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

A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)

(2016) Simon Uribe-Convers et al.   PLoS One

Natural Hybridization between Genera That Diverged from Each Other Approximately 60 Million Years Ago

(2015) Carl J. Rothfels et al.   AMERICAN NATURALIST

Parallel tagged amplicon sequencing of relatively long PCR products using the Illumina HiSeq platform and transcriptome assembly

(2015) Yan-Jie Feng et al.   Molecular Ecology Resources

Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal

(2015) Miguel Minaya et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

On the relative abundance of autopolyploids and allopolyploids

(2015) Michael S. Barker et al.   NEW PHYTOLOGIST

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

(2015) Jonathan Brassac et al.   SYSTEMATIC BIOLOGY

Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next-gen approaches

(2015) Elizabeth A. Zimmer et al.   Journal of Systematics and Evolution

The origin and evolution of phototropins

(2015) Fay-Wei Li et al.   Frontiers in Plant Science

MarkerMiner 1.0: A New Application for Phylogenetic Marker Development Using Angiosperm Transcriptomes

(2015) Srikar Chamala et al.   Applications in Plant Sciences

Evidence for reciprocal origins in Polypodium hesperium (Polypodiaceae): A fern model system for investigating how multiple origins shape allopolyploid genomes

(2014) E. M. Sigel et al.   AMERICAN JOURNAL OF BOTANY

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms

(2014) Peter A Larsen et al.   BMC GENOMICS

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing

(2014) Lisa N. Barrow et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltiset al. (2014)

(2014) Itay Mayrose et al.   NEW PHYTOLOGIST

Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayroseet al. (2011)

(2014) Douglas E. Soltis et al.   NEW PHYTOLOGIST

Independent allopolyploidization events preceded speciation in the temperate and tropical woody bamboos

(2014) Jimmy K. Triplett et al.   NEW PHYTOLOGIST

Ecological studies of polyploidy in the 100 years following its discovery

(2014) J. Ramsey et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Utility of low-copy nuclear markers in phylogenetic reconstruction of Hypericum L. (Hypericaceae)

(2014) Andrea Sánchez Meseguer et al.   PLANT SYSTEMATICS AND EVOLUTION

Maximum likelihood inference of reticulate evolutionary histories

(2014) Yun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

(2014) F.-W. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allopolyploidy, diversification, and the Miocene grassland expansion

(2014) Matt C. Estep et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Thomas Marcussen et al.   SYSTEMATIC BIOLOGY

Low-copy nuclear data confirm rampant allopolyploidy in the Cystopteridaceae (Polypodiales)

(2014) Carl J. Rothfels et al.   TAXON

Rediscovery ofCystoathyrium chinenseChing (Cystopteridaceae): Phylogenetic placement of the critically endangered fern species endemic to China

(2014) Ran WEI et al.   Journal of Systematics and Evolution

Molecular evidence for natural hybridization in the mangrove fern genus Acrostichum

(2013) Rongshu Zhang et al.   BMC PLANT BIOLOGY

Polyploids and hybrids in changing environments: winners or losers in the struggle for adaptation?

(2013) B K Mable   HEREDITY

Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools

(2013) France Dufresne et al.   MOLECULAR ECOLOGY

Development, validation and high-throughput analysis of sequence markers in nonmodel species

(2013) P. Zieliński et al.   Molecular Ecology Resources

Diversification and reticulation in the circumboreal fern genus Cryptogramma

(2013) Jordan S. Metzgar et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Spatiotemporal reconstruction of theAquilegiarapid radiation through next-generation sequencing of rapidly evolving cpDNA regions

(2013) Simone Fior et al.   NEW PHYTOLOGIST

Radiation of the Nod-independentAeschynomenerelies on multiple allopolyploid speciation events

(2013) Jean-François Arrighi et al.   NEW PHYTOLOGIST

Origin of African Physacanthus (Acanthaceae) via Wide Hybridization

(2013) Erin A. Tripp et al.   PLoS One

Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns

(2013) Carl J. Rothfels et al.   PLoS One

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

(2013) Graham Jones et al.   SYSTEMATIC BIOLOGY

Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Driven by Selection

(2013) Carl J. Rothfels et al.   SYSTEMATIC BIOLOGY

A Plastid Phylogeny of the Cosmopolitan Fern Family Cystopteridaceae (Polypodiopsida)

(2013) Carl J. Rothfels et al.   SYSTEMATIC BOTANY

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform

(2013) Erin B Fichot et al.   Microbiome

Apomixis and reticulate evolution in the Asplenium monanthes fern complex

(2012) Robert J. Dyer et al.   ANNALS OF BOTANY

Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae)

(2012) Emily B Sessa et al.   BMC EVOLUTIONARY BIOLOGY

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

Using nuclear gene data for plant phylogenetics: Progress and prospects

(2012) Elizabeth A. Zimmer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms

(2012) Ning Zhang et al.   NEW PHYTOLOGIST

A tailed PCR procedure for cost-effective, two-order multiplex sequencing of candidate genes in polyploid plants

(2012) Mahmood Gholami et al.   PLANT BIOTECHNOLOGY JOURNAL

Reticulate evolution in the Crepidomanes minutum species complex (Hymenophyllaceae)

(2011) Joel H. Nitta et al.   AMERICAN JOURNAL OF BOTANY

Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation

(2011) Rajanikanth Govindarajulu et al.   AMERICAN JOURNAL OF BOTANY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

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

THE PROMISCUOUS AND THE CHASTE: FREQUENT ALLOPOLYPLOID SPECIATION AND ITS GENOMIC CONSEQUENCES IN AMERICAN DAISIES (MELAMPODIUM SECT. MELAMPODIUM; ASTERACEAE)

(2011) Hanna Weiss-Schneeweiss et al.   EVOLUTION

DOES HYBRIDIZATION DRIVE THE TRANSITION TO ASEXUALITY IN DIPLOID BOECHERA?

(2011) James B. Beck et al.   EVOLUTION

Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

(2011) Seth M. Bybee et al.   Genome Biology and Evolution

Next-generation hybridization and introgression

(2011) A D Twyford et al.   HEREDITY

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2011) Thomas Marcussen et al.   SYSTEMATIC BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

(2010) Jill M Duarte et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary consequences of autopolyploidy

(2010) Christian Parisod et al.   NEW PHYTOLOGIST

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

Deciphering the origins of apomictic polyploids in the Cheilanthes yavapensis complex (Pteridaceae)

(2009) Amanda L. Grusz et al.   AMERICAN JOURNAL OF BOTANY

Molecular evidence of reticulate evolution in the subgenus Plantago (Plantaginaceae)

(2009) Naoko Ishikawa et al.   AMERICAN JOURNAL OF BOTANY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Influence of phylogeny and ploidy on species ranges of North American angiosperms

(2009) Sara L Martin et al.   JOURNAL OF ECOLOGY

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

The frequency of polyploid speciation in vascular plants

(2009) T. E. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Low-copy nuclear DNA sequences reveal a predominance of allopolyploids in a New Zealand Asplenium fern complex

(2008) L SHEPHERD et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Allohexaploidy, introgression, and the complex phylogenetic history of Elymus repens (Poaceae)

(2008) Roberta J. Mason-Gamer   MOLECULAR PHYLOGENETICS AND EVOLUTION

Allopolyploid speciation in Persicaria (Polygonaceae): Insights from a low-copy nuclear region

(2008) S.-T. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

The Utility of Nuclear gapCp in Resolving Polyploid Fern Origins

(2008) Eric Schuettpelz et al.   SYSTEMATIC BOTANY