Resolving phylogeny and polyploid parentage using genus-wide genome-wide sequence data from birch trees

Population structure of Betula albosinensis and Betula platyphylla: evidence for hybridization and a cryptic lineage

(2019) Ya-Nan Hu et al.   ANNALS OF BOTANY

Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

(2018) Jonna S. Eriksson et al.   BMC EVOLUTIONARY BIOLOGY

Post-polyploid diploidization and diversification through dysploid changes

(2018) Terezie Mandáková et al.   CURRENT OPINION IN PLANT BIOLOGY

Rapid allopolyploid radiation of moonwort ferns ( Botrychium ; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions

(2018) Benjamin Dauphin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

(2018) Diego F. Morales-Briones et al.   NEW PHYTOLOGIST

Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus)

(2017) Sorel Fitz-Gibbon et al.   GENOME

PhyloNetworks: A Package for Phylogenetic Networks

(2017) Claudia Solís-Lemus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

(2017) Ming-Cheng Luo et al.   NATURE

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

(2017) Jarkko Salojärvi et al.   NATURE GENETICS

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni et al.   SCIENCE

Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae

(2016) R. Massatti et al.   AMERICAN JOURNAL OF BOTANY

Molecular phylogeny and genome size evolution of the genusBetula(Betulaceae)

(2016) Nian Wang et al.   ANNALS OF BOTANY

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multispecies genetic structure and hybridization in theBetulagenus across Eurasia

(2016) Yoshiaki Tsuda et al.   MOLECULAR ECOLOGY

Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers

(2016) Jasmin Zohren et al.   MOLECULAR ECOLOGY

ddRAD-seq phylogenetics based on nucleotide, indel, and presence–absence polymorphisms: Analyses of two avian genera with contrasting histories

(2016) Jeffrey M. DaCosta et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing

(2016) Carl J. Rothfels et al.   NEW PHYTOLOGIST

Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants

(2016) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Phylogenetic relationships, molecular taxonomy, biogeography of Betula, with emphasis on phylogenetic position of Iranian populations

(2016) Hamid Bina et al.   Tree Genetics & Genomes

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

ASTRID: Accurate Species TRees from Internode Distances

(2015) Pranjal Vachaspati et al.   BMC GENOMICS

Comparative analyses of plastid and AFLP data suggest different colonization history and asymmetric hybridization betweenBetula pubescensandB. nana

(2015) Pernille Bronken Eidesen et al.   MOLECULAR ECOLOGY

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

(2015) Fuguang Li et al.   NATURE BIOTECHNOLOGY

Despite introgressive hybridization, North American birches (Betula spp.) maintain strong differentiation at nuclear microsatellite loci

(2015) Ashley M. Thomson et al.   Tree Genetics & Genomes

Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae)

(2015) Yan Hou et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Use of RAD sequencing for delimiting species

(2014) E Pante et al.   HEREDITY

Empirical Assessment of RAD Sequencing for Interspecific Phylogeny

(2014) Astrid Cruaud et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular footprints of the Holocene retreat of dwarf birch in Britain

(2014) Nian Wang et al.   MOLECULAR ECOLOGY

QDD version 3.1: a user-friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate

(2014) Emese Meglécz et al.   Molecular Ecology Resources

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

(2014) Andrew L. Hipp et al.   PLoS One

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

(2014) Thomas Marcussen et al.   SYSTEMATIC BIOLOGY

A Review of Bronze Birch Borer (Coleoptera: Buprestidae) Life History, Ecology, and Management

(2013) Vanessa L. Muilenburg et al.   ENVIRONMENTAL ENTOMOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Statistical Inference of Allopolyploid Species Networks in the Presence of Incomplete Lineage Sorting

(2013) Graham Jones et al.   SYSTEMATIC BIOLOGY

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

(2013) Marie Cariou et al.   Ecology and Evolution

Rapid, Repeated, and Clustered Loss of Duplicate Genes in Allopolyploid Plant Populations of Independent Origin

(2012) Richard J.A. Buggs et al.   CURRENT BIOLOGY

Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers

(2012) Nian Wang et al.   MOLECULAR ECOLOGY

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

Ecological and genetic factors linked to contrasting genome dynamics in seed plants

(2012) A. R. Leitch et al.   NEW PHYTOLOGIST

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

Chloroplast DNA variation of Betula humilis Schrk. in Poland and Belarus

(2012) Katarzyna A. Jadwiszczak et al.   Tree Genetics & Genomes

Identification of SNP and SSR markers in eggplant using RAD tag sequencing

(2011) Lorenzo Barchi et al.   BMC GENOMICS

Production of viable male unreduced gametes in Brassica interspecific hybrids is genotype specific and stimulated by cold temperatures

(2011) Annaliese S Mason et al.   BMC PLANT BIOLOGY

INTERSPECIFIC HYBRIDIZATION WITHIN THE GENUS BETULA

(2010) HELGE JOHNSSON   HEREDITAS

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Inferring polyploid phylogenies from multiply-labeled gene trees

(2009) Martin Lott et al.   BMC EVOLUTIONARY BIOLOGY

Cytogenetics of hybrid introgression in Icelandic birch

(2008) KESARA ANAMTHAWAT-JÓNSSON et al.   HEREDITAS

Phylogenetic relationships in Betula (Betulaceae) based on AFLP markers

(2008) Martijn F. Schenk et al.   Tree Genetics & Genomes