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Accuracy of Coalescent Likelihood Estimates: Do We Need More Sites, More Sequences, or More Loci?

https://doi.org/10.1093/molbev/msj079
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What this work says

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

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Inference from Gene Trees in a Subdivided Population
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Progress in Population Genetics and Human Evolution
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Genealogical-tree probabilities in the infinitely-many-site model
inferredcites →https://doi.org/10.1016/0040-5809(75)90020-9openalex-snapshot
On the number of segregating sites in genetical models without recombination
inferredcites →https://doi.org/10.1016/0304-4149(82)90011-4openalex-snapshot
The coalescent
inferredcites →https://doi.org/10.1017/s0016672300030354openalex-snapshot
Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates
inferredcites →https://doi.org/10.1017/s0016672300030962openalex-snapshot
Estimating effective population size from samples of sequences: a bootstrap Monte Carlo integration method
inferredcites →https://doi.org/10.1017/s0021900200034446openalex-snapshot
On the genealogy of large populations
inferredcites →https://doi.org/10.1073/pnas.081068098openalex-snapshot
Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach
inferredcites →https://doi.org/10.1089/cmb.1996.3.479openalex-snapshot
Ancestral Inference from Samples of DNA Sequences with Recombination
inferredcites →https://doi.org/10.1093/genetics/105.2.437openalex-snapshot
EVOLUTIONARY RELATIONSHIP OF DNA SEQUENCES IN FINITE POPULATIONS
inferredcites →https://doi.org/10.1093/genetics/133.3.693openalex-snapshot
Statistical tests of neutrality of mutations.
inferredcites →https://doi.org/10.1093/genetics/136.2.685openalex-snapshot
A phylogenetic estimator of effective population size or mutation rate.
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/144.3.1247openalex-snapshot
Optimal Sequencing Strategies for Surveying Molecular Genetic Diversity
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/152.2.763openalex-snapshot
Maximum-Likelihood Estimation of Migration Rates and Effective Population Numbers in Two Populations Using a Coalescent Approach
inferredcites →https://doi.org/10.1093/genetics/156.3.1393openalex-snapshot
Maximum Likelihood Estimation of Recombination Rates From Population Data
inferredcites →https://doi.org/10.1098/rstb.1994.0079openalex-snapshot
Sampling theory for neutral alleles in a varying environment
inferredcites →https://doi.org/10.1111/1467-985x.00264openalex-snapshot
Inferences from DNA Data: Population Histories, Evolutionary Processes and Forensic Match Probabilities
inferredcites →https://doi.org/10.1111/j.2517-6161.1970.tb00828.xopenalex-snapshot
Estimation of the Branch Points of a Branching Diffusion Process
inferredcites →https://doi.org/10.1146/annurev.ge.22.120188.002513openalex-snapshot
PHYLOGENIES FROM MOLECULAR SEQUENCES: INFERENCE AND RELIABILITY
inferredcites →https://doi.org/10.1214/ss/1177010378openalex-snapshot
Ancestral Inference in Population Genetics

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inferred← citeshttps://doi.org/10.1111/1755-0998.12602openalex-snapshot
Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome
inferred← citeshttps://doi.org/10.1111/1755-0998.12632openalex-snapshot
Small‐ and large‐scale heterogeneity in genetic variation across the collard flycatcher genome: implications for estimating genetic diversity in nonmodel organisms
inferred← citeshttps://doi.org/10.1111/2041-210x.12347openalex-snapshot
Theoretical expectations of the Isolation–Migration model of population evolution for inferring demographic parameters
inferred← citeshttps://doi.org/10.1111/bij.12668openalex-snapshot
Species divergence in field crickets: genetics, song, ecomorphology, and pre- and postzygotic isolation
inferred← citeshttps://doi.org/10.1111/eva.12274openalex-snapshot
Morphological and genomic comparisons of H awaiian and J apanese B lack‐footed A lbatrosses ( P hoebastria nigripes) using double digest RAD seq: implications for conservation
inferred← citeshttps://doi.org/10.1111/eva.12712openalex-snapshot
A coalescent sampler successfully detects biologically meaningful population structure overlooked by F‐statistics
inferred← citeshttps://doi.org/10.1111/eva.13495openalex-snapshot
Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec
inferred← citeshttps://doi.org/10.1111/evo.12280openalex-snapshot
THE INFLUENCE OF SAMPLING DESIGN ON SPECIES TREE INFERENCE: A NEW RELATIONSHIP FOR THE NEW WORLD CHICKADEES (AVES:POECILE)
inferred← citeshttps://doi.org/10.1111/evo.12916openalex-snapshot
Community trees: Identifying codiversification in the Páramo dipteran community
inferred← citeshttps://doi.org/10.1111/evo.12924openalex-snapshot
Phylogeographic concordance factors quantify phylogeographic congruence among co-distributed species in theSarracenia alatapitcher plant system
inferred← citeshttps://doi.org/10.1111/j.0014-3820.2006.tb01880.xopenalex-snapshot
TEST FOR SIMULTANEOUS DIVERGENCE USING APPROXIMATE BAYESIAN COMPUTATION
inferred← citeshttps://doi.org/10.1111/j.1095-8312.2011.01712.xopenalex-snapshot
Phylogeography and population structure of European sea bass in the north-east Atlantic
inferred← citeshttps://doi.org/10.1111/j.1365-2699.2012.02683.xopenalex-snapshot
Phylogeography of the medically important mosquito Aedes (Ochlerotatus) vigilax (Diptera: Culicidae) in Australasia
inferred← citeshttps://doi.org/10.1111/j.1365-2699.2012.02775.xopenalex-snapshot
Assessing model fit in phylogeographical investigations: an example from the N orth A merican sandbar willow S alix melanopsis
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2006.03085.xopenalex-snapshot
Nearshore fish (Pholis gunnellus) persists across the North Atlantic through multiple glacial episodes
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2009.04212.xopenalex-snapshot
Divergence population genetic analysis of hybridization between rhesus and cynomolgus macaques
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2009.04404.xopenalex-snapshot
Contrasting signals from multiple markers illuminate population connectivity in a marine fish
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2010.04722.xopenalex-snapshot
Lizards as model organisms for linking phylogeographic and speciation studies
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2010.04767.xopenalex-snapshot
Postglacial history of a widespread conifer produces inverse clines in selective neutrality tests
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2010.04978.xopenalex-snapshot
Phylogeography of a pan-Atlantic abyssal protobranch bivalve: implications for evolution in the Deep Atlantic
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2011.05008.xopenalex-snapshot
Mitochondrial and nuclear DNA sequences reveal recent divergence in morphologically indistinguishable petrels
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2011.05190.xopenalex-snapshot
Multilocus analysis of the evolutionary dynamics of rainforest bird populations in Southeast Asia
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2011.05307.xopenalex-snapshot
Climate-driven genetic divergence of limpets with different life histories across a southeast African marine biogeographic disjunction: different processes, same outcome
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2011.05343.xopenalex-snapshot
Isolation and gene flow: inferring the speciation history of European house mice
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2012.05576.xopenalex-snapshot
Common misconceptions in molecular ecology: echoes of the modern synthesis
inferred← citeshttps://doi.org/10.1111/j.1365-294x.2012.05700.xopenalex-snapshot
A likelihood‐based comparison of population histories in a parasitoid guild
inferred← citeshttps://doi.org/10.1111/j.1471-8286.2007.01685.xopenalex-snapshot
Mark–recapture cloning: a straightforward and cost‐effective cloning method for population genetics of single‐copy nuclear DNA sequences in diploids
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2007.00043.xopenalex-snapshot
ESTIMATING A GEOGRAPHICALLY EXPLICIT MODEL OF POPULATION DIVERGENCE
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2007.00095.xopenalex-snapshot
TESTING THE ROLE OF INTERSPECIFIC COMPETITION IN THE EVOLUTIONARY ORIGIN OF ELEVATIONAL ZONATION: AN EXAMPLE WITHBUARREMONBRUSH-FINCHES (AVES, EMBERIZIDAE) IN THE NEOTROPICAL MOUNTAINS
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2008.00414.xopenalex-snapshot
ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2008.00549.xopenalex-snapshot
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2010.01071.xopenalex-snapshot
NUCLEAR AND MITOCHONDRIAL SEQUENCE DATA REVEAL AND CONCEAL DIFFERENT DEMOGRAPHIC HISTORIES AND POPULATION GENETIC PROCESSES IN CARIBBEAN REEF FISHES
inferred← citeshttps://doi.org/10.1111/j.1558-5646.2011.01287.xopenalex-snapshot
DIVERSITY AND DEMOGRAPHY IN BERINGIA: MULTILOCUS TESTS OF PALEODISTRIBUTION MODELS REVEAL THE COMPLEX HISTORY OF ARCTIC GROUND SQUIRRELS
inferred← citeshttps://doi.org/10.1111/j.1600-0706.2009.17555.xopenalex-snapshot
On the relationship between population differentiation and sampling effort: is more always better?
inferred← citeshttps://doi.org/10.1111/j.1748-7692.2011.00551.xopenalex-snapshot
Examination of ten thousand years of mitochondrial DNA diversity and population demographics in bowhead whales (Balaena mysticetus) of the Central Canadian Arctic
inferred← citeshttps://doi.org/10.1111/j.1755-0998.2009.02574.xopenalex-snapshot
A combination of techniques proves useful in the development of nuclear markers in the newt genus Triturus
inferred← citeshttps://doi.org/10.1111/j.1755-0998.2011.03036.xopenalex-snapshot
Genotyping HapSTR loci: phase determination from direct sequencing of PCR products
inferred← citeshttps://doi.org/10.1111/jbi.12217openalex-snapshot
Phylogeography and trans‐Pacific divergence of the rocky shore gastropod Nucella lima
inferred← citeshttps://doi.org/10.1111/jbi.12434openalex-snapshot
Distributional dynamics and interspecific gene flow in Picea likiangensis and P. wilsonii triggered by climate change on the Qinghai‐Tibet Plateau
inferred← citeshttps://doi.org/10.1111/jbi.12873openalex-snapshot
Asynchronous diversification of snakes in the North American warm deserts
inferred← citeshttps://doi.org/10.1111/jbi.13382openalex-snapshot
A global analysis of bats using automated comparative phylogeography uncovers a surprising impact of Pleistocene glaciation
inferred← citeshttps://doi.org/10.1111/jbi.13503openalex-snapshot
Extending phylogeography to account for lineage fusion
inferred← citeshttps://doi.org/10.1111/jbi.13932openalex-snapshot
Efficient summary statistics for detecting lineage fusion from phylogeographic datasets
inferred← citeshttps://doi.org/10.1111/jbi.14774openalex-snapshot
Global genetic diversity and historical demography of the Bull Shark
inferred← citeshttps://doi.org/10.1111/jpy.12305openalex-snapshot
Contrasting patterns of population structure and demographic history in cryptic species of Bostrychia intricata (Rhodomelaceae, Rhodophyta) from New Zealand
inferred← citeshttps://doi.org/10.1111/mec.12066openalex-snapshot
Restricted distribution and limited gene flow in the model ciliate T etrahymena thermophila
inferred← citeshttps://doi.org/10.1111/mec.12119openalex-snapshot
The evolution of north‐east A tlantic gadfly petrels using statistical phylogeography
inferred← citeshttps://doi.org/10.1111/mec.12347openalex-snapshot
Model selection as a tool for phylogeographic inference: an example from the willow S alix melanopsis
inferred← citeshttps://doi.org/10.1111/mec.12850openalex-snapshot
Global population structure and demographic history of the grey seal
inferred← citeshttps://doi.org/10.1111/mec.12881openalex-snapshot
ABC inference of multi‐population divergence with admixture from unphased population genomic data
inferred← citeshttps://doi.org/10.1111/mec.13108openalex-snapshot
The evolution of phylogeographic data sets
inferred← citeshttps://doi.org/10.1111/mec.13212openalex-snapshot
Understanding the mechanisms of antitropical divergence in the seabird W hite‐faced S torm‐petrel ( P rocellariiformes: P elagodroma marina) using a multilocus approach
inferred← citeshttps://doi.org/10.1111/mec.13427openalex-snapshot
The large‐X effect in plants: increased species divergence and reduced gene flow on the Silene X‐chromosome
inferred← citeshttps://doi.org/10.1111/mec.13447openalex-snapshot
The aggregate site frequency spectrum for comparative population genomic inference
inferred← citeshttps://doi.org/10.1111/mec.14274openalex-snapshot
On the independent gene trees assumption in phylogenomic studies
inferred← citeshttps://doi.org/10.1111/mec.14892openalex-snapshot
Genomic data recover previously undetectable fragmentation effects in an endangered amphibian
inferred← citeshttps://doi.org/10.1111/mec.15574openalex-snapshot
Divergence, gene flow, and speciation in eight lineages of trans‐Beringian birds
inferred← citeshttps://doi.org/10.1111/mec.15626openalex-snapshot
Little genetic structure in a Bornean endemic small mammal across a steep ecological gradient
inferred← citeshttps://doi.org/10.1111/mec.16931openalex-snapshot
Genome‐wide phylogeography reveals cryptic speciation in the circumglobal planktonic calcifier Limacina bulimoides
inferred← citeshttps://doi.org/10.1111/mec.70056openalex-snapshot
Gene Flow Accompanies Divergence in Beringian Birds
inferred← citeshttps://doi.org/10.1111/plb.12654openalex-snapshot
Unexpectedly high genetic diversity and divergence among populations of the apomictic Neotropical tree Miconia albicans
inferred← citeshttps://doi.org/10.1111/plb.13273openalex-snapshot
Clone worth? Genetic diversity in obligate apomictic Miconia albicans (Melastomataceae)
inferred← citeshttps://doi.org/10.1139/x07-209openalex-snapshot
Chloroplast DNA phylogeography in long-lived Huon pine, a Tasmanian rain forest conifer
inferred← citeshttps://doi.org/10.1146/annurev-ecolsys-110316-022645openalex-snapshot
The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics
inferred← citeshttps://doi.org/10.1146/annurev-genom-090810-183123openalex-snapshot
Perspectives on Human Population Structure at the Cusp of the Sequencing Era
inferred← citeshttps://doi.org/10.1146/annurev-phyto-072910-095246openalex-snapshot
Evolution and Population Genetics of Exotic and Re-Emerging Pathogens: Novel Tools and Approaches
inferred← citeshttps://doi.org/10.11606/t.11.2016.tde-09062016-155937openalex-snapshot
Análise da estrutura populacional e do desequilíbrio de ligação de um painel de acessos de sorgo: uma abordagem usando teoria da coalescência
inferred← citeshttps://doi.org/10.11606/t.59.2015.tde-30032015-201941openalex-snapshot
História evolutiva de Drosophila serido ("cluster" Drosophila buzzatii)
inferred← citeshttps://doi.org/10.11648/j.jps.20150306.14openalex-snapshot
Looking Inside Non-coding Chloroplast Regions of Calophyllum brasiliense (Calophyllaceae) to Understand Its Southernmost Population Distribution
inferred← citeshttps://doi.org/10.1177/1176934319874792openalex-snapshot
Assexon: Assembling Exon Using Gene Capture Data
inferred← citeshttps://doi.org/10.1186/1471-2148-10-320openalex-snapshot
When environmental changes do not cause geographic separation of fauna: differential responses of Baikalian invertebrates
inferred← citeshttps://doi.org/10.1186/1471-2148-12-9openalex-snapshot
Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus)
inferred← citeshttps://doi.org/10.1186/1471-2148-13-223openalex-snapshot
Paleoclimatic modeling and phylogeography of least killifish, Heterandria formosa: insights into Pleistocene expansion-contraction dynamics and evolutionary history of North American Coastal Plain freshwater biota
inferred← citeshttps://doi.org/10.1186/1471-2148-8-252openalex-snapshot
Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839)
inferred← citeshttps://doi.org/10.1186/1471-2148-8-289openalex-snapshot
Bayesian inference of population size history from multiple loci
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