Overview

To see my google scholar with a complete list of papers please click here

bold denotes lab member

*asterisks denotes equal contribution

UIC Publications (Aug. 2021 - )

HM Robertson, JF Walker*, E Moyroud*. Investigating Phylogenetic Conflict using Homolog Trees reveals the Genetic Basis of Phenotypic Convergence in Carnivorous Sundews. 2023. In review.

N Ruiz-Vargas, K Ramanauskas, AS Tyszka, Roberta J Mason-Gamer and JF Walker. Transcriptome data from silica-preserved leaf tissue reveals gene flow patterns in a Caribbean bromeliad. 2023. In review.

AS Tyszka*, EC Bretz*, HM Robertson, MD Woodcock-Girard, K Ramanauskas, DA Larson, GW Stull and JF Walker. Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants. 2023. Frontiers in Plant Sciences.

Joseph F. Walker and SA Smith. Phylogenomic Conflict in Plants. 2023. Princeton Press.

G Reeves, A Tripathi, P Singh, MRW Jones, AK Nanda, C Musseau, M Craze, S Bowden, JF Walker, AR Bentley, CW Melnyk and JM Hibberd. Monocotyledonous plants graft at the embryonic root–shoot interface. 2022. Nature.

E Moyroud, CA Airoldi, J Ferria, C Giorio, SS Steimer, PJ Rudall, CJ Prychid, S Halliwell, JF Walker, S Robinson, M Kalberer and BJ Glover. Cuticle chemistry drives the development of diffraction gratings on the surface of Hibiscus trionum petals. 2022. Current Biology.

JF Walker, SA Smith, RGJ Hodel, E Moyroud. Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic data sets. 2022. Systematic Biology.

LC Wheeler*, JF Walker*, J Ng, R Deanna, A Dunbar-Wallis, A Backes, PH Pezzi, MV Palchetti, HM Robertson, A Monaghan, L Brandão de Freitas, GE Barboza, E Moyroud, SD Smith. Transcription factors evolve faster than their structural gene targets in the flavonoid pigment pathway. 2022. Molecular Biology and Evolution.

ALM Fairnie*, MTS Yeo*, S Gatti*, E Chan*, V Travaglia*, JF Walker*, E Moyroud. Eco-Evo-Devo of petal pigmentation patterning. 2022. Essays in Biochemistry.

Pre UIC publications (Aug. 2012 - Aug. 2021)

SA Smith*, N Walker-Hale*, JF Walker*. Intragenic Conflict in Phylogenomic Data Sets. 2020. Molecular Biology and Evolution.

DA Larson, JF Walker, OM Vargas and SA Smith. A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales. 2020. American Journal of Botany.

SA Smith, N Walker-Hale, JF Walker and JW Brown. Nested phylogenetic conflicts, combinability, and deep phylogenomics in plants. 2020. Systematic Biology.

S Tittes, JF Walker, L Torres-Martinez and N Emery. Grow where you thrive or where only you can survive? A Bayesian analysis of tolerance curve evolution in a clade with diverse habitat affinities (2019). American Naturalist.

JF Walker*, N Walker-Hale*, DA Larson, OM Vargas and GW Stull. Characterizing gene tree conflict and systematic error in plastome-inferred phylogenies (2019). PeerJ.

SA Smith and JF Walker. PyPHLAWD: A python package for phylogenetic dataset construction (2019). Methods in Ecology and Evolution.

N Wang, Y Yang, MJ Moore, SF Brockington, JF Walker, JW Brown, T Feng, A Timoneda, C Edwards, L Majure, R Puente, U Eggli, B Liang and SA Smith. Evolution of Portulacineae marked by adaptation to harsh environments, gene tree conflict, and gene family expansion (2019). Molecular Biology and Evolution.

JF Walker, JW Brown and SA Smith. Analyzing contentious relationships and outlier genes in phylogenomics (2018). Systematic Biology, 67:5.

SA Smith, JW Brown* and JF Walker*. So many genes, so little time: A practical approach to divergence time estimation in the genomic era (2018). Plos One, 13:5.

JF Walker, Y Yang, T Feng, A Timoneda, J Mikenas, V Hutchison, C Edwards, N Wang, S Ahluwalia, J Olivieri, N Walker-Hale, LC Majure, R Puente, G Kadereit, M Lauterbach, U Eggli, H Flores-Olvera, H Ochoterena, SF Brockington, MJ Moore and SA Smith. From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provides further insight to the evolution of Caryophyllales (2018). American Journal of Botany, 105:3.

JB Pease, JW Brown, JF Walker, CE Hinchliff and SA Smith. Quartet sampling distinguishes lack of support from conflicting support in plant tree of life (2018). American Journal of Botany, 105:3.

Y Yang, MJ Moore, SF Brockington, J Mikenas, J Olivieri, JF Walker and SA Smith. Improved transcriptome sampling pinpoints 26 paleopolyploidy events in Caryophyllales, including two paleo-allopolyploidy events (2018). New Phytologist, 217:2.

SA Smith, JW Brown, Y Yang, R Bruenn, CP Drummond, SF Brockington, JF Walker, N Last, NA Douglas and MJ Moore. Disparity, Diversity, and Duplications in the Caryophyllales (2018). New Phytologist, 217:2.

JF Walker, Y Yang, MJ Moore, J Mikenas, SF Brockington, A Timoneda and SA Smith. Widespread paleopolyploidy, gene tree conflict and recalcitrant relationships among the carnivorous Caryophyllales (2017). American Journal of Botany, 104:6.

JW Brown*, JF Walker* and SA Smith (2017). Phyx: Phylogenetic tools for Unix. Bioinformatics, 33:12.

Y Yang, MJ Moore, SF Brockington, A Timoneda, T Feng, H Marx, JF Walker and SA Smith (2017). An efficient field and laboratory workflow for plant phylotranscriptomic projects. Applications in Plant Sciences, 5:3.

T Casey, JF Walker, K Bhide, J Thimmapuram and J Schoonmaker. Global transcriptome difference in myokine and inflammatory genes in muscle of mature steer progeny is related to maternal lactation diet and muscle composition (2018). Physiological Genomics.

JF Walker, RK Jansen, MJ Zanis and NC Emery (2015). Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes. American Journal of Botany, 102:11.

JF Walker, MJ Zanis and NC Emery (2014). Comparative analysis of Complete Chloroplast Genome Sequence and Inversion Variation in Lasthenia Burkei (Madieae, Asteraceae). American Journal of Botany, 101:4.

AM Stoehr, JF Walker and A Monteiro (2013). Spalt expression and the development of melanic color patterns in pierid butterflies. EvoDevo, 4:6.