A need for standardized reporting of introgression: Insights from studies across eukaryotes

Dagilis, Andrius J.; Peede, David; Coughlan, Jenn M.; Jofre, Gaston I.; D'Agostino, Emmanuel R. R.; Mavengere, Heidi; Tate, Alexander D.; Matute, Daniel R.

doi:10.1002/evl3.294

Cited by 21 publications

(24 citation statements)

References 98 publications

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“…Therefore, higher amounts of ILS lead to broad increases in the occurrence of hemiplasy across multiple possible incongruent trait patterns (Guerrero and Hahn 2018; Mendes et al 2018). Introgression is a process of historical hybridization and back-crossing that, while widespread in modern phylogenomic datasets (Mallet et al 2016; Taylor and Larson 2019; Dagilis et al 2022), is often more limited to specific pairs of taxa. In particular, post-speciation introgression between non-sister lineages leads to an excess of gene trees grouping those lineages as sister (Reich et al 2009; Green et al 2010; Durand et al 2011; Patterson et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic comparative methods: accurate evolutionary inferences in the presence of gene tree discordance

Hibbins

Breithaupt

Hahn

2022

Preprint

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Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for inferences of the tempo and mode of trait evolution across species while accounting for their common ancestry. These analyses typically assume a single, bifurcating phylogenetic tree that describes the shared history among species. However, modern phylogenomic analyses have shown that genomes are often composed of a mosaic of different histories that can disagree both with the species tree and with each other-so-called discordant gene trees. These gene trees describe shared histories that are not captured by the species tree, and therefore that are unaccounted for in classic comparative approaches. The application of standard phylogenetic comparative methods to species histories containing discordance leads to incorrect inferences about the timing, direction, and rate of evolution. Here, we develop two approaches for incorporating gene tree histories into comparative methods: one involves constructing a fuller phylogenetic variance-covariance matrix that includes relationships not found in the species tree, and another that applies Felsenstein's pruning algorithm over a set of gene trees to calculate trait histories and likelihoods. Both approaches are agnostic to the biological causes of gene tree discordance, which may include incomplete lineage sorting and introgression. Using simulation, we demonstrate that our new approaches generate much more accurate estimates of tree-wide rates of trait evolution than standard methods. We apply our methods to two clades of the wild tomato genus Solanum with varying rates of discordance, demonstrating the contribution of gene tree discordance to variation in a set of floral traits and the ability of our approaches to provide more accurate inferences. Our new approaches have the potential to be applied to a broad range of classic inference problems in phylogenetics, including ancestral state reconstruction and the inference of lineage-specific rate shifts.

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Section: Introductionmentioning

confidence: 99%

Phylogenomic comparative methods: accurate evolutionary inferences in the presence of gene tree discordance

Hibbins

Breithaupt

Hahn

2022

Preprint

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“…Introgression, the process of hybridization and repeated back-crossing between previously isolated lineages, occurs frequently across the tree of life and is a common feature of modern phylogenomic datasets (Mallet et al 2016, Taylor and Larson 2019, Dagilis et al 2021). From a phylogenetic perspective, histories of introgression are not consistent with a strictly bifurcating phylogeny and are therefore often represented using phylogenetic networks (Huson and Bryant 2006, Huson et al 2010, Solis-Lemus and Ane 2016, Wen et al 2018, Wen and Nakhleh 2018).…”

Section: Introductionmentioning

confidence: 99%

Distinguishing between histories of speciation and introgression using genomic data

Hibbins

Hahn

2022

Preprint

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Introgression creates complex, non-bifurcating relationships among species. At individual loci and across the genome, both introgression and incomplete lineage sorting interact to produce a wide range of different gene tree topologies. These processes can obscure the history of speciation among lineages, and, as a result, identifying the history of speciation vs. introgression remains a challenge. Here, we use theory and simulation to investigate how introgression can mislead multiple approaches to species tree inference. We find that arbitrarily low amounts of introgression can mislead both gene tree methods and parsimony methods if the rate of incomplete lineage sorting is sufficiently high. We also show that an alternative approach based on minimum gene tree node heights is inconsistent and depends on the rate of introgression across the genome. To distinguish between speciation and introgression, we apply supervised machine learning models to a set of features that can easily be obtained from phylogenomic datasets. We find that multiple of these models are highly accurate in classifying the species history in simulated datasets. We also show that, if the histories of speciation and introgression can be identified, PhyloNet will return highly accurate estimates of the contribution of each history to the data (i.e. edge weights). Overall, our results highlight the promise of supervised machine learning as a potentially powerful complement to phylogenetic methods in the analysis of introgression from genomic data.

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“…The most popular statistical methods for making genome-wide inferences about introgression exploit asymmetries in observed site patterns (Dagilis et al, 2022). Statistical tests for site pattern asymmetries count the number of segregating sites that have a configuration of shared derived and ancestral alleles which are informative of introgression in a set of taxa.…”

Section: Introductionmentioning

confidence: 99%

The Utility of Ancestral and Derived Allele Sharing for Genome-Wide Inferences of Introgression

Peede

Vecchyo

Huerta‐Sánchez

2022

Preprint

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The past decade has ushered in a resurgence of studies highlighting the importance of introgression throughout the Tree of Life. Several methods exist for detecting and quantifying introgression on a genomic scale, yet the majority of these methods primarily utilize signals of derived allele sharing between donor and recipient populations. In this study, we exploit the fact that introgression will not only result in derived allele sharing but also the reintroduction of ancestral alleles to derive new estimators of the admixture proportion. Using coalescent simulations, we assess the performance of our new methods and the methods proposed in Lopez Fang et al. 2022 to assess the utility of incorporating shared ancestral variation into genome-wide inferences of introgression. Using coalescent theory, simulations, and applying our methods to human and canid data, we find that methods incorporating ancestral allele sharing are comparable to their derived allele sharing counterparts, in turn providing researchers with the opportunity to utilize more of the genomic signature of introgression.

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A need for standardized reporting of introgression: Insights from studies across eukaryotes

Cited by 21 publications

References 98 publications

Phylogenomic comparative methods: accurate evolutionary inferences in the presence of gene tree discordance

Phylogenomic comparative methods: accurate evolutionary inferences in the presence of gene tree discordance

Distinguishing between histories of speciation and introgression using genomic data

The Utility of Ancestral and Derived Allele Sharing for Genome-Wide Inferences of Introgression

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