

Section: Single Locus and Quantitative Trait Testsmentioning

confidence: 99%

Population genomics perspectives on convergent adaptation

Lee

Coop

2018

Preprint

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Convergent adaptation is the independent evolution of similar traits conferring a fitness advantage in two or more lineages. Cases of convergent adaptation inform our ideas about the ecological and molecular basis of adaptation. In judging the degree to which putative cases of convergent adaptation provide independent replication of the process of adaptation, it is necessary to establish the degree to which the evolutionary change is unexpected under null models and to show that selection has repeatedly, independently driven these changes. Here, we discuss the issues that arise from these questions particularly for closely-related populations, where gene flow and standing variation add additional layers of complexity. We outline a conceptual framework to guide intuition as to the extent to which evolutionary change represents the independent gain of information due to selection and show that this is a measure of how surprised we should be by convergence. Additionally, we summarize the ways population and quantitative genetics and genomics may help us address questions related to convergent adaptation, as well as open new questions and avenues of research.

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Quantifying the risk of hemiplasy in phylogenetic inference

Cited by 57 publications

References 56 publications

The perils of intralocus recombination for inferences of molecular convergence

The perils of intralocus recombination for inferences of molecular convergence

Peer Review #2 of "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (v0.1)"

Population genomics perspectives on convergent adaptation

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