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Courses
  • REE
    Research in Ecology and Evolution

  • FEG
    Functional and Evolutionary Genomics

  • B
    Bioinformatics

Grants
  • Funding agency logo
    EAGER-NEON: Genomic Plasticity in Response to Variable Environments

    Principal Investigator (PI)

    2016

    $300.0K
  • Funding agency logo
    Polyploidy and plasticity in the crop Brassicas

    Co-Investigator (COI)

    2014

    $812.5K
  • Funding agency logo
    Developing a Predictive Genomic Framework to Understand the Outcomes of Hybridization

    Principal Investigator (PI)

    2014

    $10.0K
News
  • Researchers 'Turn on the Lights' Across the Plant Tree of Life

    2019

  • UA Biologists Find Answer to 100-Year-Old Question

    2018

  • Ancient Genetic 'Baby Boom' of Conifers Uncovered

    2015

  • Research Uses DNA to Study Key Events in Plant Evolution

    2014

  • When Plants Go Polyploid

    2011

Publications (114)
Recent
  • Dynamic genome evolution in a model fern

    2022

  • Chromosome-Scale Genome Assembly of Gilia yorkii Enables Genetic Mapping of Floral Traits in an Interspecies Cross

    2022

  • Demographic history inference and the polyploid continuum

    2022

  • Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader …

    2022

  • Genome size evolution in the diverse insect order Trichoptera

    2022

  • Patterns and Processes of Diploidization in Land Plants

    2021

  • Underwater CAM photosynthesis elucidated by Isoetes genome

    2021

  • Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa

    2021

  • Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids

    2021

  • Applying Machine Learning to Classify the Origins of Gene Duplications

    2021

  • Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids

    2021

  • Data from: Development of an ultra-dense genetic map of the sunflower genome

    2021

  • Animal chromosome counts reveal a similar range of chromosome numbers but with less polyploidy in animals compared to flowering plants

    2021

  • Data from: Recently-formed polyploid plants diversify at lower rates

    2021

  • The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

    2021

  • Pilot RNA‐seq data from 24 species of vascular plants at Harvard Forest

    2021

  • Broad variation in rates of polyploidy and dysploidy across flowering plants is correlated with lineage diversification

    2021

  • Data from: Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

    2021

  • Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks

    2021

  • Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

    2020

  • Progress Towards Plant Community Transcriptomics: Pilot RNA-Seq Data from 24 Species of Vascular Plants at Harvard Forest

    2020

  • Polyploid plants have faster rates of multivariate niche differentiation than their diploid relatives

    2020

  • Polyploids increase overall diversity despite higher turnover than diploids in the Brassicaceae

    2020

  • Inferring the demographic history of inbred species from genome-wide snp frequency data

    2020

  • Animal chromosome counts reveal similar range of chromosome numbers but with less polyploidy in animals compared to flowering plants

    2020

  • Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions

    2020

  • Sequencing and analyzing the transcriptomes of a thousand species across the tree of life for green plants

    2020

  • TagSeq for gene expression in non‐model plants: A pilot study at the Santa Rita Experimental Range NEON core site

    2020

  • Phylogeny and multiple independent whole‐genome duplication events in the Brassicales

    2020

  • The Chimonanthus salicifolius genome provides insight into magnoliid evolution and flavonoid biosynthesis

    2020

  • Illumina GAII Library Construction and Sequencing for RNA Seq

    2019

  • Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)

    2019

  • Current Status and Future Prospects for Fern and Lycophyte Genomics: Introduction to an American Fern Journal Special Issue

    2019

  • Polyploid plants have faster rates of multivariate niche evolution than their diploid relatives

    2019

  • One thousand plant transcriptomes and the phylogenomics of green plants

    2019

  • Nuclear Genome Size is Positively Correlated with Mean LTR Insertion Date in Fern and Lycophyte Genomes

    2019

  • Polyploidy increases overall diversity despite higher turnover than diploids in the Brassicaceae

    2019

  • Reply to Nakatani and McLysaght: analyzing deep duplication events

    2019

  • Inferring putative ancient whole genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions

    2019

  • Sequencing protocols for the one thousand plant transcriptomes initiative

    2019

  • Hiseq 2000 Library Construction and Sequencing for RNA Seq

    2019

  • Nuclear genome size is positively correlated with median LTR-RT insertion time in fern and lycophyte genomes

    2019

  • Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus

    2019

  • Fern genomes elucidate land plant evolution and cyanobacterial symbioses

    2018

  • Multiple large-scale gene and genome duplications during the evolution of hexapods

    2018

  • Polyploid plants have faster rates of multivariate climatic niche evolution than their diploid relatives

    2018

  • Assessing the performance of Ks plots for detecting ancient whole genome duplications

    2018

  • A Gneato nuclear genome

    2018

  • Impact of whole-genome duplication events on diversification rates in angiosperms

    2018

  • Multilocus phylogenetic reconstruction informing polyploid relationships of Aconitum subgenus Lycoctonum (Ranunculaceae) in China

    2017

  • A successful in vitro propagation technique for resurrection plants of the Selaginellaceae

    2017

  • Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention

    2017

  • Genomic inferences of domestication events are corroborated by written records in Brassica rapa

    2017

  • The Compositae Tree of Life in the age of phylogenomics

    2017

  • Transcriptome-derived evidence supports recent polyploidization and a major phylogeographic division in T rithuria submersa (H ydatellaceae, N ymphaeales)

    2016

  • Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae

    2016

  • A community-derived classification for extant lycophytes and ferns

    2016

  • Is hybridization driving the evolution of climatic niche in Alyssum montanum?

    2016

  • Spreading Winge and flying high: the evolutionary importance of polyploidy after a century of study

    2016

  • The small nuclear genomes of Selaginella are associated with a low rate of genome size evolution

    2016

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

    2015

  • Early genome duplications in conifers and other seed plants

    2015

  • On the relative abundance of autopolyploids and allopolyploids

    2015

  • Transcriptome-derived evidence supports recent polyploidization and a major phylogeographic division in Trithuria submersa (Hydatellaceae, Nymphaeales)

    2015

  • The butterfly plant arms-race escalated by gene and genome duplications

    2015

  • Between two fern genomes

    2014

  • Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives

    2014

  • Phylotranscriptomic analysis of the origin and early diversification of land plants

    2014

  • Data access for the 1,000 Plants (1KP) project

    2014

  • A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys

    2013

  • Polyploidy in Plants and Animals

    2012

  • Duplications and turnover in plant genomes

    2012

  • Rarely successful polyploids and their legacy in plant genomes

    2012

  • Karyotype and genome evolution in pteridophytes

    2012

  • Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

    2012

  • Development of an ultra-dense genetic map of the sunflower genome based on single-feature polymorphisms

    2012

  • Quantitative visualization of biological data in G oogle E arth using R 2 G 2, an R CRAN package

    2012

  • Molecular evolution across the Asteraceae: micro-and macroevolutionary processes

    2011

  • Recently formed polyploid plants diversify at lower rates

    2011

  • De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum

    2011

  • The Selaginella genome identifies genetic changes associated with the evolution of vascular plants

    2011

  • The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants

    2011

  • PART OF A HIGHLIGHT ON GENES IN EVOLUTION

    2010

  • Unfurling fern biology in the genomics age

    2010

  • EvoPipes. net: bioinformatic tools for ecological and evolutionary genomics

    2010

  • Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.—the development of a library of expressed sequence tags, microsatellite loci, and the …

    2010

  • NU-IN: Nucleotide evolution and input module for the EvolSimulator genome simulation platform

    2010

  • Functional Genomics of Fern Gametophytes: Transcriptome Sequencing in Pteridium aquilinum

    2010

  • Establishing genomic tools and resources for Guizotia abyssinica (Lf) Cass.—the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome

    2010

  • Probabilistic models of chromosome number evolution and the inference of polyploidy

    2010

  • Evolutionary genomic analyses of ferns reveal that high chromosome numbers are a product of high retention and fewer rounds of polyploidy relative to angiosperms

    2009

  • The frequency of polyploid speciation in vascular plants

    2009

  • Summary of the 2008 AFS Symposium: From Gels to Genomics: The Evolving Landscape of Pteridology. A Celebration of Gerald Gastony's Contributions to Fern Evolutionary Biology

    2009

  • Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales

    2009

  • Comparative genomic and population genetic analyses indicate highly porous genomes and high levels of gene flow between divergent Helianthus species

    2009

  • SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses

    2009

  • A Brief History of Gerald J. Gastony's Botanical Career

    2009

  • Paleopolyploidy and the evolution of plants

    2009

  • Evolution of the nuclear genome of ferns and lycophytes

    2008

  • Contribution to The Pteridophyte Flora of Puerto Rico

    2008

  • Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years

    2008

  • The impact of doppler radar data on rainfall forecast: A cave study of a convective rainband event in Mississippi Delta using WRF 3D-Var [presentation]

    2007

  • Gene co-inheritance and gene transfer

    2007

  • A TAXONOMIC REVISION OF CARIBBEAN ADIANTOPSIS (PTERIDACEAE) 1, 2

    2006

  • A Natural History of Ferns

    2005

  • Lepidopteran Soral Crypsis on Caribbean Ferns1

    2005

  • Maternal expression relaxes constraint on innovation of the anterior determinant, bicoid

    2005

  • Lepidopteran soral crypsis on caribbean ferns 1

    2005

  • Notes on the genus Lygodium Sw.(Schizaeaceae) in Malaysia

    2004

  • An Adiantopsis hybrid from Northeastern Argentina and vicinity

    2003

  • Botrychium lanceolatum subsp. angustisegmentum in Ohio

    2003

  • A Revision of Caribbean Adiantopsis

    2003

  • An evaluation of Sceptridium dissectum (Ophioglossaceae) with ISSR markers: implications for Sceptridium systematics

    2003

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