(Q28610719)

English

Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci

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scholarly article

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26048340%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci (English)

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26048340%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

1 reference

based on heuristic

inferred from title

1 reference

based on heuristic

inferred from title

1 reference

based on heuristic

inferred from title

1 reference

based on heuristic

inferred from title

Jonathan Brassac

1

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26048340%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Frank R. Blattner

2

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26048340%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

author name string

Jonathan Brassac

1

0 references

Frank R Blattner

2

0 references

language of work or name

0 references

publication date

5 June 2015

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26048340%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Systematic Biology

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26048340%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

64

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26048340%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

5

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26048340%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

792-808

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26048340%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

describes a project that uses

massive parallel sequencing

1 reference

based on heuristic

inferred from title

From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

Evolutionary consequences, constraints and potential of polyploidy in plants

1 reference

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17 March 2017

A physical, genetic and functional sequence assembly of the barley genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

Bayesian phylogenetics with BEAUti and the BEAST 1.7

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

Bayesian random local clocks, or one rate to rule them all

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

BEAST: Bayesian evolutionary analysis by sampling trees

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

Multiple intercontinental dispersals shaped the distribution area of Hordeum (Poaceae)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

Phylogenetic analysis of Hordeum (Poaceae) as inferred by nuclear rDNA ITS sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

Phylogenetic methods come of age: testing hypotheses in an evolutionary context

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

The neighbor-joining method: a new method for reconstructing phylogenetic trees

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

Basic local alignment search tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

17 March 2017

jModelTest 2: more models, new heuristics and parallel computing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

7 April 2017

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

7 April 2017

Bayesian inference of species trees from multilocus data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

7 April 2017

Recent developments in the MAFFT multiple sequence alignment program

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

7 April 2017

AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

7 April 2017

Gene tree discordance, phylogenetic inference and the multispecies coalescent

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

7 April 2017

Is a new and general theory of molecular systematics emerging?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

7 April 2017

Ribosomal ITS sequences and plant phylogenetic inference

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

7 April 2017

Relationships between gene trees and species trees

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

7 April 2017

Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Ancient hybridizations among the ancestral genomes of bread wheat

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Evolutionary history of wild barley (Hordeum vulgare subsp. spontaneum) analyzed using multilocus sequence data and paleodistribution modeling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Five nuclear loci resolve the polyploid history of switchgrass (Panicum virgatum L.) and relatives

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Anchored hybrid enrichment for massively high-throughput phylogenomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Next-generation sequencing and genome evolution in allopolyploids.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Diversity and evolution of the Hordeum murinum polyploid complex in Algeria.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Phylogeographic analyses and paleodistribution modeling indicate pleistocene in situ survival of Hordeum species (Poaceae) in southern Patagonia without genetic or spatial restriction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Evolutionary genetics of genome merger and doubling in plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Parallel tagged sequencing on the 454 platform

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Combined ecological niche modelling and molecular phylogeography revealed the evolutionary history of Hordeum marinum (Poaceae)--niche differentiation, loss of genetic diversity, and speciation in Mediterranean Quaternary refugia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Inconsistency of phylogenetic estimates from concatenated data under coalescence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

A novel algorithm and web-based tool for comparing two alternative phylogenetic trees

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Ancestry of American polyploid Hordeum species with the I genome inferred from 5S and 18S-25S rDNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Utility of low-copy nuclear gene sequences in plant phylogenetics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Molecular evidence for an extinct parent of the tetraploid species Microseris acuminata and M. campestris (Asteraceae, Lactuceae).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

29 September 2017

Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

3 June 2018

The evolutionary history of sea barley (Hordeum marinum) revealed by comparative physical mapping of repetitive DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

3 June 2018

Progenitor-derivative relationships of Hordeum polyploids (Poaceae, Triticeae) inferred from sequences of TOPO6, a nuclear low-copy gene region

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

3 June 2018

A chloroplast genealogy of hordeum (poaceae): Long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inference

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

3 June 2018

Bayesian estimation of concordance among gene trees.

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Progress in phylogenetic analysis and a new infrageneric classification of the barley genus Hordeum (Poaceae: Triticeae)

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer.

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Revealing unknown or extinct lineages within Isoetes (Isoetaceae) using DNA sequencesfrom hybrids

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Localization of anchor loci representing five hundred annotated rice genes to wheat chromosomes using PLUG markers.

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Two extinct diploid progenitors were involved in allopolyploid formation in the Hordeum murinum (Poaceae: Triticeae) taxon complex

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Population demography influences climatic niche evolution: evidence from diploid American Hordeum species (Poaceae).

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

The considerable genome size variation of Hordeum species (poaceae) is linked to phylogeny, life form, ecology, and speciation rates

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Allopolyploid origin of Cardamine asarifolia (Brassicaceae): incongruence between plastid and nuclear ribosomal DNA sequences solved by a single-copy nuclear gene

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Molecular phylogeny of the genus Hordeum using three chloroplast DNA sequences

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Selecting the Best-Fit Model of Nucleotide Substitution

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Origins of polyploids: an example from peonies (Paeonia) and a model for angiosperms

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Estimating the Dimension of a Model

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Analysis of DNA sequence polymorphism at the cMWG699 locus reveals phylogenetic relationships and allopolyploidy within Hordeum murinum subspecies

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Dissecting plant genomes with the PLAZA comparative genomics platform

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae)

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

On the Origin of the Tetraploid Species Hordeum capense and H. secalinum (Poaceae)

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV035

21 January 2018

Selecting the best-fit model of nucleotide substitution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538882

27 November 2018

Polyploidy: recurrent formation and genome evolution

1 reference

https://pubmed.ncbi.nlm.nih.gov/26048340

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The evolution of the hexaploid grass Zingeriakochii (Mez) Tzvel. (2n=12) was accompanied by complex hybridization and uniparental loss of ribosomal DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/26048340

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/SYSBIO/SYV035

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26048340%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26048340%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26048340%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

ResearchGate publication ID

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