scholarly journals Gene tree discordance generates patterns of diminishing convergence over time

2016 ◽  
Author(s):  
Fabio K. Mendes ◽  
Yoonsoo Hahn ◽  
Matthew W. Hahn
Keyword(s):  
Gene Tree ◽  
Primate Species ◽  
Epistatic Interactions ◽  
Genome Wide ◽  
Tree Inference ◽  
Gene Tree Discordance ◽  
Similar Solutions ◽  
Additional Explanation ◽  
Species Tree Inference ◽  
Over Time

AbstractPhenotypic convergence is an exciting outcome of adaptive evolution, occurring when species find similar solutions to the same problem. Unraveling the molecular basis of convergence provides a way to link genotype to adaptive phenotypes, but can also shed light on the extent to which evolution is repeatable and predictable. Many recent genome-wide studies have uncovered a striking pattern of diminishing convergence over time, ascribing this pattern to the presence of intramolecular epistatic interactions. Here, we consider gene tree discordance as an alternative driver of convergence levels over time. We demonstrate that gene tree discordance can produce patterns of diminishing convergence by itself, and that controlling for discordance as a cause of apparent convergence makes the pattern disappear. We also show that synonymous substitutions, where neither selection nor epistasis should be prevalent, have the same diminishing pattern of molecular convergence among closely related primate species. Finally, we demonstrate that even in situations where biological discordance is not possible, errors in species tree inference can drive these same patterns. Though intramolecular epistasis is undoubtedly affecting many proteins, our results suggest an additional explanation for this widespread pattern. These results contribute to a growing appreciation not just of the presence of gene tree discordance, but of the unpredictable effects this discordance can have on analyses of molecular evolution.

scholarly journals Gene tree correction for reconciliation and species tree inference: Complexity and algorithms

2014 ◽  
Vol 25 ◽  
pp. 51-65 ◽  
Author(s):  
Riccardo Dondi ◽  
Nadia El-Mabrouk ◽  
Krister M. Swenson
Keyword(s):  
Gene Tree ◽  
Species Tree ◽  
Tree Inference ◽  
Species Tree Inference

scholarly journals Phylogenetic conflicts, combinability, and deep phylogenomics in plants

2018 ◽  
Author(s):  
Stephen A. Smith ◽  
Nathanael Walker-Hale ◽  
Joseph F. Walker ◽  
Joseph W. Brown
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Gene Tree ◽  
Species Tree ◽  
Gene Trees ◽  
Data Filtering ◽  
Tree Inference ◽  
Tree Methods ◽  
Inference Methods ◽  
Species Tree Inference

AbstractStudies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a dataset in order to resolve recalcitrant relationships and, importantly, identify what the dataset is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error and disambiguate sources of conflict among species tree inference methods. We demonstrate these on a large phylogenomic plant dataset. Our results support the placement of Amborella as sister to the remaining extant angiosperms, Gnetales as sister to pines, and the monophyly of extant gymnosperms. Several other contentious relationships, including the resolution of relationships within the bryophytes and the eudicots, remain uncertain given the low number of supporting gene trees. To address whether concatenation of filtered genes amplified phylogenetic signal for relationships, we implemented a combinatorial heuristic to test combinability of genes. We found that nested conflicts limited the ability of data filtering methods to fully ameliorate conflicting signal amongst gene trees. These analyses confirmed that the underlying conflicting signal does not support broad concatenation of genes. Our approach provides a means of dissecting a specific dataset to address deep phylogenetic relationships while also identifying the inferential boundaries of the dataset.

scholarly journals Using all gene families vastly expands data available for phylogenomic inference in primates

2021 ◽  
Author(s):  
Megan L Smith ◽  
Dan Vanderpool ◽  
Matthew W. Hahn
Keyword(s):  
Branch Length ◽  
Gene Families ◽  
Phylogenetic Inference ◽  
Single Copy ◽  
Decomposition Methods ◽  
Species Tree ◽  
Primate Species ◽  
Tree Inference ◽  
Inference Methods ◽  
Species Tree Inference

Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs by using clustering approaches and retaining families with a single sequence from each species. However, this approach can severely limit the amount of data available by excluding larger families. Recent methodological advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several popular methods for species tree inference appear to be robust to the inclusion of paralogs, and hence could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference using genomes from 26 primate species. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data (i.e., including orthologs and paralogs). We explore several species tree inference methods, finding that across all nodes of the tree except one, identical trees are returned across nearly all datasets and methods. As in previous studies, the relationships among Platyrrhini remain contentious; however, the tree inference methods matter more than the dataset used. We also assess the effects of each dataset on branch length estimates, measures of phylogenetic uncertainty and concordance, and in detecting introgression. Our results demonstrate that using data from larger gene families drastically increases the number of genes available for phylogenetic inference and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression.

scholarly journals Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time

2016 ◽  
Vol 33 (12) ◽  
pp. 3299-3307 ◽  
Author(s):  
Fábio K. Mendes ◽  
Yoonsoo Hahn ◽  
Matthew W. Hahn
Keyword(s):  
Gene Tree ◽  
Gene Tree Discordance ◽  
Over Time

scholarly journals Gene tree correction for reconciliation and species tree inference

2012 ◽  
Vol 7 (1) ◽  
Author(s):  
Krister M Swenson ◽  
Andrea Doroftei ◽  
Nadia El-Mabrouk
Keyword(s):  
Gene Tree ◽  
Species Tree ◽  
Tree Inference ◽  
Species Tree Inference

scholarly journals Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards

2016 ◽  
Author(s):  
Mozes P.K. Blom ◽  
Jason G. Bragg ◽  
Sally Potter ◽  
Craig Moritz
Keyword(s):  
Phylogenetic Signal ◽  
Gene Tree ◽  
Phylogenetic Inference ◽  
Species Tree ◽  
Gene Trees ◽  
Tree Inference ◽  
Tree Estimation ◽  
Tree Resolution ◽  
The Impact ◽  
Species Tree Inference

AbstractAccurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should therefore examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic datasets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ~2000 exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well-supported topology based on all loci and find that a relatively small number of high-resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent-based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low-resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated in the analysis of empirical phylogenomic datasets. This will ultimately increase our confidence in species tree estimation using summary-coalescent methods and enable us to exploit genomic data for phylogenetic inference.

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