Species-Level Phylogeny and Polyploid Relationships inHordeum(Poaceae) Inferred by Next-Generation Sequencing andIn SilicoCloning of Multiple Nuclear Loci

Evolutionary History of Wild Barley (Hordeum vulgare subsp. spontaneum) Analyzed Using Multilocus Sequence Data and Paleodistribution Modeling

(2014) Sabine S. Jakob et al.   Genome Biology and Evolution

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

Disentangling Methodological and Biological Sources of Gene Tree Discordance on Oryza (Poaceae) Chromosome 3

(2014) Derrick J. Zwickl et al.   SYSTEMATIC BIOLOGY

From Gene Trees to a Dated Allopolyploid Network: Insights from the Angiosperm Genus Viola (Violaceae)

(2014) Thomas Marcussen et al.   SYSTEMATIC BIOLOGY

Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

(2014) Zhenxiang Xi et al.   SYSTEMATIC BIOLOGY

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

(2013) Alejandro Carmona et al.   ANNALS OF BOTANY

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

(2013) Vincent Ranwez et al.   BMC BIOINFORMATICS

Evolutionary Consequences, Constraints and Potential of Polyploidy in Plants

(2013) H. Weiss-Schneeweiss et al.   CYTOGENETIC AND GENOME RESEARCH

Barley whole exome capture: a tool for genomic research in the genusHordeumand beyond

(2013) Martin Mascher et al.   PLANT JOURNAL

Next-generation sequencing and genome evolution in allopolyploids

(2012) Richard J. A. Buggs et al.   AMERICAN JOURNAL OF BOTANY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2012) Eric M. O'Neill et al.   MOLECULAR ECOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Progenitor-Derivative Relationships of Hordeum Polyploids (Poaceae, Triticeae) Inferred from Sequences of TOPO6, a Nuclear Low-Copy Gene Region

(2012) Jonathan Brassac et al.   PLoS One

Five Nuclear Loci Resolve the Polyploid History of Switchgrass (Panicum virgatum L.) and Relatives

(2012) Jimmy K. Triplett et al.   PLoS One

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Late Cenozoic glaciations in Patagonia and Tierra del Fuego: an updated review

(2011) JORGE RABASSA et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

(2011) Philippa C Griffin et al.   BMC BIOLOGY

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

(2011) Juan S Escobar et al.   BMC EVOLUTIONARY BIOLOGY

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

(2011) Gitte Petersen et al.   CLADISTICS

Diversity and evolution of the Hordeum murinum polyploid complex in Algeria

(2011) Malika Ourari et al.   GENOME

Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform

(2011) M. Van Bel et al.   PLANT PHYSIOLOGY

Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer

(2011) Yujin Chung et al.   SYSTEMATIC BIOLOGY

Inferring Species Networks from Gene Trees in High-Polyploid North American and Hawaiian Violets (Viola, Violaceae)

(2011) Thomas Marcussen et al.   SYSTEMATIC BIOLOGY

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

(2010) Bret R. Larget et al.   BIOINFORMATICS

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

(2010) Robert Schmieder et al.   BMC BIOINFORMATICS

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

(2010) Alexei J Drummond et al.   BMC BIOLOGY

Analysis of DNA sequence polymorphism at the cMWG699 locus reveals phylogenetic relationships and allopolyploidy withinHordeum murinumsubspecies

(2010) K. Tanno et al.   HEREDITAS

Population demography influences climatic niche evolution: evidence from diploid AmericanHordeumspecies (Poaceae)

(2010) SABINE S. JAKOB et al.   MOLECULAR ECOLOGY

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

(2010) Violetta Kotseruba et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny of two tetraploid Hordeum species, H. secalinum and H. capense inferred from physical mapping of 5S and 18S-25S rDNA

(2009) Shin Taketa et al.   BREEDING SCIENCE

Evolutionary process of Hordeum brachyantherum 6x and related tetraploid species revealed by nuclear DNA sequences

(2009) Takao Komatsuda et al.   BREEDING SCIENCE

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

(2009) Frank R. Blattner   BREEDING SCIENCE

Giemsa C-banding in Asiatic taxa of Hordeum section Stenostachys with notes on chromosome morphology

(2009) IB LINDE-LAURSEN et al.   HEREDITAS

Phylogeographic Analyses and Paleodistribution Modeling Indicate Pleistocene In Situ Survival of Hordeum Species (Poaceae) in Southern Patagonia without Genetic or Spatial Restriction

(2009) S. S. Jakob et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2009) Sabine S. Jakob et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Evolutionary Genetics of Genome Merger and Doubling in Plants

(2008) Jeff J. Doyle et al.   Annual Review of Genetics

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Parallel tagged sequencing on the 454 platform

(2008) Matthias Meyer et al.   Nature Protocols

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

(2008) Goro Ishikawa et al.   THEORETICAL AND APPLIED GENETICS