Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

Abstract This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny (A00), species tree estimation when the assignment and species delimitation are fixed (A01), species delimitation using a fixed guide tree (A10), and joint species delimitation and species-tree estimation or unguided species delimitation (A11). For the joint analysis (A11), two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis.

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A Simulation Study to Examine the Information Content in Phylogenomic Data Sets under the Multispecies Coalescent Model

Molecular Biology and Evolution ◽

10.1093/molbev/msaa166 ◽

2020 ◽

Vol 37 (11) ◽

pp. 3211-3224

Author(s):

Jun Huang ◽

Tomáš Flouri ◽

Ziheng Yang

Keyword(s):

Information Content ◽

Mutation Rate ◽

Species Delimitation ◽

Species Tree ◽

Data Sets ◽

Site Mutation ◽

Coalescent Model ◽

Inference Problems ◽

Multispecies Coalescent ◽

Tree Estimation

Abstract We use computer simulation to examine the information content in multilocus data sets for inference under the multispecies coalescent model. Inference problems considered include estimation of evolutionary parameters (such as species divergence times, population sizes, and cross-species introgression probabilities), species tree estimation, and species delimitation based on Bayesian comparison of delimitation models. We found that the number of loci is the most influential factor for almost all inference problems examined. Although the number of sequences per species does not appear to be important to species tree estimation, it is very influential to species delimitation. Increasing the number of sites and the per-site mutation rate both increase the mutation rate for the whole locus and these have the same effect on estimation of parameters, but the sequence length has a greater effect than the per-site mutation rate for species tree estimation. We discuss the computational costs when the data size increases and provide guidelines concerning the subsampling of genomic data to enable the application of full-likelihood methods of inference.

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MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R

Bioinformatics ◽

10.1093/bioinformatics/btaa868 ◽

2020 ◽

Author(s):

John A Rhodes ◽

Hector Baños ◽

Jonathan D Mitchell ◽

Elizabeth S Allman

Keyword(s):

Network Inference ◽

Incomplete Lineage Sorting ◽

R Package ◽

Species Tree ◽

Supplementary Information ◽

Species Trees ◽

Lineage Sorting ◽

Coalescent Model ◽

Multispecies Coalescent ◽

Tree Inference

Abstract Summary MSCquartets is an R package for species tree hypothesis testing, inference of species trees, and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package implements the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model. Availability MSCquartets is available through the Comprehensive R Archive Network: https://CRAN.R-project.org/package=MSCquartets. Supplementary information Supplementary materials, including example data and analyses, are incorporated into the package.

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Split Probabilities and Species Tree Inference Under the Multispecies Coalescent Model

Bulletin of Mathematical Biology ◽

10.1007/s11538-017-0363-5 ◽

2017 ◽

Vol 80 (1) ◽

pp. 64-103 ◽

Cited By ~ 3

Author(s):

Elizabeth S. Allman ◽

James H. Degnan ◽

John A. Rhodes

Keyword(s):

Species Tree ◽

Coalescent Model ◽

Multispecies Coalescent ◽

Tree Inference ◽

Species Tree Inference

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Complexity of the simplest species tree problem

Molecular Biology and Evolution ◽

10.1093/molbev/msab009 ◽

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.

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

Bioinformatics ◽

10.1093/bioinformatics/btaa605 ◽

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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Consistency of SVDQuartets and Maximum Likelihood for Coalescent-based Species Tree Estimation

10.1101/523050 ◽

2019 ◽

Cited By ~ 2

Author(s):

Matthew Wascher ◽

Laura Kubatko

Keyword(s):

Maximum Likelihood ◽

Species Tree ◽

Gene Trees ◽

Data Types ◽

Coalescent Model ◽

Multispecies Coalescent ◽

Consistency Results ◽

True Tree ◽

Tree Inference ◽

Statistical Consistency

AbtractNumerous methods for inferring species-level phylogenies under the coalescent model have been proposed within the last 20 years, and debates continue about the relative strengths and weaknesses of these methods. One desirable property of a phylogenetic estimator is that of statistical consistency, which means intuitively that as more data are collected, the probability that the estimated tree has the same topology as the true tree goes to 1. To date, consistency results for species tree inference under the multispecies coalescent have been derived only for summary statistics methods, such as ASTRAL and MP-EST. These methods have been found to be consistent given true gene trees, but may be inconsistent when gene trees are estimated from data for loci of finite length (Roch et al., 2019). Here we consider the question of statistical consistency for four taxa for SVDQuartets for general data types, as well as for the maximum likelihood (ML) method in the case in which the data are a collection of sites generated under the multispecies coalescent model such that the sites are conditionally independent given the species tree (we call these data Coalescent Independent Sites (CIS) data). We show that SVDQuartets is statistically consistent for all data types (i.e., for both CIS data and for multilocus data), and we derive its rate of convergence. We additionally show that ML is consistent for CIS data under the JC69 model, and discuss why a proof for the more general multilocus case is difficult. Finally, we compare the performance of maximum likelihood and SDVQuartets using simulation for both data types.

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The Impact of Cross-Species Gene Flow on Species Tree Estimation

Systematic Biology ◽

10.1093/sysbio/syaa001 ◽

2020 ◽

Vol 69 (5) ◽

pp. 830-847 ◽

Cited By ~ 1

Author(s):

Xiyun Jiao ◽

Tomáš Flouri ◽

Bruce Rannala ◽

Ziheng Yang

Keyword(s):

Gene Flow ◽

Sequence Data ◽

Majority Vote ◽

Gene Tree ◽

Species Tree ◽

Likelihood Method ◽

Estimation Methods ◽

Vote Method ◽

Multispecies Coalescent ◽

Tree Estimation

Abstract Recent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree estimation. We examine the levels of gene flow needed to mislead species tree estimation with three species and either episodic introgressive hybridization or continuous migration between an outgroup and one ingroup species. Several species tree estimation methods are examined, including the majority-vote method based on the most common gene tree topology (with either the true or reconstructed gene trees used), the UPGMA method based on the average sequence distances (or average coalescent times) between species, and the full-likelihood method based on multilocus sequence data. Our results suggest that the majority-vote method based on gene tree topologies is more robust to gene flow than the UPGMA method based on coalescent times and both are more robust than likelihood assuming a multispecies coalescent (MSC) model with no cross-species gene flow. Comparison of the continuous migration model with the episodic introgression model suggests that a small amount of gene flow per generation can cause drastic changes to the genetic history of the species and mislead species tree methods, especially if the species diverged through radiative speciation events. Estimates of parameters under the MSC with gene flow suggest that African mosquito species in the Anopheles gambiae species complex constitute such an example of extreme impact of gene flow on species phylogeny. [IM; introgression; migration; MSci; multispecies coalescent; species tree.]

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ILS-Aware Analyses of Retroelement Insertions in the Anomaly Zone

10.1101/2020.09.29.319038 ◽

2020 ◽

Author(s):

Erin K. Molloy ◽

John Gatesy ◽

Mark S. Springer

Keyword(s):

Dna Sequences ◽

Incomplete Lineage Sorting ◽

Species Tree ◽

Species Trees ◽

Lineage Sorting ◽

Short Branch ◽

Multispecies Coalescent ◽

Branch Lengths ◽

Tree Estimation ◽

Infinite Sites Model

AbstractA major shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting (ILS). Coalescence methods explicitly address this problem, but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescence methods, retroelement insertions have emerged as powerful phylogenomic markers for species tree estimation. We show that two recently proposed methods, SDPquartets and ASTRAL_BP, are statistically consistent estimators of the species tree under the multispecies coalescent model, with retroelement insertions following a neutral infinite sites model of mutation. The accuracy of these and other methods for inferring species trees with retroelements has not been assessed in simulation studies. We simulate retroelements for four different species trees, including three with short branch lengths in the anomaly zone, and assess the performance of eight different methods for recovering the correct species tree. We also examine whether ASTRAL_BP recovers accurate internal branch lengths for internodes of various lengths (in coalescent units). Our results indicate that two recently proposed ILS-aware methods, ASTRAL_BP and SDPquartets, as well as the newly proposed ASTRID_BP, always recover the correct species tree on data sets with large numbers of retroelements even when there are extremely short species-tree branches in the anomaly zone. Dollo parsimony performed almost as well as these ILS-aware methods. By contrast, unordered parsimony, polymorphism parsimony, and MDC recovered the correct species tree in the case of a pectinate tree with four ingroup taxa in the anomaly zone, but failed to recover the correct tree in more complex anomaly-zone situations with additional lineages impacted by extensive incomplete lineage sorting. Camin-Sokal parsimony always reconstructed an incorrect tree in the anomaly zone. ASTRAL_BP accurately estimated branch lengths when internal branches were very short as in anomaly zone situations, but branch lengths were upwardly biased by more than 35% when species tree branches were longer. We derive a mathematical correction for these distortions, assuming the expected number of new retroelement insertions per generation is constant across the species tree. We also show that short branches do not need to be corrected even when this assumption does not hold; therefore, the branch lengths estimates produced by ASTRAL_BP may provide insight into whether an estimated species tree is in the anomaly zone.

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Disentangling incomplete lineage sorting and introgression to refine species-tree estimates for Lake Tanganyika cichlid fishes

10.1101/039396 ◽

2016 ◽

Cited By ~ 4

Author(s):

Britta S Meyer ◽

Michael Matschiner ◽

Walter Salzburger

Keyword(s):

Adaptive Radiation ◽

Lake Tanganyika ◽

Genetic Material ◽

Species Tree ◽

Ecological Niches ◽

Species Flock ◽

Cichlid Fishes ◽

Coalescent Model ◽

Multispecies Coalescent ◽

History Of

Adaptive radiation is thought to be responsible for the evolution of a great portion of the past and present diversity of life. Instances of adaptive radiation, characterized by the rapid emergence of an array of species as a consequence to their adaptation to distinct ecological niches, are important study systems in evolutionary biology. However, because of the rapid lineage formation in these groups, and the occurrence of hybridization between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation. In this study, we present a novel approach for species-tree estimation in rapidly diversifying lineages, where introgression is known to occur, and apply it to a multimarker dataset containing up to 16 specimens per species for a set of 45 species of East African cichlid fishes (522 individuals in total), with a main focus on the cichlid species flock of Lake Tanganyika. We first identified, using age distributions of most recent common ancestors in individual gene trees, those lineages in our dataset that show strong signatures of past introgression. This led us to formulate three hypotheses of introgression between different lineages of Tanganyika cichlids: the ancestor of Boulengerochromini (or of Boulengerochromini and Bathybatini) received genomic material from the derived H-lineage; the common ancestor of Cyprichromini and Perissodini experienced, in turn, introgression from Boulengerochromini and/or Bathybatini; and the Lake Tanganyika Haplochromini and closely related riverine lineages received genetic material from Cyphotilapiini. We then applied the multispecies coalescent model to estimate the species tree of Lake Tanganyika cichlids, but excluded the lineages involved in these introgression events, as the multispecies coalescent model does not incorporate introgression. This resulted in a robust species tree, in which the Lamprologini were placed as sister lineage to the H-lineage (including the Eretmodini), and we identify a series of rapid splitting events at the base of the H-lineage. Divergence ages estimated with the multispecies coalescent model were substantially younger than age estimates based on concatenation, and agree with the geological history of the Great Lakes of East Africa. Finally, we formally tested the three hypotheses of introgression using a likelihood framework, and find strong support for introgression between some of the cichlid tribes of Lake Tanganyika.

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