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Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent

https://doi.org/10.1093/molbev/msac161
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
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Estimating the pattern of nucleotide substitution
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
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Evolutionary trees from DNA sequences: A maximum likelihood approach
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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
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An evaluation of the molecular clock hypothesis using mammalian DNA sequences
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Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent
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Evolution of Protein Molecules
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Molecular clocks
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Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics
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Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds
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Gene trees and species trees are not the same
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Gibbon genome and the fast karyotype evolution of small apes
inferredcites →https://doi.org/10.1038/nrg.2015.8openalex-snapshot
Bayesian molecular clock dating of species divergences in the genomics era
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The fossilized birth–death process for coherent calibration of divergence-time estimates
inferredcites →https://doi.org/10.1073/pnas.1515798113openalex-snapshot
Life history effects on the molecular clock of autosomes and sex chromosomes
inferredcites →https://doi.org/10.1080/10635150701420643openalex-snapshot
Inferring Speciation Times under an Episodic Molecular Clock
inferredcites →https://doi.org/10.1093/acprof:oso/9780199602605.001.0001openalex-snapshot
Molecular Evolution
inferredcites →https://doi.org/10.1093/bioinformatics/btv234openalex-snapshot
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
inferredcites →https://doi.org/10.1093/czoolo/61.5.854openalex-snapshot
The BPP program for species tree estimation and species delimitation
inferredcites →https://doi.org/10.1093/czoolo/61.5.874openalex-snapshot
The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times
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/molbev/msaa166openalex-snapshot
A Simulation Study to Examine the Information Content in Phylogenomic Data Sets under the Multispecies Coalescent Model
inferredcites →https://doi.org/10.1093/molbev/msab009openalex-snapshot
Complexity of the simplest species tree problem
inferredcites →https://doi.org/10.1093/molbev/msj024openalex-snapshot
Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds
inferredcites →https://doi.org/10.1093/molbev/msm193openalex-snapshot
A General Comparison of Relaxed Molecular Clock Models
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Estimation of Hominoid Ancestral Population Sizes under Bayesian Coalescent Models Incorporating Mutation Rate Variation and Sequencing Errors
inferredcites →https://doi.org/10.1093/molbev/msu279openalex-snapshot
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci
inferredcites →https://doi.org/10.1093/molbev/msw079openalex-snapshot
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
inferredcites →https://doi.org/10.1093/molbev/msx277openalex-snapshot
Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons
inferredcites →https://doi.org/10.1093/molbev/msy147openalex-snapshot
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent
inferredcites →https://doi.org/10.1093/molbev/msy158openalex-snapshot
Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex
inferredcites →https://doi.org/10.1093/molbev/msz296openalex-snapshot
A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis
inferredcites →https://doi.org/10.1093/nsr/nwab127openalex-snapshot
Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003811openalex-snapshot
Performance of a Divergence Time Estimation Method under a Probabilistic Model of Rate Evolution
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025892openalex-snapshot
Estimating the rate of evolution of the rate of molecular evolution
inferredcites →https://doi.org/10.1093/sysbio/46.3.523openalex-snapshot
Gene Trees in Species Trees
inferredcites →https://doi.org/10.1093/sysbio/syab047openalex-snapshot
Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model
inferredcites →https://doi.org/10.1093/sysbio/syac009openalex-snapshot
Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of the erato-sara Group of Heliconius Butterflies
inferredcites →https://doi.org/10.1093/sysbio/syac010openalex-snapshot
StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent
inferredcites →https://doi.org/10.1093/sysbio/syp082openalex-snapshot
Bayesian Dating of Shallow Phylogenies with a Relaxed Clock
inferredcites →https://doi.org/10.1093/sysbio/syr027openalex-snapshot
Estimating Species Trees from Unrooted Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/sys058openalex-snapshot
A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
inferredcites →https://doi.org/10.1093/sysbio/syu020openalex-snapshot
The Impact of the Rate Prior on Bayesian Estimation of Divergence Times with Multiple Loci
inferredcites →https://doi.org/10.1093/sysbio/syu048openalex-snapshot
The Inference of Gene Trees with Species Trees
inferredcites →https://doi.org/10.1093/sysbio/syu109openalex-snapshot
Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci
inferredcites →https://doi.org/10.1093/sysbio/syv080openalex-snapshot
Total-Evidence Dating under the Fossilized Birth–Death Process
inferredcites →https://doi.org/10.1093/sysbio/syv118openalex-snapshot
Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods
inferredcites →https://doi.org/10.1093/sysbio/syw119openalex-snapshot
Efficient Bayesian Species Tree Inference under the Multispecies Coalescent
inferredcites →https://doi.org/10.1093/sysbio/syy061openalex-snapshot
Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods
inferredcites →https://doi.org/10.1093/sysbio/syz015openalex-snapshot
Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters
inferredcites →https://doi.org/10.1093/sysbio/syz019openalex-snapshot
Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone
inferredcites →https://doi.org/10.1098/rspb.2004.3035openalex-snapshot
Phylogenetics of modern birds in the era of genomics
inferredcites →https://doi.org/10.1098/rstb.2015.0126openalex-snapshot
Dating species divergences using rocks and clocks
inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00549.xopenalex-snapshot
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
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/10.1186/1471-2148-8-77openalex-snapshot
Birth-death prior on phylogeny and speed dating
inferredcites →https://doi.org/10.1198/106186006x136976openalex-snapshot
Validation of Software for Bayesian Models Using Posterior Quantiles
inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1534/genetics.112.149039openalex-snapshot
Improved Reversible Jump Algorithms for Bayesian Species Delimitation
inferredcites →https://doi.org/10.1534/genetics.115.174425openalex-snapshot
Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach
inferredcites →https://doi.org/10.1534/genetics.116.190173openalex-snapshot
Challenges in Species Tree Estimation Under the Multispecies Coalescent Model
inferredcites →https://doi.org/10.2183/pjab.60.95openalex-snapshot
A new molecular clock of mitochondrial DNA and the evolution of hominoids.
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Cases in which Parsimony or Compatibility Methods Will be Positively Misleading

What points at this work

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

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Coalescent-delimitation framework disentangles species boundaries within the Neotropical mouse-opossums subgenus Marmosops
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Beyond Level-1: Identifiability of a Class of Galled Tree-Child Networks
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Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family
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Efficient Bayesian inference under the multispecies coalescent with migration
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Effect of Different Types of Sequence Data on Palaeognath Phylogeny
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Low accuracy of complex admixture graph inference from f -statistics
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PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance
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Estimation of species divergence times in presence of cross-species gene flow
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Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information
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Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences
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Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila
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Bayesian Test of Gene Flow between Sister Lineages Using Genomic Data
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Diversification over deep and shallow temporal scales in the Holarctic genus Perpolita (Gastropoda: Gastrodontidae)
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PhyloAcc-GT: A Bayesian method for inferring patterns of substitution rate shifts and associations with binary traits under gene tree discordance
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CASTER: Direct species tree inference from whole-genome alignments
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Natural selection and recombination at host-interacting lipoprotein loci drive genome diversification of Lyme disease and related bacteria
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Common Methods for Phylogenetic Tree Construction and Their Implementation in R
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Prevalence and Genetic Characterization of Mammalian Orthoreoviruses in Diarrheic Cattle from Guangxi, China
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Integrating Morphological, Molecular and Whole Genome (Mitogenomic) Approaches in Indian Lepidoptera
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Phylogenetic tree inference using generative models
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