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Molecular dating for phylogenies containing a mix of populations and species

https://doi.org/10.1101/536656
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What this work says

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

inferredcites →https://doi.org/10.1002/0471667196.ess1571.pub2openalex-snapshot
Maximum Likelihood Estimation
inferredcites →https://doi.org/10.1007/978-3-319-16859-3_20openalex-snapshot
Die Grundlagen der Volterraschen Theorie des Kampfes ums Dasein in wahrscheinlichkeitstheoretischer Behandlung
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Die Grundlagen der Volterraschen Theorie des Kampfes ums Dasein in wahrscheinlichkeitstheoretischer Behandlung
inferredcites →https://doi.org/10.1007/bf02101694openalex-snapshot
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
inferredcites →https://doi.org/10.1016/j.ajhg.2008.01.019openalex-snapshot
A Bayesian Evaluation of Human Mitochondrial Substitution Rates
inferredcites →https://doi.org/10.1016/j.biocon.2017.11.017openalex-snapshot
Conservation phylogenetics and computational species delimitation of Neotropical primates
inferredcites →https://doi.org/10.1016/j.cub.2014.06.034openalex-snapshot
Phylogenomics Resolves a Spider Backbone Phylogeny and Rejects a Prevailing Paradigm for Orb Web Evolution
inferredcites →https://doi.org/10.1016/j.cub.2015.09.066openalex-snapshot
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales
inferredcites →https://doi.org/10.1016/j.tig.2015.08.001openalex-snapshot
Dating Tips for Divergence-Time Estimation
inferredcites →https://doi.org/10.1016/j.tree.2014.07.004openalex-snapshot
The changing face of the molecular evolutionary clock
inferredcites →https://doi.org/10.1016/j.ympev.2011.12.007openalex-snapshot
Applications of next-generation sequencing to phylogeography and phylogenetics
inferredcites →https://doi.org/10.1016/j.ympev.2014.05.032openalex-snapshot
The impact of calibration and clock-model choice on molecular estimates of divergence times
inferredcites →https://doi.org/10.1038/s41467-018-05479-9openalex-snapshot
Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes
inferredcites →https://doi.org/10.1038/s42003-018-0176-6openalex-snapshot
Incomplete lineage sorting rather than hybridization explains the inconsistent phylogeny of the wisent
inferredcites →https://doi.org/10.1073/pnas.1213199109openalex-snapshot
Estimating divergence times in large molecular phylogenies
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/18.2.337openalex-snapshot
Generating samples under a Wright–Fisher neutral model of genetic variation
inferredcites →https://doi.org/10.1093/bioinformatics/btq062openalex-snapshot
Phybase: an R package for species tree analysis
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/genetics/110.2.325openalex-snapshot
GENE GENEALOGY AND VARIANCE OF INTERPOPULATIONAL NUCLEOTIDE DIFFERENCES
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/140.4.1421openalex-snapshot
Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling.
inferredcites →https://doi.org/10.1093/genetics/149.1.429openalex-snapshot
Maximum Likelihood Estimation of Population Growth Rates Based on the Coalescent
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/msg067openalex-snapshot
Heterogeneity of Nucleotide Frequencies Among Evolutionary Lineages and Phylogenetic Inference
inferredcites →https://doi.org/10.1093/molbev/msi103openalex-snapshot
Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences
inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot
Bayesian Inference of Species Trees from Multilocus Data
inferredcites →https://doi.org/10.1093/molbev/msr045openalex-snapshot
Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times
inferredcites →https://doi.org/10.1093/molbev/msr100openalex-snapshot
Fast and Slow Implementations of Relaxed-Clock Methods Show Similar Patterns of Accuracy in Estimating Divergence Times
inferredcites →https://doi.org/10.1093/molbev/msu200openalex-snapshot
Prospects for Building Large Timetrees Using Molecular Data with Incomplete Gene Coverage among Species
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/msu325openalex-snapshot
Phylogeny of Zebrafish, a “Model Species,” within Danio, a “Model Genus”
inferredcites →https://doi.org/10.1093/molbev/msv037openalex-snapshot
Tree of Life Reveals Clock-Like Speciation and Diversification
inferredcites →https://doi.org/10.1093/molbev/msv075openalex-snapshot
A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla
inferredcites →https://doi.org/10.1093/molbev/msv154openalex-snapshot
Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations
inferredcites →https://doi.org/10.1093/molbev/msw054openalex-snapshot
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
inferredcites →https://doi.org/10.1093/molbev/msw247openalex-snapshot
Fast and Accurate Estimates of Divergence Times from Big Data
inferredcites →https://doi.org/10.1093/molbev/msw267openalex-snapshot
Evolutionary History of the Asian Horned Frogs (Megophryinae): Integrative Approaches to Timetree Dating in the Absence of a Fossil Record
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/molbev/msx324openalex-snapshot
Phylogenomic Data Yield New and Robust Insights into the Phylogeny and Evolution of Weevils
inferredcites →https://doi.org/10.1093/molbev/msy044openalex-snapshot
Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates
inferredcites →https://doi.org/10.1093/molbev/msy096openalex-snapshot
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms
inferredcites →https://doi.org/10.1093/molbev/msy103openalex-snapshot
Undersampling Genomes has Biased Time and Rate Estimates Throughout the Tree of Life
inferredcites →https://doi.org/10.1093/molbev/msz014openalex-snapshot
A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies
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/sysbio/46.3.523openalex-snapshot
Gene Trees in Species Trees
inferredcites →https://doi.org/10.1093/sysbio/syr029openalex-snapshot
Simulating Trees with a Fixed Number of Extant Species
inferredcites →https://doi.org/10.1093/sysbio/sys051openalex-snapshot
High-Throughput Identification of Informative Nuclear Loci for Shallow-Scale Phylogenetics and Phylogeography
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/syy001openalex-snapshot
Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case
inferredcites →https://doi.org/10.1098/rsos.161061openalex-snapshot
Identifying hybridization and admixture using SNPs: application of the DArTseq platform in phylogeographic research on vertebrates
inferredcites →https://doi.org/10.1098/rspb.2012.0705openalex-snapshot
Single-locus species delimitation: a test of the mixed Yule–coalescent model, with an empirical application to Philippine round-leaf bats
inferredcites →https://doi.org/10.1098/rspb.2014.1013openalex-snapshot
Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors
inferredcites →https://doi.org/10.1098/rspb.2017.0227openalex-snapshot
Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution
inferredcites →https://doi.org/10.1111/1755-0998.12176openalex-snapshot
Next‐Gen phylogeography of rainforest trees: exploring landscape‐level cp DNA variation from whole‐genome sequencing
inferredcites →https://doi.org/10.1111/1755-0998.12320openalex-snapshot
Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
inferredcites →https://doi.org/10.1111/j.0014-3820.2000.tb01231.xopenalex-snapshot
PERSPECTIVE: GENE DIVERGENCE, POPULATION DIVERGENCE, AND THE VARIANCE IN COALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIES
inferredcites →https://doi.org/10.1111/j.0014-3820.2005.tb01072.xopenalex-snapshot
SPECIATIONAL HISTORY OF AUSTRALIAN GRASS FINCHES (POEPHILA) INFERRED FROM THIRTY GENE TREES
inferredcites →https://doi.org/10.1111/jbi.12591openalex-snapshot
Mitochondrial phylogeography and cryptic divergence in the stickleback genusPungitius
inferredcites →https://doi.org/10.1186/s12862-018-1160-yopenalex-snapshot
Phylogenomics and barcoding of Panax: toward the identification of ginseng species
inferredcites →https://doi.org/10.1214/aoms/1177730285openalex-snapshot
On the Generalized "Birth-and-Death" Process
inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1371/journal.pcbi.1003537openalex-snapshot
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
inferredcites →https://doi.org/10.1534/genetics.116.190173openalex-snapshot
Challenges in Species Tree Estimation Under the Multispecies Coalescent Model
inferredcites →https://doi.org/10.1554/0014-3820(2000)054[1839:pgdpda]2.0.co;2openalex-snapshot
PERSPECTIVE: GENE DIVERGENCE, POPULATION DIVERGENCE, AND THE VARIANCE INCOALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIES
inferredcites →https://doi.org/10.1554/04-385openalex-snapshot
GENE TREE DISTRIBUTIONS UNDER THE COALESCENT PROCESS
inferredcites →https://doi.org/10.25225/fozo.v64.i3.a2.2015openalex-snapshot
Next-generation sequencing and the expanding domain of phylogeography

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inferred← citeshttps://doi.org/10.1177/1176934319855988openalex-snapshot
The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis
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