In defence of model-based inference in phylogeography. (Q47169104)

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8 April 2020

title

In defence of model-based inference in phylogeography (English)

1 reference

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8 April 2020

0 references

1

1 reference

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8 April 2020

Rasmus Nielsen

2

1 reference

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8 April 2020

Christian Robert

3

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8 April 2020

Oscar E Gaggiotti

5

1 reference

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8 April 2020

Scott A. Sisson

11

1 reference

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Nelson Jurandi Rosa Fagundes

8 April 2020

12

1 reference

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8 April 2020

Lounes Chikhi

13

1 reference

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8 April 2020

Peter Beerli

14

1 reference

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8 April 2020

Renaud Vitalis

15

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8 April 2020

Matthieu Foll

18

1 reference

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8 April 2020

Francois Rousset

20

1 reference

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8 April 2020

David J. Balding

21

1 reference

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8 April 2020

Laurent Excoffier

22

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8 April 2020

7

Arnaud Estoup

1 reference

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8 April 2020

4

Jody Hey

1 reference

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8 April 2020

16

Jean-Marie Cornuet

1 reference

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8 April 2020

author name string

Lacey Knowles

6

1 reference

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8 April 2020

Jukka Corander

9

1 reference

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8 April 2020

Mike Hickerson

10

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8 April 2020

John Huelsenbeck

17

1 reference

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8 April 2020

Ziheng Yang

19

1 reference

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8 April 2020

Mahesh Panchal

8

1 reference

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8 April 2020

publication date

11 January 2010

1 reference

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8 April 2020

number of pages

11

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based on heuristic

inferred from page(s)

published in

Molecular Ecology

1 reference

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8 April 2020

volume

19

1 reference

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8 April 2020

issue

3

1 reference

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8 April 2020

page(s)

436-446

1 reference

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TESTING THE CONSTANT-RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA.

8 April 2020

cites work

1 reference

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Coalescent-based, maximum likelihood inference in phylogeography

23 May 2018

1 reference

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Bayesian computation and model selection without likelihoods

23 May 2018

1 reference

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The origins of lactase persistence in Europe

23 May 2018

1 reference

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The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Model criticism based on likelihood-free inference, with an application to protein network evolution

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood.

23 May 2018

1 reference

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Why does a method that fails continue to be used? The answer

23 May 2018

1 reference

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Gene tree discordance, phylogenetic inference and the multispecies coalescent

23 May 2018

1 reference

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Statistical inferences in phylogeography

23 May 2018

1 reference

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Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems.

23 May 2018

1 reference

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Statistical hypothesis testing in intraspecific phylogeography: nested clade phylogeographical analysis vs. approximate Bayesian computation

23 May 2018

1 reference

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Approximate bayesian computation without summary statistics: the case of admixture

23 May 2018

1 reference

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Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Why does a method that fails continue to be used?

23 May 2018

1 reference

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Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

23 May 2018

1 reference

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Genes mirror geography within Europe

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Nested clade analysis: an extensively validated method for strong phylogeographic inference

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Statistical evaluation of alternative models of human evolution

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Strong Inference: Certain systematic methods of scientific thinking may produce much more rapid progress than others

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Genetics and recent human evolution.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

The automation and evaluation of nested clade phylogeographic analysis

23 May 2018

1 reference

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Genetic structure of chimpanzee populations

23 May 2018

1 reference

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Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Sequential Monte Carlo without likelihoods

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Modern computational approaches for analysing molecular genetic variation data

23 May 2018

1 reference

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Bayesian clustering using hidden Markov random fields in spatial population genetics

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

How reliable are empirical genomic scans for selective sweeps?

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

The geographic spread of the CCR5 Delta32 HIV-resistance allele

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Genomics refutes an exclusively African origin of humans

23 May 2018

1 reference

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Bayesian estimation of recent migration rates after a spatial expansion

23 May 2018

1 reference

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Bayesian analysis of an admixture model with mutations and arbitrarily linked markers

23 May 2018

1 reference

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A spatial statistical model for landscape genetics

23 May 2018

1 reference

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The burgeoning field of statistical phylogeography

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Markov chain Monte Carlo without likelihoods

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci

23 May 2018

1 reference

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The study of structured populations--new hope for a difficult and divided science

23 May 2018

1 reference

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Approximate Bayesian computation in population genetics

23 May 2018

1 reference

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Statistical phylogeography

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Optimal randomization strategies when testing the existence of a phylogeographic structure

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Out of Africa again and again.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Using linked markers to infer the age of a mutation

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Population growth of human Y chromosomes: a study of Y chromosome microsatellites

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Genealogical inference from microsatellite data

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Population paths implied by the mean number of pairwise nucleotide differences among mitochondrial DNA sequences.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Heterogeneity of microsatellite mutations within and between loci, and implications for human demographic histories

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Inferring coalescence times from DNA sequence data

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type I sequences

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Evolutionary trees from DNA sequences: A maximum likelihood approach

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Evolutionary relationship of DNA sequences in finite populations

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

The Icelandic admixture problem.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Relationships between gene trees and species trees

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Evaluating nested clade phylogeographic analysis under models of restricted gene flow

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

PopABC: a program to infer historical demographic parameters

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Approximately sufficient statistics and bayesian computation

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

On the validity of nested clade phylogeographical analysis

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

The coup de grâce for the nested clade phylogeographic analysis?

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

PHYLOGENETIC ANALYSIS: MODELS AND ESTIMATION PROCEDURES

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5743441

Gene trees and species trees are not the same

29 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29284924

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Statistical phylogeography: methods of evaluating and minimizing inference errors

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29284924

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1111/J.1365-294X.2009.04515.X

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29284924%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29284924%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

PubMed publication ID

29284924

1 reference