An Efficient Method for DNA-Based Species Assignment via Gene Tree and Species Tree Reconciliation

2010 ◽  
pp. 300-311 ◽  
Author(s):  
Louxin Zhang ◽  
Yun Cui
Keyword(s):  
Efficient Method ◽  
Gene Tree ◽  
Species Tree ◽  
Tree Reconciliation ◽  
Species Assignment

scholarly journals BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

2010 ◽  
Vol 26 (22) ◽  
pp. 2910-2911 ◽  
Author(s):  
Bret R. Larget ◽  
Satish K. Kotha ◽  
Colin N. Dewey ◽  
Cécile Ané
Keyword(s):  
Tree Species ◽  
Gene Tree ◽  
Species Tree ◽  
Tree Reconciliation ◽  
Concordance Analysis

scholarly journals Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates

2019 ◽  
Vol 36 (7) ◽  
pp. 1384-1404 ◽  
Author(s):  
Arthur Zwaenepoel ◽  
Yves Van de Peer
Keyword(s):  
Maximum Likelihood ◽  
Gene Duplication ◽  
Gene Tree ◽  
Probabilistic Approach ◽  
Species Tree ◽  
Rate Variation ◽  
Whole Genome ◽  
Tree Reconciliation ◽  
Gene Duplication And Loss ◽  
Loss Rates

Abstract Gene tree–species tree reconciliation methods have been employed for studying ancient whole-genome duplication (WGD) events across the eukaryotic tree of life. Most approaches have relied on using maximum likelihood trees and the maximum parsimony reconciliation thereof to count duplication events on specific branches of interest in a reference species tree. Such approaches do not account for uncertainty in the gene tree and reconciliation, or do so only heuristically. The effects of these simplifications on the inference of ancient WGDs are unclear. In particular, the effects of variation in gene duplication and loss rates across the species tree have not been considered. Here, we developed a full probabilistic approach for phylogenomic reconciliation-based WGD inference, accounting for both gene tree and reconciliation uncertainty using a method based on the principle of amalgamated likelihood estimation. The model and methods are implemented in a maximum likelihood and Bayesian setting and account for variation of duplication and loss rates across the species tree, using methods inspired by phylogenetic divergence time estimation. We applied our newly developed framework to ancient WGDs in land plants and investigated the effects of duplication and loss rate variation on reconciliation and gene count based assessment of these earlier proposed WGDs.

scholarly journals Terraces in Gene Tree Reconciliation-Based Species Tree Inference

2020 ◽  
Author(s):  
Michael J. Sanderson ◽  
Michelle M. McMahon ◽  
Mike Steel
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Solution Space ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Data Set ◽  
Tree Reconciliation ◽  
The Impact

AbstractTerraces in phylogenetic tree space are sets of trees with identical optimality scores for a given data set, arising from missing data. These were first described for multilocus phylogenetic data sets in the context of maximum parsimony inference and maximum likelihood inference under certain model assumptions. Here we show how the mathematical properties that lead to terraces extend to gene tree - species tree problems in which the gene trees are incomplete. Inference of species trees from either sets of gene family trees subject to duplication and loss, or allele trees subject to incomplete lineage sorting, can exhibit terraces in their solution space. First, we show conditions that lead to a new kind of terrace, which stems from subtree operations that appear in reconciliation problems for incomplete trees. Then we characterize when terraces of both types can occur when the optimality criterion for tree search is based on duplication, loss or deep coalescence scores. Finally, we examine the impact of assumptions about the causes of losses: whether they are due to imperfect sampling or true evolutionary deletion.

scholarly journals ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony: Table 1.

2016 ◽  
Vol 32 (13) ◽  
pp. 2056-2058 ◽  
Author(s):  
Edwin Jacox ◽  
Cedric Chauve ◽  
Gergely J. Szöllősi ◽  
Yann Ponty ◽  
Celine Scornavacca
Keyword(s):  
Tree Species ◽  
Gene Tree ◽  
Species Tree ◽  
Tree Reconciliation

scholarly journals Phylogenomic Analyses Of 2,786 Genes In 158 Lineages Support a Root of The Eukaryotic Tree of Life Between Opisthokonts (Animals, Fungi and Their Microbial Relatives) and All Other Lineages

2021 ◽  
Author(s):  
Mario A Ceron Romero ◽  
Miguel M Fonseca ◽  
Leonardo de Oliveira Martins ◽  
David Posada ◽  
Laura A Katz
Keyword(s):  
Tree Species ◽  
High Throughput Sequencing ◽  
Single Gene ◽  
Gene Tree ◽  
Gene Families ◽  
Species Tree ◽  
Tree Of Life ◽  
Gene Duplications ◽  
Tree Reconciliation ◽  
Phylogenomic Analyses

Advances in phylogenetics and high throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single gene fusion. Subsequent highly cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within Excavata. However, concatenation of genes neither considers phylogenetically informative events (i.e. gene duplications and losses), nor provides an estimate of the root. A more recent study using gene tree / species tree reconciliation methods suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we apply a gene tree / species tree reconciliation approach to a gene-rich and taxon rich dataset (i.e. 2,786 gene families from two sets of 158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. We estimate a root between Fungi and all other eukaryotes, or between Opisthokonta and all other eukaryotes, and reject alternative roots from the literature. Based on further analysis of genome size we propose Opisthokonta + others as the most likely root.

scholarly journals Gene tree species tree reconciliation with gene conversion

2019 ◽  
Vol 78 (6) ◽  
pp. 1981-2014 ◽  
Author(s):  
Damir Hasić ◽  
Eric Tannier
Keyword(s):  
Gene Conversion ◽  
Tree Species ◽  
Gene Tree ◽  
Species Tree ◽  
Tree Reconciliation

scholarly journals Fungi ligE-type glutathione S-transferases horizontally transferred into plants and a protozoan

2020 ◽  
Author(s):  
Dan Li ◽  
Meng Zhang
Keyword(s):  
Green Algae ◽  
Tree Species ◽  
Gene Tree ◽  
Acanthamoeba Castellanii ◽  
Transgenic Crops ◽  
Species Tree ◽  
Glutathione S Transferase ◽  
Tree Reconciliation ◽  
Glutathione S Transferases ◽  
Thinopyrum Elongatum

AbstractHorizontal gene transfers (HGT) were considered as common evolution approaches for organisms. However, most HGT especially those HGT among distant species, like microbes to plants, were over-estimated because they were just identified based on the criteria of Blast searches and gene tree–species tree reconciliation. Recently, a ligE-type glutathione S-transferase (GST), Fhb7-GST was considered as an HGT from Epichloë to Thinopyrum elongatum. To confirm and clarify the occurring patterns of this HGT, homologue searches were conducted. Although TeFhb7-GST was not found in other plants, ligE-GSTs were found in not only plants but also an ameba protozoan. Additionally, ligE-GSTs were likely to horizontally transfer from fungi to other organisms. LigE-GSTs evolve in various fungi, but they only exist in some liverworts and green algae. Interestingly, all these ligE-GST genes in these plants share more than 90% similarities with that from fungus Coniosporium apollinis. More than that, the protozoan homologue from Acanthamoeba castellanii have 94.9% similiarity with that from C. apollinis. Actually, only a few substitutions were found in two homologues except a 111-bp lost in A. castellanii ligE-GST. All these results suggested HGT is an important evolutionary method for all organisms. Notably, natural HGT remind us to reevaluate the transgenic crops.

scholarly journals Ancient whole genome duplications and the evolution of the gene duplication and loss rate

2019 ◽  
Author(s):  
Arthur Zwaenepoel ◽  
Yves Van de Peer
Keyword(s):  
Maximum Likelihood ◽  
Gene Duplication ◽  
Loss Rate ◽  
Gene Tree ◽  
Probabilistic Approach ◽  
Species Tree ◽  
Rate Variation ◽  
Whole Genome ◽  
Tree Reconciliation ◽  
Gene Duplication And Loss

AbstractGene tree - species tree reconciliation methods have been employed for studying ancient whole genome duplication (WGD) events across the eukaryotic tree of life. Most approaches have relied on using maximum likelihood trees and the maximum parsimony reconciliation thereof to count duplication events on specific branches of interest in a reference species tree. Such approaches do not account for uncertainty in the gene tree and reconciliation, or do so only heuristically. The effects of these simplifications on the inference of ancient WGDs are unclear. In particular the effects of variation in gene duplication and loss rates across the species tree have not been considered. Here, we developed a full probabilistic approach for phylogenomic reconciliation based WGD inference, accounting for both gene tree and reconciliation uncertainty using a method based on the principle of amalgamated likelihood estimation. The model and methods are implemented in a maximum likelihood and Bayesian setting and account for variation of duplication and loss rate across the species tree, using methods inspired by phylogenetic divergence time estimation. We applied our newly developed framework to ancient WGDs in land plants and investigate the effects of duplication and loss rate variation on reconciliation and gene count based assessment of these earlier proposed WGDs.

scholarly journals The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales

2020 ◽  
Author(s):  
Liming Cai ◽  
Zhenxiang Xi ◽  
Emily Moriarty Lemmon ◽  
Alan R Lemmon ◽  
Austin Mast ◽  
...  
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Estimation Error ◽  
Gene Tree ◽  
Species Tree ◽  
Flowering Plant ◽  
Estimation Methods ◽  
Lineage Sorting ◽  
Tree Estimation ◽  
Perfect Storm

Abstract The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes nine of the top ten most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0%, 34.8%, and 21.4% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.

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