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Species Tree Inference on Data with Paralogs is Accurate Using Methods Intended to Deal with Incomplete Lineage Sorting

https://doi.org/10.1101/498378
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-030-10837-3_13openalex-snapshot
Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization
inferredcites →https://doi.org/10.1007/978-3-319-59575-7_18openalex-snapshot
Coestimation of Gene Trees and Reconciliations Under a Duplication-Loss-Coalescence Model
inferredcites →https://doi.org/10.1007/978-3-642-29627-7_23openalex-snapshot
Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis
inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot
Comparison of phylogenetic trees
inferredcites →https://doi.org/10.1016/j.jtbi.2013.01.009openalex-snapshot
Identifying a species tree subject to random lateral gene transfer
inferredcites →https://doi.org/10.1016/j.tig.2020.08.012openalex-snapshot
New Approaches for Inferring Phylogenies in the Presence of Paralogs
inferredcites →https://doi.org/10.1016/j.tree.2009.01.009openalex-snapshot
Gene tree discordance, phylogenetic inference and the multispecies coalescent
inferredcites →https://doi.org/10.1016/j.tree.2013.09.004openalex-snapshot
Computational approaches to species phylogeny inference and gene tree reconciliation
inferredcites →https://doi.org/10.1016/j.ympev.2009.05.033openalex-snapshot
Coalescent methods for estimating phylogenetic trees
inferredcites →https://doi.org/10.1038/nature08064openalex-snapshot
Evolution of pathogenicity and sexual reproduction in eight Candida genomes
inferredcites →https://doi.org/10.1038/nrg2689openalex-snapshot
The evolution of gene duplications: classifying and distinguishing between models
inferredcites →https://doi.org/10.1073/pnas.1407950111openalex-snapshot
Maximum likelihood inference of reticulate evolutionary histories
inferredcites →https://doi.org/10.1073/pnas.91.15.6721openalex-snapshot
Tempo, mode, the progenote, and the universal root.
inferredcites →https://doi.org/10.1080/10635150390235520openalex-snapshot
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
inferredcites →https://doi.org/10.1089/cmb.2011.0174openalex-snapshot
Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles
inferredcites →https://doi.org/10.1089/cmb.2012.0234openalex-snapshot
Recovering the Treelike Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis
inferredcites →https://doi.org/10.1089/cmb.2020.0424openalex-snapshot
Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
inferredcites →https://doi.org/10.1093/bioinformatics/13.3.235openalex-snapshot
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/btaa444openalex-snapshot
FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models
inferredcites →https://doi.org/10.1093/bioinformatics/btu462openalex-snapshot
ASTRAL: genome-scale coalescent-based species tree estimation
inferredcites →https://doi.org/10.1093/genetics/122.4.957openalex-snapshot
Gene genealogy in three related populations: consistency probability between gene and population trees.
inferredcites →https://doi.org/10.1093/genetics/132.4.1161openalex-snapshot
Population genetics of polymorphism and divergence.
inferredcites →https://doi.org/10.1093/genetics/164.4.1645openalex-snapshot
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci
inferredcites →https://doi.org/10.1093/jhered/esp047openalex-snapshot
Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates
inferredcites →https://doi.org/10.1093/molbev/msaa139openalex-snapshot
ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy
inferredcites →https://doi.org/10.1093/molbev/msq189openalex-snapshot
A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction
inferredcites →https://doi.org/10.1093/molbev/msu245openalex-snapshot
Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msx126openalex-snapshot
StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates
inferredcites →https://doi.org/10.1093/sysbio/46.3.523openalex-snapshot
Gene Trees in Species Trees
inferredcites →https://doi.org/10.1093/sysbio/syaa084openalex-snapshot
The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution
inferredcites →https://doi.org/10.1093/sysbio/syab097openalex-snapshot
The Frequency and Topology of Pseudoorthologs
inferredcites →https://doi.org/10.1093/sysbio/syr027openalex-snapshot
Estimating Species Trees from Unrooted Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/syv082openalex-snapshot
SimPhy : Phylogenomic Simulation of Gene, Locus, and Species Trees
inferredcites →https://doi.org/10.1093/sysbio/syw030openalex-snapshot
Inconsistency of Species Tree Methods under Gene Flow
inferredcites →https://doi.org/10.1093/sysbio/syw082openalex-snapshot
Incomplete Lineage Sorting in Mammalian Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syw101openalex-snapshot
Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses
inferredcites →https://doi.org/10.1093/sysbio/syy015openalex-snapshot
Inferring Phylogenetic Networks Using PhyloNet
inferredcites →https://doi.org/10.1093/sysbio/syy020openalex-snapshot
The Effect of Gene Flow on Coalescent-based Species-Tree Inference
inferredcites →https://doi.org/10.1101/267914openalex-snapshot
STAG: Species Tree Inference from All Genes
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
inferredcites →https://doi.org/10.1101/gr.123901.111openalex-snapshot
Unified modeling of gene duplication, loss, and coalescence using a locus tree
inferredcites →https://doi.org/10.1101/gr.141978.112openalex-snapshot
Genome-scale coestimation of species and gene trees
inferredcites →https://doi.org/10.1111/j.1558-5646.1983.tb05528.xopenalex-snapshot
TESTING THE CONSTANT-RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA
inferredcites →https://doi.org/10.1111/nyas.12747openalex-snapshot
Estimating phylogenetic trees from genome‐scale data
inferredcites →https://doi.org/10.1145/1502793.1502796openalex-snapshot
The gene evolution model and computing its associated probabilities
inferredcites →https://doi.org/10.1145/3233547.3233600openalex-snapshot
Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence Model
inferredcites →https://doi.org/10.1146/annurev.genet.39.073003.114725openalex-snapshot
Orthologs, Paralogs, and Evolutionary Genomics
inferredcites →https://doi.org/10.1186/1471-2148-10-302openalex-snapshot
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
inferredcites →https://doi.org/10.1186/1471-2164-16-s10-s10openalex-snapshot
A maximum pseudo-likelihood approach for phylogenetic networks
inferredcites →https://doi.org/10.1186/1471-2164-16-s8-s1openalex-snapshot
Better prediction of functional effects for sequence variants
inferredcites →https://doi.org/10.1186/s12859-016-1269-1openalex-snapshot
In the light of deep coalescence: revisiting trees within networks
inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
inferredcites →https://doi.org/10.1186/s13059-019-1925-7openalex-snapshot
Gene content evolution in the arthropods
inferredcites →https://doi.org/10.1371/journal.pcbi.1000501openalex-snapshot
Species Tree Inference by Minimizing Deep Coalescences
inferredcites →https://doi.org/10.1371/journal.pgen.0020173openalex-snapshot
Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1371/journal.pgen.0030197openalex-snapshot
Gene Family Evolution across 12 Drosophila Genomes
inferredcites →https://doi.org/10.1534/g3.116.034744openalex-snapshot
Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data
inferredcites →https://doi.org/10.1534/genetics.107.071506openalex-snapshot
Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1534/genetics.113.151670openalex-snapshot
Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster
inferredcites →https://doi.org/10.48550/arxiv.2004.04299openalex-snapshot
Quartet-Based Inference Methods are Statistically Consistent Under the Unified Duplication-Loss-Coalescence Model
inferredcites →https://doi.org/10.6084/m9.figshare.1466899openalex-snapshot
SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/ajb2.16025openalex-snapshot
Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification
inferred← citeshttps://doi.org/10.1007/978-3-030-45257-5_8openalex-snapshot
Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106668openalex-snapshot
A phylogenomic analysis of Nepenthes (Nepenthaceae)
inferred← citeshttps://doi.org/10.1017/9781139047678openalex-snapshot
Cladistics
inferred← citeshttps://doi.org/10.1017/9781139047678.001openalex-snapshot
Preface
inferred← citeshttps://doi.org/10.1017/9781139047678.002openalex-snapshot
Introduction: Carving Nature at Its Joints, or Why Birds Are Not Dinosaurs and Men Are Not Apes
inferred← citeshttps://doi.org/10.1017/9781139047678.003openalex-snapshot
The Interrelationships of Organisms
inferred← citeshttps://doi.org/10.1017/9781139047678.004openalex-snapshot
What This Book Is About
inferred← citeshttps://doi.org/10.1017/9781139047678.005openalex-snapshot
Classification
inferred← citeshttps://doi.org/10.1017/9781139047678.006openalex-snapshot
Systematics: Exposing Myths
inferred← citeshttps://doi.org/10.1017/9781139047678.007openalex-snapshot
Relationship Diagrams
inferred← citeshttps://doi.org/10.1017/9781139047678.008openalex-snapshot
Essentialism and Typology
inferred← citeshttps://doi.org/10.1017/9781139047678.009openalex-snapshot
Monothetic and Polythetic Taxa
inferred← citeshttps://doi.org/10.1017/9781139047678.010openalex-snapshot
Non-taxa or the Absence of –Phyly: Paraphyly and Aphyly
inferred← citeshttps://doi.org/10.1017/9781139047678.011openalex-snapshot
The Cladistic Programme
inferred← citeshttps://doi.org/10.1017/9781139047678.012openalex-snapshot
Parameters of Classification:Ordo Ab Chao
inferred← citeshttps://doi.org/10.1017/9781139047678.013openalex-snapshot
How to Study Classification
inferred← citeshttps://doi.org/10.1017/9781139047678.014openalex-snapshot
Modern Artificial Methods and Raw Data
inferred← citeshttps://doi.org/10.1017/9781139047678.015openalex-snapshot
How to Study Classification: Consensus Techniques and General Classifications
inferred← citeshttps://doi.org/10.1017/9781139047678.016openalex-snapshot
How to Study Classification: ‘Total Evidence’ vs. ‘Consensus’, Character Congruence vs. Taxonomic Congruence, Simultaneous Analysis vs. Partitioned Data
inferred← citeshttps://doi.org/10.1017/9781139047678.017openalex-snapshot
How to Study Classification
inferred← citeshttps://doi.org/10.1017/9781139047678.018openalex-snapshot
How to Study Classification
inferred← citeshttps://doi.org/10.1017/9781139047678.019openalex-snapshot
Beyond Classification
inferred← citeshttps://doi.org/10.1017/9781139047678.020openalex-snapshot
Beyond Classification: How to Study Phylogeny
inferred← citeshttps://doi.org/10.1017/9781139047678.021openalex-snapshot
The Separation of Classification and Phylogenetics
inferred← citeshttps://doi.org/10.1017/9781139047678.022openalex-snapshot
Further Myths and More Misunderstandings
inferred← citeshttps://doi.org/10.1017/9781139047678.023openalex-snapshot
Afterword
inferred← citeshttps://doi.org/10.1017/9781139047678.024openalex-snapshot
Index
inferred← citeshttps://doi.org/10.1017/9781139047678.025openalex-snapshot
Systematics Association Special Volumes
inferred← citeshttps://doi.org/10.1089/cmb.2020.0424openalex-snapshot
Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
inferred← citeshttps://doi.org/10.1089/cmb.2021.0011openalex-snapshot
Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa444openalex-snapshot
FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models
inferred← citeshttps://doi.org/10.1093/gbe/evad034openalex-snapshot
Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae
inferred← citeshttps://doi.org/10.1093/molbev/msac112openalex-snapshot
Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference
inferred← citeshttps://doi.org/10.1093/sysbio/syac040openalex-snapshot
Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication
inferred← citeshttps://doi.org/10.1146/annurev-ecolsys-012121-095340openalex-snapshot
Multispecies Coalescent: Theory and Applications in Phylogenetics
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