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A new method for detecting autocorrelation of evolutionary rates in large phylogenies

https://doi.org/10.1101/346635
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Mammalian Evolutionary Morphology
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
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Detecting Regular Sound Changes in Linguistics as Events of Concerted Evolution
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Machine learning for ecosystem services
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Evolution of the mutation rate
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Supervised Machine Learning for Population Genetics: A New Paradigm
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Watching the clock: Studying variation in rates of molecular evolution between species
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The Neutral Theory of Molecular Evolution
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Evolution of the Rodents
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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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Zika virus evolution and spread in the Americas
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Machine learning: supervised methods
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Bayesian molecular clock dating of species divergences in the genomics era
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Molecular clocks: four decades of evolution
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The Neutral Theory of Molecular Evolution
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Mutation rates in mammalian genomes
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An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants
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Estimating divergence times in large molecular phylogenies
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Phylotranscriptomic analysis of the origin and early diversification of land plants
inferredcites →https://doi.org/10.1073/pnas.1423653112openalex-snapshot
Early evolution of the angiosperm clade Asteraceae in the Cretaceous of Antarctica
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Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
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Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary
inferredcites →https://doi.org/10.1073/pnas.80.14.4394openalex-snapshot
Birds, behavior, and anatomical evolution.
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The molecular clock may be an episodic clock.
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Correlates of Diversification in the Plant Clade Dipsacales: Geographic Movement and Evolutionary Innovations
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Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
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TimeTree: a public knowledge-base of divergence times among organisms
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MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis
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Global Rate Variation in Bony Vertebrates
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/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msm193openalex-snapshot
A General Comparison of Relaxed Molecular Clock Models
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A Major Clade of Prokaryotes with Ancient Adaptations to Life on Land
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Performance of Relaxed-Clock Methods in Estimating Evolutionary Divergence Times and Their Credibility Intervals
inferredcites →https://doi.org/10.1093/molbev/msr284openalex-snapshot
Selective Sweep of a cis-Regulatory Sequence in a Non-African Population of Drosophila melanogaster
inferredcites →https://doi.org/10.1093/molbev/mss243openalex-snapshot
Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics
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/msv266openalex-snapshot
The Impact of Missing Data on Species Tree Estimation
inferredcites →https://doi.org/10.1093/molbev/msw026openalex-snapshot
Advances in Time Estimation Methods for Molecular Data
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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
inferredcites →https://doi.org/10.1093/molbev/msx285openalex-snapshot
Mode and Rate of Evolution of Haemosporidian Mitochondrial Genomes: Timing the Radiation of Avian Parasites
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/oso/9780199535033.001.0001openalex-snapshot
The Timetree of Life
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.a025731openalex-snapshot
A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy
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/oxfordjournals.molbev.a040454openalex-snapshot
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
inferredcites →https://doi.org/10.1093/sysbio/syp017openalex-snapshot
The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference
inferredcites →https://doi.org/10.1093/sysbio/syq085openalex-snapshot
Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection
inferredcites →https://doi.org/10.1093/sysbio/syr009openalex-snapshot
Evaluation of Bayesian Models of Substitution Rate Evolution—Parental Guidance versus Mutual Independence
inferredcites →https://doi.org/10.1093/sysbio/syt072openalex-snapshot
Molecular Dating, Evolutionary Rates, and the Age of the Grasses
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/syu036openalex-snapshot
Mixture Models of Nucleotide Sequence Evolution that Account for Heterogeneity in the Substitution Process Across Sites and Across Lineages
inferredcites →https://doi.org/10.1093/sysbio/syv027openalex-snapshot
Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms
inferredcites →https://doi.org/10.1093/sysbio/syw086openalex-snapshot
Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale
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/rspb.2001.1782openalex-snapshot
Evolution of the angiosperms: calibrating the family tree
inferredcites →https://doi.org/10.1098/rspb.2012.0683openalex-snapshot
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
inferredcites →https://doi.org/10.1098/rstb.2015.0132openalex-snapshot
A mixed relaxed clock model
inferredcites →https://doi.org/10.1109/ijcnn.2017.7966298openalex-snapshot
Using synthetic data to train neural networks is model-based reasoning
inferredcites →https://doi.org/10.1111/1755-0998.12320openalex-snapshot
Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
inferredcites →https://doi.org/10.1111/2041-210x.13256openalex-snapshot
Applications for deep learning in ecology
inferredcites →https://doi.org/10.1111/boj.12260openalex-snapshot
Phylogenetics, divergence times and diversification from three genomic partitions in monocots
inferredcites →https://doi.org/10.1111/mec.12953openalex-snapshot
Molecular‐clock methods for estimating evolutionary rates and timescales
inferredcites →https://doi.org/10.1111/nph.15011openalex-snapshot
Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution
inferredcites →https://doi.org/10.1126/sciadv.1501005openalex-snapshot
A new time tree reveals Earth history’s imprint on the evolution of modern birds
inferredcites →https://doi.org/10.1126/science.1206375openalex-snapshot
The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals
inferredcites →https://doi.org/10.1126/science.1211028openalex-snapshot
Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification
inferredcites →https://doi.org/10.1126/science.1253451openalex-snapshot
Whole-genome analyses resolve early branches in the tree of life of modern birds
inferredcites →https://doi.org/10.1126/science.1257570openalex-snapshot
Phylogenomics resolves the timing and pattern of insect evolution
inferredcites →https://doi.org/10.1186/1471-2148-11-311openalex-snapshot
A Bayesian framework to estimate diversification rates and their variation through time and space
inferredcites →https://doi.org/10.1186/1471-2148-14-23openalex-snapshot
From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
inferredcites →https://doi.org/10.1186/1471-2164-15-977openalex-snapshot
Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria
inferredcites →https://doi.org/10.1186/1741-7007-6-6openalex-snapshot
Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages
inferredcites →https://doi.org/10.1186/s12983-016-0162-0openalex-snapshot
Evolution of body morphology and beak shape revealed by a morphometric analysis of 14 Paridae species
inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1371/journal.pgen.1005928openalex-snapshot
S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning
inferredcites →https://doi.org/10.1371/journal.pone.0107679openalex-snapshot
Phylogeny and Divergence Times of Gymnosperms Inferred from Single-Copy Nuclear Genes
inferredcites →https://doi.org/10.1371/journal.ppat.1005574openalex-snapshot
The Ancient Evolutionary History of Polyomaviruses
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/10.3724/sp.j.1002.2008.08040openalex-snapshot
Missing data and the accuracy of Bayesian phylogenetics
inferredcites →https://doi.org/10.3732/ajb.0900346openalex-snapshot
The age and diversification of the angiosperms re‐revisited
inferredcites →https://doi.org/10.3732/ajb.1200416openalex-snapshot
Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates
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Synthetic Data Generation for Deep Learning in Counting Pedestrians

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

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Isolation and characterization of PoWRKY, an abiotic stress-related WRKY transcription factor from Polygonatum odoratum
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Transmission of SARS-CoV-2 in South Asian countries: molecular evolutionary model based phylogenetic and mutation analysis
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Morphological and molecular analysis of the freshwater copepod Heliodiaptomus viduus (Calanoida: Diaptomidae)
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A new method for inferring timetrees from temporally sampled molecular sequences
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