Author

J. F. Walker

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Evolutionary Biology· 12

Signature Assays, Organisms & Methods

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Organism:plant (other)· 11 Research Focus:phylogenetics / evolution· 10 Approach:statistical model· 8 Assay:DNA methylation· 5 Assay:whole-genome sequencing· 4 Assay:bulk RNA-seq· 2 Approach:comparative / phylogenetic analysis· 2 Research Focus:development & morphogenesis· 2

Frequent Co-Authors

S. A. Smith· 7 shared J. W. Brown· 5 shared S. F. Brockington· 3 shared Y. Yang· 3 shared A. Timoneda· 2 shared D. A. Larson· 2 shared E. Moyroud· 2 shared J. Mikenas· 2 shared

Activity by Year

2017-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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7 shared papersEvolutionary Biology

S. A. Smith

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12 papers

Recent·Most cited

CAnDI: a new tool to investigate conflict in homologous gene trees and explain convergent trait evolution

H. M. Robertson, J. F. Walker, E. Moyroud

CAnDI identifies conflicts in homologous gene trees to better understand convergent trait evolution, showing genomic evidence for shared molecular bases in carnivorous plant traps.

bioRxiv · Nov 18, 2023Evolutionary Biology

Transcriptome data from silica-preserved leaf tissue reveals gene flow patterns in a Caribbean bromeliad

N. Ruiz-Vargas, K. Ramanauskas, A. S. Tyszka, R. J. Mason-Gamer, J. F. Walker

The paper demonstrates that high-quality transcriptomes can be obtained from silica-preserved leaf tissue and uses them to study gene flow patterns in Pitcairnia species in the Dominican Republic.

bioRxiv · Jun 16, 2023Evolutionary Biology

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

J. F. Walker, X.-X. Shen, A. Rokas, S. A. Smith, E. Moyroud

The paper identifies four factors causing outlier genes in phylogenomic matrices and shows how excluding them can mislead evolutionary inferences.

bioRxiv · Apr 20, 2020 · PreprintEvolutionary Biology

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

D. A. Larson, J. F. Walker, O. M. Vargas, S. A. Smith

This study uses a consensus phylogenomic approach to analyze Ericales' evolutionary history, finding unresolved ancient relationships and evidence of a whole genome duplication.

bioRxiv · Dec 9, 2019Evolutionary Biology

Phylogenetic conflicts, combinability, and deep phylogenomics in plants

S. A. Smith, J. F. Walker, J. Brown, N. Walker-Hale

The paper dissects phylogenetic signal in a plant dataset to resolve conflicts and identify unresolved relationships, finding support for certain placements but uncertainty in others.

bioRxiv · Oct 17, 2019Evolutionary Biology

Characterizing gene tree conflict in plastome-inferred phylogenies

J. F. Walker, G. W. Stull, N. Walker-Hale, O. M. Vargas, D. A. Larson

The paper examines gene tree conflict in plastome-inferred phylogenies and identifies rpoC2 as a superior marker for angiosperm phylogeny reconstruction.

bioRxiv · Jan 4, 2019Evolutionary Biology

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

N. Wang, Y. Yang, M. J. Moore, S. F. Brockington, J. F. Walker, J. W. Brown, B. Liang, T. Feng, C. Edwards, J. Mikenas, J. Olivieri, V. Hutchison, A. Timoneda, T. Stoughton, R. Puente, , S. A. Smith

This study reconstructs the phylogeny of Portulacineae and examines molecular evolution correlates with adaptation to harsh environments, identifying gene duplications and expansions linked to stress responses.

bioRxiv · Aug 13, 2018Evolutionary Biology

Analyzing contentious relationships and outlier genes in phylogenomics

J. F. Walker, J. W. Brown, S. A. Smith

The paper identifies outlier genes causing conflict between supermatrix and coalescent-based species trees in two datasets and proposes a framework for examining alternative edges in phylogenomic analyses.

bioRxiv · Jun 4, 2018Evolutionary Biology

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

S. Smith, J. W. Brown, J. F. Walker

The paper introduces a method to improve divergence-time estimation by filtering genes from phylogenomic datasets based on clock-likeness and topological compatibility, showing it reduces error in time inference.

bioRxiv · Feb 22, 2018Evolutionary Biology

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

J. B. Pease, J. W. Brown, J. F. Walker, C. E. Hinchliff, S. A. Smith

The paper introduces Quartet Sampling (QS), a method to distinguish conflicting support from poor support in plant phylogenies, showing it effectively identifies discordant evolutionary relationships.

bioRxiv · Aug 18, 2017Evolutionary Biology

Disparity, Diversity, And Duplications In The Caryophyllales

S. Smith, J. W. Brown, Y. Yang, S. F. Brockington, R. Bruenn, C. P. Drummond, J. F. Walker, N. Last, N. A. Douglas, M. Moore

The paper maps whole genome duplications (WGDs) and diversification shifts in Caryophyllales, finding some correlations but no tight link between WGDs and diversification rates.

bioRxiv · Jul 24, 2017Evolutionary Biology

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

J. F. Walker, Y. Yang, M. J. Moore, J. Mikenas, A. Timoneda, S. F. Brockington, S. A. Smith

The paper uses phylogenomic data to analyze relationships among carnivorous Caryophyllales, finding gene tree conflict, paleopolyploidy events, and unresolved relationships.

bioRxiv · Mar 10, 2017Evolutionary Biology