(Q111742440)

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

author

Oksana Vernygora

1

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Erin O Campbell

2

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Nick Grishin

3

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Felix A. H. Sperling

4

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Julian R. Dupuis

5

object named as

Julian R. Dupuis

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

publication date

June 2022

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

published in

Molecular Phylogenetics and Evolution

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

volume

171

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

page(s)

107465

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107465

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

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Time to standardize taxonomies

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Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies.

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Genome-wide data delimits multiple climate-determined species ranges in a widespread Australian fish, the golden perch (Macquaria ambigua).

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BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

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Bayesian molecular dating: opening up the black box.

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Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.

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Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support

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Data partitioning and correction for ascertainment bias reduce the uncertainty of placental mammal divergence times inferred from the morphological clock

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Would an RRS by any other name sound as RAD?

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Single nucleotide polymorphism‐based species phylogeny of greater fritillary butterflies (Lepidoptera: Nymphalidae: Speyeria ) demonstrates widespread mitonuclear discordance

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The implications of lineage-specific rates for divergence time estimation

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Insights from Empirical Analyses and Simulations on Using Multiple Fossil Calibrations with Relaxed Clocks to Estimate Divergence Times

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Uncertainty in divergence time estimation

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Stacks: building and genotyping Loci de novo from short-read sequences

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Papilio phylogeny based on mitochondrial cytochrome oxidase I and II genes

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Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

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Global biogeographical pattern of swallowtail diversification demonstrates alternative colonization routes in the Northern and Southern hemispheres

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What causes latitudinal gradients in species diversity? Evolutionary processes and ecological constraints on swallowtail biodiversity

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Tiger Swallowtail Genome Reveals Mechanisms for Speciation and Caterpillar Chemical Defense

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ddRAD-seq phylogenetics based on nucleotide, indel, and presence-absence polymorphisms: Analyses of two avian genera with contrasting histories

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The variant call format and VCFtools

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ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

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Solid-phase reversible immobilization for the isolation of PCR products

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex.

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Hybrid dynamics in a species group of swallowtail butterflies

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Worldwide phylogeny of three-spined sticklebacks

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Rates of niche and phenotype evolution lag behind diversification in a temperate radiation

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

New skulls and skeletons of the Cretaceous legged snake Najash, and the evolution of the modern snake body plan

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short‐necked turtles (Chelidae: Emydura ) of eastern Australia

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Dental evolutionary rates and its implications for the Neanderthal-modern human divergence.

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Correction to 'Extraordinarily rapid life-history divergence between Cryptasterina sea star species'

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

North Pacific seasonality and the glaciation of North America 2.7 million years ago.

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

The fossilized birth-death process for coherent calibration of divergence-time estimates

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Bayesian inference of species trees from multilocus data

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

The Timing and Direction of Introgression Under the Multispecies Network Coalescent

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Time-dependent rates of molecular evolution

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Reconciling hierarchical taxonomy with molecular phylogenies

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

A simulation study to examine the information content in phylogenomic datasets under the multispecies coalescent model

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

The Origin of Grass-Dominated Ecosystems

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

The Multispecies Coalescent Model Outperforms Concatenation across Diverse Phylogenomic Data Sets

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Did the pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshopprers

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K.

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

A temporal banding approach for consistent taxonomic ranking above the species level.

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Inconsistency of phylogenetic estimates from concatenated data under coalescence

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Sex chromosome mosaicism and hybrid speciation among tiger swallowtail butterflies

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Fast gapped-read alignment with Bowtie 2

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Species delimitation using genome-wide SNP data

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

popart : full‐feature software for haplotype network construction

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Renewing Felsenstein's phylogenetic bootstrap in the era of big data.

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

A likelihood approach to estimating phylogeny from discrete morphological character data

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

The Sequence Alignment/Map format and SAMtools

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

StructureSelector: A web-based software to select and visualize the optimal number of clusters using multiple methods.

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

BEST: Bayesian estimation of species trees under the coalescent model.

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

The evolutionary history of the embiotocid surfperch radiation based on genome-wide RAD sequence data

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Optimization of Genotype by Sequencing data for phylogenetic purposes

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Single nucleotide polymorphisms (SNPs) provide unprecedented resolution of species boundaries, phylogenetic relationships, and genetic diversity in the mastiff bats (Molossus)

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Gene flow and climate-associated genetic variation in a vagile habitat specialist

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Atlantic forests to the all Americas: Biogeographical history and divergence times of Neotropical Ficus (Moraceae).

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Cutadapt removes adapter sequences from high-throughput sequencing reads

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays.

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Applications of next-generation sequencing to phylogeography and phylogenetics

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Tempo and timing of ecological trait divergence in bird speciation

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Hybridization leads to host-use divergence in a polyphagous butterfly sibling species pair

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Diversification of host use in two polyphagous butterflies: differences in oviposition specificity or host rank hierarchy?

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

ASTRAL: genome-scale coalescent-based species tree estimation

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Implementing Large Genomic SNP Datasets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Phylogeny of Hawaiian Melicope (Rutaceae): RAD-seq Resolves Species Relationships and Reveals Ancient Introgression

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Use of RAD sequencing for delimiting species

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Inference of population structure using multilocus genotype data

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Regional climate shifts caused by gradual global cooling in the Pliocene epoch

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent.

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Closing the gap between rocks and clocks using total-evidence dating

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Ascertainment correction for a population tree via a pruning algorithm for likelihood computation

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Climate-mediated hybrid zone movement revealed with genomics, museum collection, and simulation modeling.

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Species trees from consensus Single Nucleotide Polymorphism (SNP) data: testing phylogenetic approaches with simulated and empirical data.

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Reciprocal latitudinal clines in oviposition behavior ofPapilio glaucus andP. canadensis across the Great Lakes hybrid zone: possible sex-linkage of oviposition preferences.

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

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https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Bayesian Divergence-Time Estimation with Genome-Wide SNP Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus.

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Tempo and mode of speciation in Holacanthus angelfishes based on RADseq markers

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Molecules and fossils tell distinct yet complementary stories of mammal diversification

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Total evidence or taxonomic congruence? A comparison of methods for combining biological evidence

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Coalescent-based species delimitation in the sand lizards of the Liolaemus wiegmannii complex (Squamata: Liolaemidae)

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Ice sheets promote speciation in boreal birds

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Phylogeny and Historical Biogeography of Asian Pterourus Butterflies (Lepidoptera: Papilionidae): A Case of Intercontinental Dispersal from North America to East Asia

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Terrestrial mountain islands and Pleistocene climate fluctuations as motors for speciation: A case study on the genus Pseudovelia (Hemiptera: Veliidae)

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Molecular phylogeny, historical biogeography, and divergence time estimates for swallowtail butterflies of the genus Papilio (Lepidoptera: Papilionidae).

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling.

1 reference

https://api.crossref.org/v1/works/10.1016/j.ympev.2022.107465

Simple cDNA normalization using kamchatka crab duplex-specific nuclease

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