Multilocus phylogeography and phylogenetics using sequence-based markers (Q37225449)

19 August 2017

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title

Multilocus phylogeography and phylogenetics using sequence-based markers (English)

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19 August 2017

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2

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19 August 2017

Patrícia H Brito

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19 August 2017

language of work or name

English

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publication date

24 July 2008

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19 August 2017

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19 August 2017

volume

135

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19 August 2017

issue

3

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19 August 2017

page(s)

439-455

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Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics

19 August 2017

cites work

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Phylogenetic analysis. Models and estimation procedures

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A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora.

21 January 2018

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EVOLUTIONARY TREES FROM GENE FREQUENCIES AND QUANTITATIVE CHARACTERS: FINDING MAXIMUM LIKELIHOOD ESTIMATES.

21 January 2018

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PERSPECTIVE: HIGHLY VARIABLE LOCI AND THEIR INTERPRETATION IN EVOLUTION AND CONSERVATION.

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Mathematical consequences of the genealogical species concept.

21 January 2018

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Estimating a geographically explicit model of population divergence

21 January 2018

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https://api.crossref.org/works/10.1007/S10709-008-9293-3

Direct evidence for homologous recombination in mussel (Mytilus galloprovincialis) mitochondrial DNA.

21 January 2018

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https://api.crossref.org/works/10.1007/S10709-008-9293-3

Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives

21 January 2018

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https://api.crossref.org/works/10.1007/S10709-008-9293-3

Chromosomal phylogeny and evolution of gibbons (Hylobatidae)

21 January 2018

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https://api.crossref.org/works/10.1007/S10709-008-9293-3

Nuclear loci and coalescent methods support ancient hybridization as cause of mitochondrial paraphyly between gadwall and falcated duck (Anas spp.).

21 January 2018

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Bushes in the tree of life

21 January 2018

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https://api.crossref.org/works/10.1007/S10709-008-9293-3

A multilocus perspective on colonization accompanied by selection and gene flow

21 January 2018

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https://api.crossref.org/works/10.1007/S10709-008-9293-3

A fine-scale spatial analysis of the mosaic hybrid zone between Gryllus firmus and Gryllus pennsylvanicus.

21 January 2018

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https://api.crossref.org/works/10.1007/S10709-008-9293-3

The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs.

21 January 2018

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https://api.crossref.org/works/10.1007/S10709-008-9293-3

Paternal, maternal, and biparental molecular markers provide unique windows onto the evolutionary history of macaque monkeys

21 January 2018

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https://api.crossref.org/works/10.1007/S10709-008-9293-3

Inferences of species phylogeny in relation to segregation of ancient polymorphisms

21 January 2018

1 reference

12 December 2020

Gene trees, species trees and the segregation of ancestral alleles

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12 December 2020

Delimiting species without monophyletic gene trees

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12 December 2020

Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies

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12 December 2020

Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees

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12 December 2020

Highly parallel SNP genotyping

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12 December 2020

Population size does not influence mitochondrial genetic diversity in animals

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12 December 2020

Delimiting species in recent radiations

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12 December 2020

A retroposon analysis of Afrotherian phylogeny

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12 December 2020

Mitochondrial DNA under siege in avian phylogeography

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12 December 2020

Insertion-deletion polymorphisms (indels) as genetic markers in natural populations

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12 December 2020

Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data

1 reference

12 December 2020

Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings

1 reference

12 December 2020

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers

1 reference

12 December 2020

The causes of phylogenetic conflict in a classic Drosophila species group.

1 reference

12 December 2020

Inference of population structure using multilocus genotype data

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12 December 2020

MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution

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12 December 2020

The Bayesian revolution in genetics

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12 December 2020

Thrice out of Africa: ancient and recent expansions of the honey bee, Apis mellifera

1 reference

12 December 2020

Hitchhiking mapping: a population-based fine-mapping strategy for adaptive mutations in Drosophilamelanogaster

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12 December 2020

Phylogenetics of modern birds in the era of genomics.

1 reference

12 December 2020

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

1 reference

12 December 2020

Gene Flow and Natural Selection in the Origin of Drosophila pseudoobscura and Close Relatives

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12 December 2020

Recombination in animal mitochondrial DNA: evidence from published sequences

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12 December 2020

Inferences about human demography based on multilocus analyses of noncoding sequences.

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12 December 2020

Rates and patterns of scnDNA and mtDNA divergence within the Drosophila melanogaster subgroup

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12 December 2020

Insertion/deletion and nucleotide polymorphism data reveal constraints in Drosophila melanogaster introns and intergenic regions

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12 December 2020

msBayes: pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation

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12 December 2020

Targeted high-throughput sequencing of tagged nucleic acid samples

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12 December 2020

Extreme genomic variation in a natural population

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12 December 2020

Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation

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12 December 2020

Distinguishing migration from isolation: a Markov chain Monte Carlo approach

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12 December 2020

Inferring the mode of speciation from genomic data: a study of the great apes

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12 December 2020

Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers

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12 December 2020

Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales

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12 December 2020

Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa

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12 December 2020

Approximate Bayesian computation in population genetics

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12 December 2020

Using genome scans of DNA polymorphism to infer adaptive population divergence

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12 December 2020

How reliable are empirical genomic scans for selective sweeps?

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12 December 2020

The coalescent in an exponentially growing metapopulation and its application to Arabidopsis thaliana

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12 December 2020

Statistical properties of the number of recombination events in the history of a sample of DNA sequences

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12 December 2020

Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques

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12 December 2020

Shifting distributions and speciation: species divergence during rapid climate change.

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12 December 2020

MAXIMUM-LIKELIHOOD ESTIMATION OF POPULATION DIVERGENCE TIMES AND POPULATION PHYLOGENY IN MODELS WITHOUT MUTATION.

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12 December 2020

Ancient differentiation in the single-island avian radiation of endemic Hispaniolan chat-tanagers (Aves: Calyptophilus).

1 reference

12 December 2020

The complex evolutionary history of gorillas: insights from genomic data

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12 December 2020

Population structure in the American oyster as inferred by nuclear gene genealogies

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12 December 2020

Conflicting patterns of mitochondrial and nuclear DNA diversity in Phylloscopus warblers.

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12 December 2020

Bayesian phylogenetic analysis of combined data

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12 December 2020

A new approach to estimate parameters of speciation models with application to apes

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12 December 2020

Sampling properties of DNA sequence data in phylogenetic analysis

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12 December 2020

Phylogenomics and the reconstruction of the tree of life

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12 December 2020

Genome-scale evolution: reconstructing gene orders in the ancestral species.

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12 December 2020

Population genomics: genome-wide sampling of insect populations

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12 December 2020

Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies

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12 December 2020

Genome-scale approaches to resolving incongruence in molecular phylogenies

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12 December 2020

Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae).

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12 December 2020

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

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12 December 2020

A cladistic measure of gene flow inferred from the phylogenies of alleles

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12 December 2020

Hypervariabflity of simple sequences as a general source for polymorphic DNA markers

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12 December 2020

Using genomic data to unravel the root of the placental mammal phylogeny

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12 December 2020

Gene genealogy in three related populations: consistency probability between gene and population trees

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12 December 2020

Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions

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12 December 2020

INFERRING PHYLOGENIES FROM mtDNA VARIATION: MITOCHONDRIAL-GENE TREES VERSUS NUCLEAR-GENE TREES.

1 reference

12 December 2020

Molecular phylogenetics of the lizard genus Microlophus (squamata:tropiduridae): aligning and retrieving indel signal from nuclear introns

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12 December 2020

The sampling theory of selectively neutral alleles

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12 December 2020

L1 (LINE-1) retrotransposon evolution and amplification in recent human history

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12 December 2020

Gene translocation links insects and crustaceans.

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12 December 2020

PCR-based assays of mendelian polymorphisms from anonymous single-copy nuclear DNA: techniques and applications for population genetics

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12 December 2020

Estimating species trees using multiple-allele DNA sequence data

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12 December 2020

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

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12 December 2020

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

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12 December 2020

Testing congruence in phylogenomic analysis

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12 December 2020

Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs

1 reference

12 December 2020

The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) Genome: a high frequency of deletions in tandem duplicates

1 reference

12 December 2020

Intron variation in marbled murrelets detected using analyses of single-stranded conformational polymorphisms.

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12 December 2020

Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome

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12 December 2020

A phylogenetic foundation for comparative mammalian genomics

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12 December 2020

Statistical phylogeography

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12 December 2020

Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes

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12 December 2020

LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters

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12 December 2020

Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting

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12 December 2020

Optimal sequencing strategies for surveying molecular genetic diversity.

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12 December 2020

Global patterns of human mitochondrial DNA and Y-chromosome structure are not influenced by higher migration rates of females versus males

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12 December 2020

Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model

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12 December 2020

Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci?

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12 December 2020

Rapid evolution of animal mitochondrial DNA

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12 December 2020

Microsatellite diversity and the demographic history of modern humans

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12 December 2020

Recent trends in population genetics: more data! More math! Simple models?

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12 December 2020

Genetic traces of ancient demography

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12 December 2020

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

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12 December 2020

Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data

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12 December 2020

The homozygosity test of neutrality.

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12 December 2020

A standardized genetic differentiation measure

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12 December 2020

Rooted triple consensus and anomalous gene trees

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12 December 2020

Microsatellite and trinucleotide-repeat evolution: evidence for mutational bias and different rates of evolution in different lineages

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12 December 2020

A "Long Indel" model for evolutionary sequence alignment

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12 December 2020

SINEs of speciation: tracking lineages with retroposons

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12 December 2020

SINE evolution, missing data, and the origin of whales.

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12 December 2020

Rare genomic changes as a tool for phylogenetics

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12 December 2020

High-resolution species trees without concatenation

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12 December 2020

A multilocus perspective on refugial isolation and divergence in rainforest skinks (Carlia).

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12 December 2020

Long-distance gene flow in a cooperative breeder detected in genealogies of mitochondrial DNA sequences

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12 December 2020

Genetic evidence for complex speciation of humans and chimpanzees

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12 December 2020

Low mitochondrial variability in birds may indicate Hill-Robertson effects on the W chromosome.

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12 December 2020

Inconsistency of phylogenetic estimates from concatenated data under coalescence

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12 December 2020

Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis

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12 December 2020

The power and promise of population genomics: from genotyping to genome typing

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12 December 2020

Gene sampling strategies for multi-locus population estimates of genetic diversity (theta).

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12 December 2020

From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem

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12 December 2020

Inferring phylogeny despite incomplete lineage sorting

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12 December 2020

Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees

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12 December 2020

Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data

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12 December 2020

Microsatellites: simple sequences with complex evolution

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12 December 2020

A New Statistical Method for Haplotype Reconstruction from Population Data

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12 December 2020

BEAST: Bayesian evolutionary analysis by sampling trees

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12 December 2020

Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects

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12 December 2020

Relationships between gene trees and species trees

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12 December 2020

Maximum likelihood estimation of population growth rates based on the coalescent

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12 December 2020

An initial map of insertion and deletion (INDEL) variation in the human genome.

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12 December 2020

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events

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12 December 2020

Single nucleotide polymorphisms and recombination rate in humans

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12 December 2020

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing.

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12 December 2020

Ascertainment bias in spatially structured populations: a case study in the eastern fence lizard

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12 December 2020

Animal evolution and the molecular signature of radiations compressed in time

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12 December 2020

10.1007/S10709-008-9293-3

Identifiers

DOI

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19 August 2017

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