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Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees

https://doi.org/10.1101/260745
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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/bf00137351openalex-snapshot
Dollo on Dollo's law: Irreversibility and the status of evolutionary laws
inferredcites →https://doi.org/10.1016/j.cell.2008.06.030openalex-snapshot
Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution
inferredcites →https://doi.org/10.1016/j.cell.2014.05.034openalex-snapshot
Expansion of Biological Pathways Based on Evolutionary Inference
inferredcites →https://doi.org/10.1016/j.celrep.2012.08.032openalex-snapshot
A “Forward Genomics” Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species
inferredcites →https://doi.org/10.1016/j.cub.2016.10.029openalex-snapshot
Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites
inferredcites →https://doi.org/10.1016/j.tig.2004.09.005openalex-snapshot
Mammalian phylogenomics comes of age
inferredcites →https://doi.org/10.1016/j.tree.2014.04.001openalex-snapshot
Molecular evolution tracks macroevolutionary transitions in Cetacea
inferredcites →https://doi.org/10.1016/j.ydbio.2005.04.005openalex-snapshot
Foxg1 is required for specification of ventral telencephalon and region-specific regulation of dorsal telencephalic precursor proliferation and apoptosis
inferredcites →https://doi.org/10.1016/j.ydbio.2007.03.166openalex-snapshot
Gas1 extends the range of hedgehog action by facilitating its signaling
inferredcites →https://doi.org/10.1038/nature09774openalex-snapshot
Human-specific loss of regulatory DNA and the evolution of human-specific traits
inferredcites →https://doi.org/10.1038/nature10530openalex-snapshot
A high-resolution map of human evolutionary constraint using 29 mammals
inferredcites →https://doi.org/10.1038/nature12511openalex-snapshot
Genome-wide signatures of convergent evolution in echolocating mammals
inferredcites →https://doi.org/10.1038/nbt.1630openalex-snapshot
GREAT improves functional interpretation of cis-regulatory regions
inferredcites →https://doi.org/10.1038/ng.3198openalex-snapshot
Convergent evolution of the genomes of marine mammals
inferredcites →https://doi.org/10.1038/nrg.2016.11openalex-snapshot
Causes of molecular convergence and parallelism in protein evolution
inferredcites →https://doi.org/10.1038/nrg3098openalex-snapshot
Variation in the mutation rate across mammalian genomes
inferredcites →https://doi.org/10.1038/nrg3483openalex-snapshot
The genetic causes of convergent evolution
inferredcites →https://doi.org/10.1038/s41467-018-07122-zopenalex-snapshot
Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution
inferredcites →https://doi.org/10.1073/pnas.0803242105openalex-snapshot
Phylogenomic evidence for multiple losses of flight in ratite birds
inferredcites →https://doi.org/10.1073/pnas.1818532116openalex-snapshot
A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales
inferredcites →https://doi.org/10.1074/jbc.m603984200openalex-snapshot
TTLL7 Is a Mammalian β-Tubulin Polyglutamylase Required for Growth of MAP2-positive Neurites
inferredcites →https://doi.org/10.1080/01621459.1994.10476829openalex-snapshot
The Collapsed Gibbs Sampler in Bayesian Computations with Applications to a Gene Regulation Problem
inferredcites →https://doi.org/10.1080/10635150701420643openalex-snapshot
Inferring Speciation Times under an Episodic Molecular Clock
inferredcites →https://doi.org/10.1093/bib/bbq072openalex-snapshot
PHAST and RPHAST: phylogenetic analysis with space/time models
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/molbev/msh039openalex-snapshot
Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot
Bayesian Inference of Species Trees from Multilocus Data
inferredcites →https://doi.org/10.1093/molbev/msq244openalex-snapshot
A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters
inferredcites →https://doi.org/10.1093/molbev/msq263openalex-snapshot
A Likelihood Method for Detecting Trait-Dependent Shifts in the Rate of Molecular Evolution
inferredcites →https://doi.org/10.1093/molbev/msr255openalex-snapshot
A Dirichlet Process Prior for Estimating Lineage-Specific Substitution Rates
inferredcites →https://doi.org/10.1093/molbev/msr279openalex-snapshot
The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome
inferredcites →https://doi.org/10.1093/molbev/msu153openalex-snapshot
Genomic Support for a Moa–Tinamou Clade and Adaptive Morphological Convergence in Flightless Ratites
inferredcites →https://doi.org/10.1093/molbev/msv344openalex-snapshot
Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor
inferredcites →https://doi.org/10.1093/molbev/msw001openalex-snapshot
“Reverse Genomics” Predicts Function of Human Conserved Noncoding Elements
inferredcites →https://doi.org/10.1093/molbev/msw098openalex-snapshot
Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species’ Phenotypic and Genomic Differences
inferredcites →https://doi.org/10.1093/molbev/msw112openalex-snapshot
Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals
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/nar/gky741openalex-snapshot
Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals
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/22.3.240openalex-snapshot
Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters
inferredcites →https://doi.org/10.1093/sysbio/syw018openalex-snapshot
Gene Tree Discordance Causes Apparent Substitution Rate Variation
inferredcites →https://doi.org/10.1093/sysbio/syx032openalex-snapshot
An Integrated Model of Phenotypic Trait Changes and Site-Specific Sequence Evolution
inferredcites →https://doi.org/10.1098/rsbl.2007.0191openalex-snapshot
The olfactory receptor gene repertoires in secondary-adapted marine vertebrates: evidence for reduction of the functional proportions in cetaceans
inferredcites →https://doi.org/10.1101/gr.097857.109openalex-snapshot
Detection of nonneutral substitution rates on mammalian phylogenies
inferredcites →https://doi.org/10.1101/gr.1933104openalex-snapshot
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
inferredcites →https://doi.org/10.1101/gr.3715005openalex-snapshot
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
inferredcites →https://doi.org/10.1111/evo.12832openalex-snapshot
Irrational exuberance for resolved species trees
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/10.1111/j.2041-210x.2011.00169.xopenalex-snapshot
phytools: an R package for phylogenetic comparative biology (and other things)
inferredcites →https://doi.org/10.1126/science.1098119openalex-snapshot
Ultraconserved Elements in the Human Genome
inferredcites →https://doi.org/10.1126/science.1130708openalex-snapshot
Ancient Noncoding Elements Conserved in the Human Genome
inferredcites →https://doi.org/10.1126/science.1212986openalex-snapshot
The Molecular Diversity of Adaptive Convergence
inferredcites →https://doi.org/10.1126/science.1251981openalex-snapshot
Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution
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.1254390openalex-snapshot
Evidence for a single loss of mineralized teeth in the common avian ancestor
inferredcites →https://doi.org/10.1126/science.276.5310.227openalex-snapshot
Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context
inferredcites →https://doi.org/10.1126/science.aat7244openalex-snapshot
Convergent regulatory evolution and loss of flight in paleognathous birds
inferredcites →https://doi.org/10.1128/mcb.25.13.5699-5711.2005openalex-snapshot
Transcription Factor KLF7 Is Important for Neuronal Morphogenesis in Selected Regions of the Nervous System
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110512-135828openalex-snapshot
Genomics and the Evolution of Phenotypic Traits
inferredcites →https://doi.org/10.1146/annurev-ecolsys-120213-091851openalex-snapshot
The Molecular Basis of Phenotypic Convergence
inferredcites →https://doi.org/10.1146/annurev-genom-082908-150001openalex-snapshot
Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes
inferredcites →https://doi.org/10.1146/annurev.ecolsys.28.1.437openalex-snapshot
Phylogeny Estimation and Hypothesis Testing Using Maximum Likelihood
inferredcites →https://doi.org/10.1186/1741-7007-8-114openalex-snapshot
Bayesian random local clocks, or one rate to rule them all
inferredcites →https://doi.org/10.1198/jcgs.2009.06134openalex-snapshot
Examples of Adaptive MCMC
inferredcites →https://doi.org/10.1214/18-aoas1208openalex-snapshot
Bayesian hidden Markov tree models for clustering genes with shared evolutionary history
inferredcites →https://doi.org/10.1371/journal.pbio.0030007openalex-snapshot
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development
inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1371/journal.pbio.0060063openalex-snapshot
Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation
inferredcites →https://doi.org/10.1371/journal.pcbi.1003537openalex-snapshot
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
inferredcites →https://doi.org/10.1371/journal.pgen.0020168openalex-snapshot
Forces Shaping the Fastest Evolving Regions in the Human Genome
inferredcites →https://doi.org/10.1371/journal.pgen.1003684openalex-snapshot
A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1005738openalex-snapshot
Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus
inferredcites →https://doi.org/10.1554/04-309openalex-snapshot
THE PROBABILITY OF PARALLEL EVOLUTION
inferredcites →https://doi.org/10.2307/2291091openalex-snapshot
Bayes Factors
inferredcites →https://doi.org/10.7554/elife.25884openalex-snapshot
Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling

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

inferred← citeshttps://doi.org/10.1093/bioinformatics/btz468openalex-snapshot
RERconverge: an R package for associating evolutionary rates with convergent traits
inferred← citeshttps://doi.org/10.1126/science.aat7244openalex-snapshot
Convergent regulatory evolution and loss of flight in paleognathous birds
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