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 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 DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition

2021 ◽  
Author(s):  
James Willson ◽  
Mrinmoy Saha Roddur ◽  
Baqiao Liu ◽  
Paul Zaharias ◽  
Tandy Warnow
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Gene Tree ◽  
Single Copy ◽  
Species Tree ◽  
Family Tree ◽  
Tree Inference ◽  
Gene Duplication And Loss ◽  
Species Tree Inference ◽  
Family Trees

Abstract Species tree inference from gene family trees is a significant problem in computational biology. However, gene tree heterogeneity, which can be caused by several factors including gene duplication and loss, makes the estimation of species trees very challenging. While there have been several species tree estimation methods introduced in recent years to specifically address gene tree heterogeneity due to gene duplication and loss (such as DupTree, FastMulRFS, ASTRAL-Pro, and SpeciesRax), many incur high cost in terms of both running time and memory. We introduce a new approach, DISCO, that decomposes the multi-copy gene family trees into many single copy trees, which allows for methods previously designed for species tree inference in a single copy gene tree context to be used. We prove that using DISCO with ASTRAL (i.e., ASTRAL-DISCO) is statistically consistent under the GDL model, provided that ASTRAL-Pro correctly roots and tags each gene family tree. We evaluate DISCO paired with different methods for estimating species trees from single copy genes (e.g., ASTRAL, ASTRID, and IQ-TREE) under a wide range of model conditions, and establish that high accuracy can be obtained even when ASTRAL-Pro is not able to correctly roots and tags the gene family trees. We also compare results using MI, an alternative decomposition strategy from Yang Y. and Smith S.A. (2014), and find that DISCO provides better accuracy, most likely as a result of covering more of the gene family tree leafset in the output decomposition. [Concatenation analysis; gene duplication and loss; species tree inference; summary method.]

scholarly journals FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models

2020 ◽  
Vol 36 (Supplement_1) ◽  
pp. i57-i65 ◽  
Author(s):  
Erin K Molloy ◽  
Tandy Warnow
Keyword(s):  
Gene Duplication ◽  
Species Tree ◽  
Supplementary Information ◽  
Biological Research ◽  
Generic Model ◽  
Species Trees ◽  
Basic Part ◽  
Gene Duplication And Loss ◽  
Tree Estimation ◽  
Scalable Methods

Abstract Motivation Species tree estimation is a basic part of biological research but can be challenging because of gene duplication and loss (GDL), which results in genes that can appear more than once in a given genome. All common approaches in phylogenomic studies either reduce available data or are error-prone, and thus, scalable methods that do not discard data and have high accuracy on large heterogeneous datasets are needed. Results We present FastMulRFS, a polynomial-time method for estimating species trees without knowledge of orthology. We prove that FastMulRFS is statistically consistent under a generic model of GDL when adversarial GDL does not occur. Our extensive simulation study shows that FastMulRFS matches the accuracy of MulRF (which tries to solve the same optimization problem) and has better accuracy than prior methods, including ASTRAL-multi (the only method to date that has been proven statistically consistent under GDL), while being much faster than both methods. Availability and impementation FastMulRFS is available on Github (https://github.com/ekmolloy/fastmulrfs). Supplementary information Supplementary data are available at Bioinformatics online.

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 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 Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

2019 ◽  
Vol 68 (6) ◽  
pp. 937-955 ◽  
Author(s):  
Alison Cloutier ◽  
Timothy B Sackton ◽  
Phil Grayson ◽  
Michele Clamp ◽  
Allan J Baker ◽  
...  
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Estimation Error ◽  
Gene Tree ◽  
Species Tree ◽  
Tree Topology ◽  
Whole Genome ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Genome Analyses

Abstract Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.

scholarly journals Complexity of the simplest species tree problem

2021 ◽  
Author(s):  
Tianqi Zhu ◽  
Ziheng Yang
Keyword(s):  
Maximum Likelihood ◽  
Estimation Error ◽  
Gene Tree ◽  
Species Tree ◽  
Ancestral Population ◽  
Statistical Efficiency ◽  
Multispecies Coalescent ◽  
Full Likelihood ◽  
Tree Methods ◽  
Tree Estimation

Abstract The multispecies coalescent (MSC) model provides a natural framework for species tree estimation accounting for gene-tree conflicts. While a number of species tree methods under the MSC have been suggested and evaluated using simulation, their statistical properties remain poorly understood. Here we use mathematical analysis aided by computer simulation to examine the identifiability, consistency, and efficiency of different species tree methods in the case of three species and three sequences under the molecular clock. We consider four major species-tree methods including concatenation, two-step, independent-sites maximum likelihood (ISML) and maximum likelihood (ML). We develop approximations that predict that the probit transform of the species tree estimation error decreases linearly with the square root of the number of loci. Even in this simplest case major differences exist among the methods. Fulllikelihood methods are considerably more efficient than summary methods such as concatenation and two-step. They also provide estimates of important parameters such as species divergence times and ancestral population sizes while these parameters are not identifiable by summary methods. Our results highlight the need to improve the statistical efficiency of summary methods and the computational efficiency of full likelihood methods of species tree estimation.

scholarly journals PRANC: ML species tree estimation from the ranked gene trees under coalescence

2020 ◽  
Vol 36 (18) ◽  
pp. 4819-4821
Author(s):  
Anastasiia Kim ◽  
James H Degnan
Keyword(s):  
Maximum Likelihood ◽  
Gene Tree ◽  
Species Tree ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Gene Trees ◽  
Multispecies Coalescent ◽  
Branch Lengths ◽  
Tree Topologies ◽  
Tree Estimation

Abstract Summary PRANC computes the Probabilities of RANked gene tree topologies under the multispecies coalescent. A ranked gene tree is a gene tree accounting for the temporal ordering of internal nodes. PRANC can also estimate the maximum likelihood (ML) species tree from a sample of ranked or unranked gene tree topologies. It estimates the ML tree with estimated branch lengths in coalescent units. Availability and implementation PRANC is written in C++ and freely available at github.com/anastasiiakim/PRANC. Supplementary information Supplementary data are available at Bioinformatics online.

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