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List of works by Joseph W Brown

A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves).

scientific article

A molecular genetic timescale for the diversification of autotrophic stramenopiles (Ochrophyta): substantive underestimation of putative fossil ages

scientific article

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

Analyzing contentious relationships and outlier genes in phylogenomics

Ancient divergence and biogeography of Raukaua (Araliaceae) and close relatives in the southern hemisphere

scientific article published in 2012

Angiosperm phylogeny inferred from sequences of four mitochondrial genes

article

Appraisal of the consequences of the DDT-induced bottleneck on the level and geographic distribution of neutral genetic variation in Canadian peregrine falcons, Falco peregrinus

scientific article

BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

scientific article published in 2014

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

Beyond aridification: multiple explanations for the elevated diversification of cacti in the New World Succulent Biome

scientific article

Confidence intervals in molecular dating by maximum likelihood

Constructing a broadly inclusive seed plant phylogeny

scientific article published on 14 February 2018

Directional gene flow patterns in disjunct populations of the black ratsnake (Pantheropis obsoletus) and the Blanding’s turtle (Emydoidea blandingii)

Disparity, Diversity, and Duplications in the Caryophyllales

Disparity, diversity, and duplications in the Caryophyllales

scientific article

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

article

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

Evolving Perceptions on the Antiquity of the Modern Avian Tree

Goldilocks Meets Santa Rosalia: An Ephemeral Speciation Model Explains Patterns of Diversification Across Time Scales

scientific article (publication date: June 2012)

Multi-locus phylogenetic inference among New World Vultures (Aves: Cathartidae).

scientific article

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

scientific article published on 4 June 2015

Nuclear DNA does not reconcile 'rocks' and 'clocks' in Neoaves: a comment on Ericson et al

scientific article

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 conflicts, combinability, and deep phylogenomics in plants

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

scientific article (publication date: 13 May 2013)

Phyx: phylogenetic tools for unix

scientific article

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

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

scientific article published on 17 May 2018

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

Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages

scientific article

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

scientific article

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

The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates

scientific article published on 13 March 2019

The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates

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

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

scientific article published on 07 August 2017

The use of genetics for the management of a recovering population: temporal assessment of migratory peregrine falcons in North America

scientific article

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion

scientific article published on 15 February 2019

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion

What drives results in Bayesian morphological clock analyses?

geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees

scientific article

rotl : an R package to interact with the Open Tree of Life data

article

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