Topic 83

inference evolutionary estimates estimation methods tree estimating statistical simulated estimate method data population phylogenetic inferring trees bayesian coalescent framework model models rates simulations infer inferences demographic likelihood assumptions can genetics history approach inferred scenarios error populations under when sampling empirical simulation rate selection phylogenies parameters bias accuracy paper uncertainty based individuals estimated genetic parameter time species use accounting sample markov it show number propose sampled sets approximate used size genomic be applied genotype variation accurate datasets performance analyses information package using statistics given real standard from approaches fit often distribution apply large illustrate tests errors test histories existing genealogies make

245 items. Top items listed below.

Towards an evolutionarily appropriate null model: jointly inferring demography and purifying selection 83 21 5 4

Estimating divergence times from DNA sequences 83 21 4

A minimal yet flexible likelihood framework to assess correlated evolution 83 21 4

Inference of Population Admixture Network from Local Gene Genealogies: a Coalescent-based Maximum Likelihood Approach 83 4

Detecting and quantifying natural selection at two linked loci from time series data of allele frequencies with forward-in-time simulations 83 4

Inferring the ancestry of parents and grandparents from genetic data 83 4

When species trees disagree: an approach consistent with the coalescent that quantifies phylogenomic support for contentious relationships 83 40 4

Efficient inference, potential, and limitations of site-specific substitution model 83 21 4

Limits and Convergence properties of the Sequentially Markovian Coalescent 83 4

On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo 83 4

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data 83 13 4

Exact decoding of the sequentially Markov coalescent 83 4

Inference of population genetic parameters from the continuously serial-sampled sequences of human seasonal influenza A/H3N2 83 21 4

Using high-throughput phenotypes to enable genomic selection by inferring genotypes 145 53 19 4

Variational Inference Using Approximate Likelihood Under the Coalescent With Recombination 83 4

Hierarchical modeling of haplotype effects based on a phylogeny 83 4

Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts 83 40 21 4

Identification of hidden population structure in time-scaled phylogenies 83 40 21 5 4

Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging 83 21 5 4

Inferring transmission bottleneck size from viral sequence data using a novel haplotype reconstruction method 83 41 4

Species Tree Inference under the Multispecies Coalescent on Data with Paralogs is Accurate 83 40 21 4

On the effects of selection and mutation on species tree inference 83 21 5 4

A computationally tractable birth-death model that combines phylogenetic and epidemiological data 83 4

Are skyline plot-based demographic estimates overly dependent on smoothing prior assumptions? 83 4

Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees 83 4

Accounting for Gene Flow from Unsampled `Ghost' Populations while Estimating Evolutionary History under the Isolation with Migration Model 83 21 5 4

Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic experiment 83 4

Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data 83 4

Maximum likelihood estimation of natural selection and allele age from time series data of allele frequencies 83 4

Using a supervised principal components analysis for variable selection in high-dimensional datasets reduces false discovery rates 123 83 4

On the effect of asymmetrical trait inheritance on models of trait evolution 83 21 5 4

Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy 83 40 4

SNP heritability: What are we estimating? 83 19 4

Multiple merger genealogies in outbreaks of Mycobacterium tuberculosis 83 21 5 4

Permutation tests for hypothesis testing with animal social data: problems and potential solutions 123 83 4

Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks 83 26 4

ModelTeller: model selection for optimal phylogenetic reconstruction using machine learning 83 26 4

Inferring number of populations and changes in connectivity under the n-island model 83 21 5 4

A Phylogenetic Approach to Inferring the Order in Which Mutations Arise during Cancer Progression 83 14 4

Phylogenetic signal is associated with the degree of variation in root-to-tip distances 83 40 21 5 4

On the automatic annotation of gene functions using observational data and phylogenetic trees 162 13 4

A Bayesian inference tool for identifying artifactual calls from differential transcript abundance analyses 83 4

Widespread selection against deleterious mutations in the Drosophila genome 83 21 4

Nucleotide substitutions during speciation may explain substitution rate variation 83 40 21 5

Inferring the Allelic Series at QTL in Multiparental Populations 145 83 19 4

Power analysis of transcriptome-wide association study: implications for practical protocol choice 145 123 19 4

Log Transformation Improves Dating of Phylogenies 83 4

Using visual encounter data to improve capture-recapture abundance estimates 83 4

Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression 83 40 21 4

Consistency of SVDQuartets and Maximum Likelihood for Coalescent-based Species Tree Estimation 83 40 4

Fast and accurate approximation of the joint site frequency spectrum of multiple populations 145 83 4

Deep learning for population size history inference: design, comparison and combination with approximate Bayesian computation 83 26 4

Efficient approaches for large scale GWAS studies with genotype uncertainty 145 83 4

Controlling for Human Population Stratification in Rare Variant Association Studies 145 123 19 4

Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations 21 5 4

Testing for Dependence on Tree Structures 123 83 4

Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes 83 4

Estimating cumulative incidence of SARS-CoV-2 with imperfect serological tests: a cutoff-free approach 83 4

Phylogeographic model selection using convolutional neural networks 83 26 21 5 4

Joint nonparametric coalescent inference of mutation spectrum history and demography 83 21 5 4

An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data 83 5 4

Ignoring fossil age uncertainty leads to inaccurate topology and divergence times in time calibrated tree inference 83 40 4

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations 83 40 21 4

Efficiently summarizing relationships in large samples: a general duality between statistics of genealogies and genomes 83 4

A deep learning framework for characterization of genotype data 26 4

Expanding the utility of sequence comparisons using data from whole genomes 83 4

Relative model fit does not predict topological accuracy in single-gene protein phylogenetics 83 4

Spatial Proximity Moderates Genotype Uncertainty in Genetic Tagging Studies 83 4

QMaker: Fast and accurate method to estimate empirical models of protein evolution 83 62 4

Detecting adaptive introgression in human evolution using convolutional neural networks 83 21 4

Capturing biodiversity complexities while accounting for imperfect detection: the application of occupancy-based diversity profiles. 83 17 5 4

Assessing the Performance of qpAdm: A Statistical Tool for Studying Population Admixture 145 83 4

Variation in recombination rate affects detection of outliers in genome scans under neutrality 21 5 4

Macroevolutionary analysis of discrete character evolution using parsimony-informed likelihood 83 21 4

Comparison of methods for estimating genetic correlation between complex traits using GWAS summary statistics 19 4

Detecting sex-linked genes using genotyped individuals sampled in natural populations 145 83 4

Multiple Haplotype Reconstruction from Allele Frequency Data 145 83 4

Estimating predator functional responses using the times between prey captures 83 38 17 4

GxEsum: genotype-by-environment interaction model based on summary statistics 19 4

ILS-Aware Analyses of Retroelement Insertions in the Anomaly Zone 83 40 4

GeneRax: A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss. 162 83 13 4

How well do crop modeling groups predict wheat phenology, given calibration data from the target population? 182 83 38 4

Evaluation of the minimum sampling design for population genomic and microsatellite studies. An analysis based on wild maize. 145 83 21 5 4

iucn_sim: A new program to simulate future extinctions based on IUCN threat status 83 4

MRLocus: identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity 19 13 4

A General Birth-Death-Sampling Model for Epidemiology and Macroevolution 83 38 4

The impact of purifying and background selection on the inference of population history: problems and prospects 83 21 5 4

A hierarchical point process model for spatial capture-recapture data 83 4

Inferring Causal Direction Between Two Traits in the Presence of Horizontal Pleiotropy with GWAS Summary Data 123 83 19 4

Ancestral Haplotype Reconstruction in Endogamous Populations using Identity-By-Descent 145 83 4

Jointly modeling prevalence, sensitivity and specificity for optimal sample allocation 83 4

Precision as a metric for acoustic survey design using occupancy or spatial capture-recapture 83 4

Numerical simulation of the two-locus Wright-Fisher stochastic differential equation with application to approximating transition probability densities 83 38 4

Estimating and accounting for genotyping errors in RAD-seq experiments 145 83 4

The Multispecies Coalescent in Space and Time 83 40 21 5 4

Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring 43 4

Rare variant enriched identity-by-descent enables the detection of distant relatedness and older divergence between populations 145 83 4

Robust Genomic Modelling Using Expert Knowledge about Additive, Dominance and Epistasis Variation 83 53 4

Estimation of Non-null SNP Effect Size Distributions Enables the Detection of Enriched Genes Underlying Complex Traits 19 4

Testing for population decline using maximal linkage disequilibrium blocks 83 4