Stephen A. Smith

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Synthesis of phylogeny and taxonomy into a comprehensive tree of life

J. G. Burleigh, Lyndon M. Coghill, Cody E. Hinchliff, 2014, Proceedings of the National Academy of Sciences.

Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis.

Stephen A. Smith, R. Ree, 2008, Systematic biology.

Climate, Niche Evolution, and Diversification of the “Bird‐Cage” Evening Primroses (Oenothera, Sections Anogra and Kleinia)

Margaret E K Evans, M. Donoghue, Stephen A. Smith, 2008, The American Naturalist.

Broad phylogenomic sampling improves resolution of the animal tree of life

David Q. Matus, Stephen A. Smith, M. Martindale, 2008, Nature.

Resolving the evolutionary relationships of molluscs with phylogenomic tools

Stephen A. Smith, G. Rouse, G. Giribet, 2011, Nature.

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

Stephen A. Smith, Ya Yang, 2014, Molecular biology and evolution.

The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution

Nicholas H. Putnam, T. Wolfsberg, J. Mullikin, 2013, Science.

Three keys to the radiation of angiosperms into freezing environments

David C. Tank, Stephen A. Smith, D. Soltis, 2013, Nature.

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

Stephen A. Smith, Ya Yang, 2013, BMC Genomics.

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

M. Donoghue, Stephen A. Smith, 2008, Science.

Phylogenomic Analyses Support Traditional Relationships within Cnidaria

Samuel H. Church, Stephen A. Smith, Mark Howison, 2015, bioRxiv.

An r package and online resource for macroevolutionary studies using the ray‐finned fish tree of life

Stephen A. Smith, D. Rabosky, M. Alfaro, 2019, Methods in Ecology and Evolution.

A targeted phylogenetic approach helps explain New World functional diversity patterns of two eudicot lineages

Stephen A. Smith, H. Figueroa, 2020, Journal of Biogeography.

Constructing a broadly inclusive seed plant phylogeny.

Stephen A. Smith, Joseph W. Brown, Stephen A Smith, 2018, American journal of botany.

The bien r package: A tool to access the Botanical Information and Ecology Network (BIEN) database

Brian J. McGill, Brody Sandel, Susan K. Wiser, 2017 .

Exploring the phylogeny of rosids with a five-locus supermatrix from GenBank

Charlotte C. Germain-Aubrey, Matthew A. Gitzendanner, Stephen A. Smith, 2019, bioRxiv.

Challenges of comprehensive taxon sampling in comparative biology: Wrestling with rosids.

Stephen A. Smith, D. Soltis, P. Soltis, 2018, American journal of botany.

Intragenic conflict in phylogenomic datasets

Stephen A. Smith, Nathanael Walker-Hale, Joseph F. Walker, 2020, bioRxiv.

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Stephen A. Smith, Ya Yang, Joseph W. Brown, 2015, BMC Evolutionary Biology.

Analyzing contentious relationships and outlier genes in phylogenomics

Stephen A. Smith, Joseph W. Brown, Joseph F Walker, 2017, bioRxiv.

Understanding Angiosperm Diversification Using Small and Large Phylogenetic Trees 1

Alexandros Stamatakis, M. Donoghue, Stephen A. Smith, 2022 .

Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective.

Stephen A. Smith, C. Moritz, D. Rabosky, 2020, Systematic biology.

Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

Diego F. Morales-Briones, Stephen A. Smith, W. C. Yim, 2020, Systematic biology.

Disentangling Sources of Gene Tree Discordance in Phylogenomic Datasets: Testing Ancient Hybridizations in Amaranthaceae s.l

Diego F. Morales-Briones, Stephen A. Smith, W. C. Yim, 2020 .

A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales.

Oscar M. Vargas, Drew A. Larson, Stephen A. Smith, 2020, American journal of botany.

Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments

Stephen A. Smith, Tao Feng, U. Eggli, 2018, bioRxiv.

Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments

Stephen A. Smith, Tao Feng, U. Eggli, 2018, bioRxiv.

Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events.

Stephen A. Smith, Ya Yang, S. Brockington, 2018, The New phytologist.

Improved transcriptome sampling pinpoints 26 paleopolyploidy events in Caryophyllales, including two paleo-allopolyploidy events

Stephen A. Smith, Ya Yang, S. Brockington, 2017, bioRxiv.

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

Yinlong Xie, Gane Ka-Shu Wong, Douglas E. Soltis, 2015, Molecular biology and evolution.

Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrapping.

M. Donoghue, Stephen A. Smith, B. R. Moore, 2006, Systematic biology.

Another look at the root of the angiosperms reveals a familiar tale.

Matthew A. Gitzendanner, B. G. Briggs, Stephen A. Smith, 2014, Systematic biology.

Target sequence capture in the Brazil nut family (Lecythidaceae): Marker selection and in silico capture from genome skimming data.

Oscar M. Vargas, Stephen A. Smith, M. Heuertz, 2019, Molecular phylogenetics and evolution.

Phylogenomic conflict coincides with rapid morphological innovation

Gregory W. Stull, Stephen A. Smith, C. Parins-Fukuchi, 2020, Proceedings of the National Academy of Sciences.

Plastid phylogenomic insights into the evolution of Caryophyllales.

Stephen A. Smith, D. Soltis, P. Soltis, 2019, Molecular phylogenetics and evolution.

Inferring and Postprocessing Huge Phylogenies

Stephen A. Smith, A. Stamatakis, 2013 .

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

M. Donoghue, Stephen A. Smith, J. Beaulieu, 2009, BMC Evolutionary Biology.

PyPHLAWD: A python tool for phylogenetic dataset construction

Stephen A. Smith, Joseph F. Walker, Stephen A. Smith, 2018, Methods in Ecology and Evolution.

Nested phylogenetic conflicts, combinability, and deep phylogenomics in plants

Stephen A. Smith, Joseph W. Brown, Nathanael Walker-Hale, 2018, bioRxiv.

Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows

Mark D. Robinson, Steven H. D. Haddock, Casey W. Dunn, 2011, PloS one.

A roadmap for global synthesis of the plant tree of life.

Alexey M. Kozlov, J. G. Burleigh, JAN T. Kim, 2018, American journal of botany.

On the Tempo of Genome Size Evolution in Angiosperms

Stephen A. Smith, I. Leitch, J. Beaulieu, 2010 .

The evolutionary assembly of forest communities along environmental gradients: recent diversification or sorting of pre-adapted clades?

Stephen A. Smith, Y. Malhi, A. Zanne, 2020, bioRxiv.

The development of scientific consensus: analyzing conflict and concordance among Avian phylogenies

Stephen A. Smith, Joseph W. Brown, Ning Wang, 2017, bioRxiv.

Corrigendum: Three keys to the radiation of angiosperms into freezing environments

David C. Tank, Stephen A. Smith, D. Soltis, 2014, Nature.

Erratum: Three keys to the radiation of angiosperms into freezing environments (Nature (2014) 506 (89-92) (Doi:10.1038/nature12872))

David C. Tank, Stephen A. Smith, D. Soltis, 2014 .

The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates

Stephen A. Smith, Joseph W. Brown, 2017, bioRxiv.

Cause of gene tree discord? Distinguishing incomplete lineage sorting and lateral gene transfer in phylogenetics

Stephen A. Smith, L. Knowles, Jeet Sukumaran, 2017 .

Evolution of l‐DOPA 4,5‐dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales

M. Sanderson, Stephen A. Smith, W. C. Yim, 2019, The New phytologist.

Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales

G. Wong, Stephen A. Smith, R. Sage, 2015, The New phytologist.

Some Limitations of Public Sequence Data for Phylogenetic Inference (in Plants)

Cody E. Hinchliff, Stephen A. Smith, 2014, PloS one.

Global variation in diversification rate and species richness are unlinked in plants

Stephen A. Smith, R. Govaerts, A. Antonelli, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Disparity, diversity, and duplications in the Caryophyllales.

Stephen A. Smith, Ya Yang, Joseph W. Brown, 2018, The New phytologist.

Disparity, Diversity, and Duplications in the Caryophyllales

Stephen A. Smith, Ya Yang, Joseph W. Brown, 2017, bioRxiv.

The Darwinian shortfall in plants: phylogenetic knowledge is driven by range size

Stephen A. Smith, R. Govaerts, J. Svenning, 2022, Ecography.

Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree

J. Cracraft, Stephen A. Smith, E. Braun, 2021, bioRxiv.

Site and gene-wise likelihoods unmask influential outliers in phylogenomic analyses

Stephen A. Smith, Joseph W. Brown, Joseph F. Walker, 2017 .

An efficient field and laboratory workflow for plant phylotranscriptomic projects1

Stephen A. Smith, Tao Feng, Hannah E. Marx, 2017, Applications in Plant Sciences.

An efficient field and laboratory workflow for plant phylotranscriptomic projects

Stephen A. Smith, Tao Feng, Hannah E. Marx, 2016, bioRxiv.

Compositional shifts associated with major evolutionary transitions in plants 1 2

Stephen A. Smith, Nathanael Walker-Hale, Caroline Parins Fukuchi, 2022 .

LIKELIHOOD AND OUTLIERS IN PHYLOGENOMICS 1 2 Title : Site and gene-wise likelihoods unmask influential outliers in phylogenomic 3 analyses 4 5

Stephen A. Smith, Joseph W. Brown, Joseph F. Walker, 2017 .

Lagrange-NG: The next generation of Lagrange

Stephen A. Smith, A. Stamatakis, Ben Bettisworth, 2022, bioRxiv.

The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation

Stephen A. Smith, W. Eiserhardt, W. Baker, 2022, Systematic Biology.

A NGIOSPERM PHYLOGENY : 17 GENES , 640 TAXA 1

Catherine A. Rushworth, David C. Tank, Matthew A. Gitzendanner, 2011 .

Molecular early burst associated with the diversification of birds at the K–Pg boundary

Stephen A. Smith, E. Braun, S. Singhal, 2022, bioRxiv.

Contrasting patterns of phylogenetic diversity and alpine specialization across the alpine flora of the American mountain range system

Stephen A. Smith, D. Soltis, P. Soltis, 2021, Alpine Botany.

Reply to “Doubtful pathways to cold tolerance in plants”

David C. Tank, Stephen A. Smith, D. Soltis, 2015 .

Functional distinctiveness of major plant lineages

Matthew W. Pennell, David C. Tank, Stephen A. Smith, 2014 .

M. Donoghue, Stephen A. Smith, J. Beaulieu, 2010, Proceedings of the National Academy of Sciences.

The Origins of C4 Grasslands: Integrating Evolutionary and Ecosystem Science

Stephen A. Smith, C. Osborne, E. Edwards, 2010, Science.

Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

L. Harder, Stephen A. Smith, P. Stevens, 2016, Proceedings of the Royal Society B: Biological Sciences.

Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

Stephen A. Smith, D. Rabosky, F. Santini, 2013, Nature Communications.

Life history influences rates of climatic niche evolution in flowering plants

Stephen A. Smith, J. Beaulieu, Jeremy M Beaulieu, 2009, Proceedings of the Royal Society B: Biological Sciences.

Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales.

Stephen A. Smith, Ya Yang, Joseph F. Walker, 2017, American journal of botany.

Phylogenetic analyses reveal the shady history of C4 grasses

Stephen A. Smith, E. Edwards, 2010, Proceedings of the National Academy of Sciences.

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Stephen A. Smith, Ya Yang, Joseph W. Brown, 2015, BMC Evolutionary Biology.

Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees

Alexandros Stamatakis, Fernando Izquierdo-Carrasco, Stephen A. Smith, 2011, BMC Bioinformatics.

Bioactive Endophytes Warrant Intensified Exploration and Conservation

David C. Tank, M. Schorn, M. Donoghue, 2008, PloS one.

treePL: divergence time estimation using penalized likelihood for large phylogenies

Brian C. O'Meara, Stephen A. Smith, Stephen A. Smith, 2012, Bioinform..

Relaxation of tyrosine pathway regulation underlies the evolution of betalain pigmentation in Caryophyllales.

Stephen A. Smith, Tao Feng, Ya Yang, 2018, The New phytologist.

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

Casey W. Dunn, Stephen A. Smith, Stephen A. Smith, 2008, Bioinform..

Patterns in the assembly of temperate forests around the Northern Hemisphere.

M. Donoghue, Stephen A. Smith, 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

Joseph W. Brown, Stephen A. Smith, Cody E. Hinchliff, 2013, PLoS Comput. Biol..

Morphogenera, monophyly, and macroevolution

Stephen A. Smith, B. O’Meara, 2009, Proceedings of the National Academy of Sciences.

Species Selection Maintains Self-Incompatibility

Boris Igić, R. Lande, Stephen A. Smith, 2010, Science.

The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates

Stephen A. Smith, Joseph W. Brown, 2017, bioRxiv.

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life.

Cody E. Hinchliff, Stephen A. Smith, J. Pease, 2018, American journal of botany.

Quartet Sampling distinguishes lack of support from conflicting support in the plant tree of life

Cody E. Hinchliff, Stephen A. Smith, J. Pease, 2017, bioRxiv.

flowering plants Life history influences rates of climatic niche evolution in

Stephen A. Smith, J. Beaulieu, Jeremy M Beaulieu, 2009 .

Disentangling Sources of Gene Tree Discordance in Phylotranscriptomic Datasets: A Case Study from Amaranthaceae s.l.

Diego F. Morales-Briones, Stephen A. Smith, J. Cushman, 2019 .

Implications for Cell Type Evolution and Its Mnemiopsis leidyi The Genome of the Ctenophore

Nicholas H. Putnam, T. Wolfsberg, J. Mullikin, 2014 .

RAxML-Light: a tool for computing terabyte phylogenies

Alexandros Stamatakis, Fernando Izquierdo-Carrasco, Stephen A. Smith, 2012, Bioinform..

A Comparison of Pan Trap and Intensive Net Sampling Techniques for Documenting a Bee (Hymenoptera: Apiformes) Fauna

Stephen A. Smith, T. Roulston, Amanda L. Brewster, 2007 .

Evolution of carnivory in angiosperms

Stephen A. Smith, T. Givnish, J. Schlauer, 2018 .

Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic datasets.

Stephen A. Smith, Edwige Moyroud, Joseph F. Walker, 2021, Systematic biology.

Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms

Gregory W. Stull, Stephen A. Smith, D. Soltis, 2021, Nature Plants.

Phylogenomic conflict coincides with rapid morphological innovation

Gregory W. Stull, Stephen A. Smith, C. Parins-Fukuchi, 2020, Proceedings of the National Academy of Sciences.

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

Stephen A Smith, Joseph W Brown, Joseph F Walker, 2018, PloS one.

So many genes, so little time: comments on divergence-time estimation in the genomic era

Joseph W. Brown, Stephen A. Smith, Joseph F. Walker, 2017, bioRxiv.

Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny

Stephen A. Smith, James Pease, Stephen A. Smith, 2016, Briefings Bioinform..

Plant Functional Diversity and the Biogeography of Biomes in North and South America

Nathan J B Kraft, Stephen A. Smith, A. Kerkhoff, 2018, Front. Ecol. Evol..

Bayesian and likelihood phylogenetic reconstructions of morphological traits are not discordant when taking uncertainty into consideration: a comment on Puttick et al.

Gregory W. Stull, Oscar M. Vargas, Stephen A. Smith, 2017, Proceedings of the Royal Society B: Biological Sciences.

Evolutionary history of the angiosperm flora of China

Stephen A. Smith, D. Soltis, P. Soltis, 2018, Nature.

Phyx: phylogenetic tools for unix

Joseph W. Brown, Stephen A. Smith, Joseph F. Walker, 2017, Bioinform..

10KP: A phylodiverse genome sequencing plan

Xun Xu, Pamela S Soltis, Huanming Yang, 2018, GigaScience.

Intragenic conflict in phylogenomic datasets.

Stephen A. Smith, Nathanael Walker-Hale, Joseph F. Walker, 2020, Molecular biology and evolution.

Chloranthus genome provides insights into the early diversification of angiosperms

Stephen A. Smith, D. Soltis, P. Soltis, 2021, Nature Communications.

Disparity , Diversity , and Duplications in the Caryophyllales 1

Stephen A. Smith, Ya Yang, Joseph W. Brown, 2017 .

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages.

Gregory W. Stull, Matthew A. Gitzendanner, Stephen A. Smith, 2020, American journal of botany.

Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

Stephen A. Smith, Ya Yang, Joseph F. Walker, 2017, bioRxiv.

PHYLOGENETIC CONFLICTS, COMBINABILITY, AND DEEP PHYLOGENOMICS IN PLANTS.

Stephen A. Smith, Joseph W. Brown, Nathanael Walker-Hale, 2019, Systematic biology.

From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales.

Ning Wang, Tao Feng, Helga Ochoterena, 2018, American journal of botany.

Noise does not equal bias in assessing the evolutionary history of the angiosperm flora of China: A response to Qian (2019)

Stephen A. Smith, D. Soltis, P. Soltis, 2020, Journal of Biogeography.

Spatial phylogenetics of the North American flora

Julie M. Allen, Stephen A. Smith, D. Soltis, 2020 .

Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates

W. M. Whitten, Charlotte C. Germain-Aubrey, Julie M. Allen, 2018, iScience.

Combining historical biogeography with niche modeling in the Caprifolium clade of Lonicera (Caprifoliaceae, Dipsacales).

M. Donoghue, Stephen A. Smith, 2010, Systematic biology.

Taking into account phylogenetic and divergence‐time uncertainty in a parametric biogeographical analysis of the Northern Hemisphere plant clade Caprifolieae

Stephen A. Smith, 2009 .

Compositional shifts associated with major evolutionary transitions in plants

Stephen A. Smith, Nathanael Walker-Hale, C. T. Parins Fukuchi, 2023, bioRxiv.

Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices

Antonis Rokas, Stephen A. Smith, Xing-Xing Shen, 2020, bioRxiv.

Molecular early burst associated with the diversification of birds at the K–Pg boundary

Stephen A. Smith, E. Braun, S. Singhal, 2023, bioRxiv.

Is the age of plant communities predicted by the age, stability and soil composition of the underlying landscapes? An investigation of OCBILs

Stephen A. Smith, D. Soltis, P. Soltis, 2020, Biological Journal of the Linnean Society.

PUmPER: phylogenies updated perpetually

Alexandros Stamatakis, John Cazes, Fernando Izquierdo-Carrasco, 2014, Bioinform..

Synthesizing tree biodiversity data to understand global patterns and processes of vegetation

Sam C. Levin, Stephen A. Smith, H. Kreft, 2021, Journal of Vegetation Science.

When species trees disagree: an approach consistent with the coalescent that quantifies phylogenomic support for contentious relationships

Stephen A. Smith, Joseph F. Walker, Richard G.J. Hodel, 2020, bioRxiv.

Corrigendum: Three keys to the radiation of angiosperms into freezing environments

David C. Tank, Stephen A. Smith, D. Soltis, 2014, Nature.

Phylesystem: a git-based data store for community-curated phylogenetic estimates

Karen Cranston, Jonathan Rees, Joseph W. Brown, 2015, Bioinform..

Using and navigating the plant tree of life.

Stephen A. Smith, D. Soltis, P. Soltis, 2018, American journal of botany.

Zanne et al. reply

David C. Tank, Stephen A. Smith, D. Soltis, 2015, Nature.

Contrasting patterns of phylogenetic diversity and alpine specialization across the alpine flora of the American mountain range system

Stephen A. Smith, D. Soltis, P. Soltis, 2021, Alpine Botany.

The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data.

Drew A. Larson, Stephen A. Smith, D. Soltis, 2023, Molecular phylogenetics and evolution.

A consensus phylogenomic approach highlights the ancient rapid radiation of Ericales

Oscar M. Vargas, Stephen A. Smith, Joseph F. Walker, 2019, bioRxiv.

Current climate, isolation and history drive global patterns of tree phylogenetic endemism

Sam C. Levin, Stephen A. Smith, H. Kreft, 2019, Global Ecology and Biogeography.

The development of scientific consensus: Analyzing conflict and concordance among avian phylogenies.

Ning Wang, Stephen A. Smith, Joseph W. Brown, 2017, Molecular phylogenetics and evolution.

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

Stephen A. Smith, Ya Yang, 2013, BMC Genomics.

RAxML-Light: a tool for computing terabyte phylogenies

Stephen A. Smith, A. Stamatakis, S. Berger, 2012, Bioinform..

Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method

Stephen A. Smith, D. Soltis, P. Soltis, 2023, Systematic biology.

A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories.

Stephen A. Smith, L. Knowles, Jeet Sukumaran, 2018, American journal of botany.

Challenges of comprehensive taxon sampling in comparative biology: Wrestling with rosids.

Stephen A. Smith, D. Soltis, P. Soltis, 2018, American journal of botany.

Target sequence capture in the Brazil nut family (Lecythidaceae): Marker selection and in silico capture from genome skimming data.

Oscar M. Vargas, Stephen A. Smith, M. Heuertz, 2019, Molecular phylogenetics and evolution.

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

J. G. Burleigh, Lyndon M. Coghill, Cody E. Hinchliff, 2014, Proceedings of the National Academy of Sciences.

Global hotspots of plant phylogenetic diversity.

Stephen A. Smith, F. Forest, R. Govaerts, 2023, The New phytologist.

Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates

W. M. Whitten, Charlotte C. Germain-Aubrey, Julie M. Allen, 2018, iScience.

Genome duplications, genomic conflict, and rapid phenotypic evolution characterize the Cretaceous radiation of Fagales

Gregory W. Stull, Stephen A. Smith, Hong Ma, 2023, bioRxiv.