List of works - Stephen A. Smith

10KP: A phylodiverse genome sequencing plan.

scientific article

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

scientific article published on 29 April 2020

A roadmap for global synthesis of the plant tree of life

scientific article published on 30 March 2018

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

scientific article

An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants

scientific article (publication date: 30 March 2010)

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

scientific article published on 5 August 2015

Analyzing Contentious Relationships and Outlier Genes in Phylogenomics

scientific article published on 01 September 2018

Analyzing and synthesizing phylogenies using tree alignment graphs

scientific article

Angiosperm phylogeny: 17 genes, 640 taxa

scientific article

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

scientific article

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

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

scientific article published in October 2017

Bioactive endophytes warrant intensified exploration and conservation

scientific article

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

scientific article published on 01 March 2018

Climate, niche evolution, and diversification of the "bird-cage" evening primroses (Oenothera, sections Anogra and Kleinia).

scientific article published in February 2009

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

scientific article published on 22 March 2010

Constructing a broadly inclusive seed plant phylogeny

scientific article published on 14 February 2018

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

scientific article published in Nature

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

scholarly article published in Nature

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

scientific article published on 02 September 2019

Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows

scientific article

Disparity, diversity, and duplications in the Caryophyllales

scientific article

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

scientific article

Elucidating the evolutionary history of the Southeast Asian, holoparasitic, giant-flowered Rafflesiaceae: pliocene vicariance, morphological convergence and character displacement.

scientific article

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

article

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

scientific article published on 01 August 2019

Evolutionary history of the angiosperm flora of China

scientific article published on 31 January 2018

Global hotspots of plant phylogenetic diversity

scientific article published in 2023

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

scientific article published on 29 June 2022

Historical biogeography of the endemic Campanulaceae of Crete

scholarly article by Nicoletta Cellinese et al published July 2009 in Journal of Biogeography

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

scientific article published in 2023

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

scientific article

Life history influences rates of climatic niche evolution in flowering plants.

scientific article

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

scientific article

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

scientific article

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

scientific article

Morphogenera, monophyly, and macroevolution

scientific article published on September 2009

New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins

scientific article (publication date: 24 November 2011)

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

scientific article published on 28 September 2020

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

scientific article published on 13 May 2020

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

scientific article

Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics

scientific article

PUmPER: phylogenies updated perpetually.

scientific article published on 28 January 2014

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

scientific article

Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants

scientific article published on 20 November 2019

Phylogenetic analyses reveal the shady history of C4 grasses

scientific article

Phylogenetic conflicts, combinability, and deep phylogenomics in plants

Phylogenomic Analyses Support Traditional Relationships within Cnidaria

scientific article

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

scientific article

Phyx: phylogenetic tools for unix

scientific article

Plastid phylogenomic insights into the evolution of Caryophyllales

scientific article published on 05 February 2019

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

scientific article

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

scientific article published on 10 June 2017

RAxML-Light: a tool for computing terabyte phylogenies

scientific article

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

scientific article

Resolving the evolutionary relationships of molluscs with phylogenomic tools

scientific article

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

scientific article published on 17 May 2018

Some limitations of public sequence data for phylogenetic inference (in plants)

scientific article

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

scholarly article published 8 December 2018

Species selection maintains self-incompatibility

scientific article

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

scientific article

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

scientific article

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

scientific article published on 25 February 2019

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

scientific article published in 2022

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

scientific article

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

scientific article published on 07 August 2017

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

scientific article published on 11 August 2021

The macroevolutionary singularity of snakes

scientific article published on 22 February 2024

The origins of C4 grasslands: integrating evolutionary and ecosystem science.

scientific article

Three keys to the radiation of angiosperms into freezing environments

scientific article with two erratum

Understanding angiosperm diversification using small and large phylogenetic trees ⬇️

scientific article published on March 2, 2011

Using and navigating the plant tree of life

scientific article published on 01 March 2018

Zanne et al. reply

scientific article

treePL: divergence time estimation using penalized likelihood for large phylogenies ⬇️

scientific article published on August 20, 2012

List of works by Stephen A. Smith

10KP: A phylodiverse genome sequencing plan.

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

A roadmap for global synthesis of the plant tree of life

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

An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants

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

Analyzing Contentious Relationships and Outlier Genes in Phylogenomics

Analyzing and synthesizing phylogenies using tree alignment graphs

Angiosperm phylogeny: 17 genes, 640 taxa

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

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

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

Bioactive endophytes warrant intensified exploration and conservation

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

Climate, niche evolution, and diversification of the "bird-cage" evening primroses (Oenothera, sections Anogra and Kleinia).

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

Constructing a broadly inclusive seed plant phylogeny

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

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

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

Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows

Disparity, diversity, and duplications in the Caryophyllales

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

Elucidating the evolutionary history of the Southeast Asian, holoparasitic, giant-flowered Rafflesiaceae: pliocene vicariance, morphological convergence and character displacement.

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

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

Evolutionary history of the angiosperm flora of China

Global hotspots of plant phylogenetic diversity

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

Historical biogeography of the endemic Campanulaceae of Crete

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

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

Life history influences rates of climatic niche evolution in flowering plants.

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

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

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

Morphogenera, monophyly, and macroevolution

New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins

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

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

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

Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics

PUmPER: phylogenies updated perpetually.

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

Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants

Phylogenetic analyses reveal the shady history of C4 grasses

Phylogenetic conflicts, combinability, and deep phylogenomics in plants

Phylogenomic Analyses Support Traditional Relationships within Cnidaria

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

Phyx: phylogenetic tools for unix

Plastid phylogenomic insights into the evolution of Caryophyllales

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

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

RAxML-Light: a tool for computing terabyte phylogenies

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

Resolving the evolutionary relationships of molluscs with phylogenomic tools

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

Some limitations of public sequence data for phylogenetic inference (in plants)

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

Species selection maintains self-incompatibility

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

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

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

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

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

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

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

The macroevolutionary singularity of snakes

The origins of C4 grasslands: integrating evolutionary and ecosystem science.

Three keys to the radiation of angiosperms into freezing environments

Understanding angiosperm diversification using small and large phylogenetic trees ⬇️

Using and navigating the plant tree of life

Zanne et al. reply

treePL: divergence time estimation using penalized likelihood for large phylogenies ⬇️