scholarly journals Quantifying the risk of hemiplasy in phylogenetic inference

2018 ◽  
Author(s):  
Rafael F. Guerrero ◽  
Matthew W. Hahn
Keyword(s):  
Risk Factor ◽  
Convergent Evolution ◽  
Phylogenetic Inference ◽  
Species Tree ◽  
New Method ◽  
Gene Trees ◽  
Arbitrary Length ◽  
Wide Range

AbstractConvergent evolution is often inferred when a trait is incongruent with the species tree. However, trait incongruence can also arise from changes that occur on discordant gene trees, a process referred to as hemiplasy. Hemiplasy is rarely taken into account in studies of convergent evolution, despite the fact that phylogenomic studies have revealed rampant discordance. Here, we study the relative probabilities of homoplasy (including convergence and reversal) and hemiplasy for an incongruent trait. We derive expressions for the probabilities of the two events, showing that they depend on many of the same parameters. We find that hemiplasy is as likely— or more likely—than homoplasy for a wide range of conditions, even when levels of discordance are low. We also present a new method to calculate the ratio of these two probabilities (the “hemiplasy risk factor”) along the branches of a phylogeny of arbitrary length. Such calculations can be applied to any tree in order to identify when and where incongruent traits may be more likely to be due to hemiplasy than homoplasy.

scholarly journals Quantifying the risk of hemiplasy in phylogenetic inference

2018 ◽  
Vol 115 (50) ◽  
pp. 12787-12792 ◽  
Author(s):  
Rafael F. Guerrero ◽  
Matthew W. Hahn
Keyword(s):  
Risk Factor ◽  
Convergent Evolution ◽  
Phylogenetic Inference ◽  
Species Tree ◽  
Character State ◽  
Gene Trees ◽  
Arbitrary Length ◽  
Wide Range

Convergent evolution—the appearance of the same character state in apparently unrelated organisms—is often inferred when a trait is incongruent with the species tree. However, trait incongruence can also arise from changes that occur on discordant gene trees, a process referred to as hemiplasy. Hemiplasy is rarely taken into account in studies of convergent evolution, despite the fact that phylogenomic studies have revealed rampant discordance. Here, we study the relative probabilities of homoplasy (including convergence and reversal) and hemiplasy for an incongruent trait. We derive expressions for the probabilities of the two events, showing that they depend on many of the same parameters. We find that hemiplasy is as likely—or more likely—than homoplasy for a wide range of conditions, even when levels of discordance are low. We also present a method to calculate the ratio of these two probabilities (the “hemiplasy risk factor”) along the branches of a phylogeny of arbitrary length. Such calculations can be applied to any tree to identify when and where incongruent traits may be due to hemiplasy.

scholarly journals Revisiting the phylogeny of Zoanthidea (Cnidaria: Anthozoa): staggered alignment of hypervariable sequences improves species tree inference

2017 ◽  
Author(s):  
Timothy D. Swain
Keyword(s):  
Sequence Alignment ◽  
Language Translation ◽  
Phylogenetic Inference ◽  
Species Tree ◽  
Gene Trees ◽  
Species Discovery ◽  
Conserved Genes ◽  
Tree Inference ◽  
Data Content ◽  
Conserved Gene

AbstractThe recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea.ResumenSpanish language translation by Lisbeth O. Swain, DePaul University, Chicago, Illinois, 60604, USA.Aunque la proliferación reciente y acelerada en la identificación de taxones en Zoanthidea ha sido acompañada por una propagación paralela de los árboles de genes como una herramienta en el descubrimiento de especies, no hay una correspondencia en cuanto a la ampliación de nuestro conocimiento en filogenia. Esta disparidad, es causada por la competencia entre la capacidad de los alineamientos de secuencia del ácido desoxirribonucleico (ADN) automatizados y la información contenida en los datos de genes que se aplican a los métodos de inferencia filogenética en este grupo de Zoanthidea. Las regiones o segmentos de genes conservados son fácilmente alineados dentro del orden; sin embargo, producen árboles de genes con resultados paupérrimos; además, aunque estas regiones hipervariables de genes o segmentos contienen las señas evolutivas necesarias para apoyar la construcción robusta y completa de árboles filogenéticos, estos genes producen alineamientos de secuencia abrumadores. Los alineamientos escalonados de secuencias son una forma de alineamientos informados por la filogenia y compuestos de un mosaico de regiones locales y universales que permiten que inferencias filogenéticas sean aplicadas a todos los nucleótidos de regiones hipervariables y de genes o segmentos conservados. Las comparaciones entre especies de árboles filogenéticos quese infirieron de los datos de alineamientos escalonados y los datos hipervariables excluidos (alineamiento estandarizado), demuestran un mejoramiento en la confiabilidad y un mayor acuerdo tipológico con respecto a otras fuentes que contienen árboles filogenéticos hechos de datos más completos. Esta nueva forma escalonada de filogenia es una de los más compresibles hasta la fecha (en términos de taxones y datos) y que pueden servir como una herramienta de amplificación para probar la hipótesis evolutiva de Zoanthidea.

scholarly journals The Influence of Model Violation on Phylogenetic Inference: A Simulation Study

2021 ◽  
Author(s):  
Suha Naser-Khdour ◽  
Rob Lanfear ◽  
Bui Quang Minh
Keyword(s):  
Maximum Likelihood ◽  
Simulation Study ◽  
Convergent Evolution ◽  
Real Data ◽  
Phylogenetic Inference ◽  
Likelihood Inference ◽  
Simulation Studies ◽  
Worst Case ◽  
Wide Range

Phylogenetic inference typically assumes that the data has evolved under Stationary, Reversible and Homogeneous (SRH) conditions. Many empirical and simulation studies have shown that assuming SRH conditions can lead to significant errors in phylogenetic inference when the data violates these assumptions. Yet, many simulation studies focused on extreme non-SRH conditions that represent worst-case scenarios and not the average empirical dataset. In this study, we simulate datasets under various degrees of non-SRH conditions using empirically derived parameters to mimic real data and examine the effects of incorrectly assuming SRH conditions on inferring phylogenies. Our results show that maximum likelihood inference is generally quite robust to a wide range of SRH model violations but is inaccurate under extreme convergent evolution.

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.

scholarly journals Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

2020 ◽  
Vol 36 (18) ◽  
pp. 4822-4824 ◽  
Author(s):  
Nicolas Comte ◽  
Benoit Morel ◽  
Damir Hasić ◽  
Laurent Guéguen ◽  
Bastien Boussau ◽  
...  
Keyword(s):  
Open Source ◽  
Source Code ◽  
Phylogenetic Inference ◽  
Species Tree ◽  
Gene Trees ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Tree Reconciliation ◽  
Multiple Sequence Alignments ◽  
Multiple Alignments

Abstract Motivation Gene and species tree reconciliation methods are used to interpret gene trees, root them and correct uncertainties that are due to scarcity of signal in multiple sequence alignments. So far, reconciliation tools have not been integrated in standard phylogenetic software and they either lack performance on certain functions, or usability for biologists. Results We present Treerecs, a phylogenetic software based on duplication-loss reconciliation. Treerecs is simple to install and to use. It is fast and versatile, has a graphic output, and can be used along with methods for phylogenetic inference on multiple alignments like PLL and Seaview. Availability and implementation Treerecs is open-source. Its source code (C++, AGPLv3) and manuals are available from https://project.inria.fr/treerecs/.

scholarly journals Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

2019 ◽  
Author(s):  
Nicolas Comte ◽  
Benoit Morel ◽  
Damir Hasic ◽  
Laurent Guéguen ◽  
Bastien Boussau ◽  
...  
Keyword(s):  
Open Source ◽  
Source Code ◽  
Phylogenetic Inference ◽  
Species Tree ◽  
Gene Trees ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Tree Reconciliation ◽  
Multiple Sequence Alignments ◽  
Multiple Alignments

AbstractMotivationGene and species tree reconciliation methods are used to interpret gene trees, root them and correct uncertainties that are due to scarcity of signal in multiple sequence alignments. So far, reconciliation tools have not been integrated in standard phylogenetic software and they either lack performance on certain functions, or usability for biologists.ResultsWe present Treerecs, a phylogenetic software based on duplication-loss reconciliation. Treerecs is simple to install and to use. It is fast and versatile, has a graphic output, and can be used along with methods for phylogenetic inference on multiple alignments like PLL and Seaview.AvailabilityTreerecs is open-source. Its source code (C++, AGPLv3) and manuals are available from https://project.inria.fr/treerecs/[email protected] or [email protected]

scholarly journals MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers

2017 ◽  
Author(s):  
Cédric Chauve ◽  
Akbar Rafiey ◽  
Adrián A. Davín ◽  
Celine Scornavacca ◽  
Philippe Veber ◽  
...  
Keyword(s):  
Significant Proportion ◽  
Time Consistency ◽  
Confidence Score ◽  
Species Tree ◽  
Time Constraints ◽  
Gene Trees ◽  
Transfer Event ◽  
Maximum Time ◽  
Wide Range ◽  
History Of

AbstractLateral gene transfers between ancient species contain information about the relative timing of species diversification. Specifically, the ancestors of a donor species must have existed before the descendants of the recipient species. Hence, the detection of a transfer event can be translated into a time constraint between nodes of a phylogeny if the donor and recipient can be identified. When a set of transfers is detected by interpreting the phylogenetic discordance between gene trees and a species tree, the set of all deduced time constraints can be used to rank the species tree,i.e.order totally its internal nodes. Unfortunately lateral gene transfer detection is challenging and current methods produce a significant proportion of false positives. As a result, often, no ranking of the species tree is compatible with the full set of time constraints deduced from predicted transfers. Here we propose a method, implemented in a software called MaxTiC (Maximum Time Consistency), which takes as input a species tree and a series of (possibly inconsistent) time constraints between its internal nodes, weighted by confidence scores. MaxTiC outputs a ranked species tree compatible with a subset of constraints with maximum cumulated confidence score. We extensively test the method on simulated datasets, under a wide range of conditions that we compare to measures on biological datasets. In most conditions the obtained ranked tree is very close to the real one, confirming the potential of dating the history of life with transfers by maximizing time consistency. MaxTiC is freely available, distributed along with a documentation and several examples:https://github.com/ssolo/ALE/tree/master/maxtic.

scholarly journals Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1645-1656 ◽  
Author(s):  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Dna Sequences ◽  
Gene Tree ◽  
Species Tree ◽  
Bayes Estimation ◽  
Ancestral Population ◽  
Divergence Times ◽  
Gene Trees ◽  
Species Divergence ◽  
Multiple Loci ◽  
Population Sizes

Abstract The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be ∼20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

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