Matt Johnson, Ph.D.

Research Interests

The Johnson Lab at Texas Tech University is focused on plant phylogenomics: using the relationships among species to reveal the evolution of plant genomes. Our research is aimed at one of the central questions of biology: what forces drive the origin and maintenance of biodiversity?

Phylogenomics is a kind of applied phylogenetics, using species relationships to reconstruct the evolution of genomic traits. Although we work on many different groups of plants, bryophytes are of particular interest because the genomic causes of key innovations associated with rapid radiations in bryophytes are poorly understood.

In plants, whole genome duplication (WGD) is common– all flowering plants descend from an ancestor that experienced one or more WGD events. Following these WGD events, plant lineages quickly return to functioning as diploid organisms, but multiple copies of some genes are retained.

In this context we are interested in using genomic techniques to ask the following questions:

• Are gene duplication events clustered on the phylogeny a result of whole genome duplication or several small-scale duplications?
• Is there a functional bias to which genes retain multiple copies following?
• Are gene duplications associated with a relaxation in purifying selection?

To address these questions, we need a solid understanding of phylogenetic relationships using molecular systmatics. This requires many nuclear genes to accurately reconstruct the phylogeny, which can be difficult in non-model organisms. In our lab we use a targeted sequencing technique called HybSeq to efficiently capture hundreds of loci for dozens of specimens. We can even get material from 100+ year-old herbarium specimens, eliminating one of the common barriers to building phylogenies with complete taxon sampling.

Effectively answering our research questions often involves lots of computational analysis. Work in our lab frequently involves adapting bioinformatics tools built for model organisms to address our data from non-model organisms in natural populations.

Selected Publications

H. Hale, E.M. Gardner, J. Viruel, L. Pokorny, and M.G. Johnson. 2020. Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants. Applications in Plant Sciences 8(4). e11337 doi:/10.1002/aps3.11337

Johnson, M. G., L. Pokorny, S. Dodsworth, L.R. Botigue, R.S. Cowan, A. Devault, W.L. Eiserhardt, N. Epitawalage, F. Forest, J.T. Kim, J.H. Leebens-Mack, I.J. Leitch, O. Maurin, D.E. Soltis, P.S. Soltis, G.K. Wong, W.J. Baker, and N.J. Wickett. 2019. A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering. Systematic Biology. 68(4):594-606. doi:10.1093/sysbio/syy086

Liu, Y., M. G. Johnson, C.J. Cox, R. Medina, N. Devos, A. Vanderpoorten, L. Hedenas, N. Bell, J.R. Shevock, B. Aguero, D. Quandt, N.J. Wickett, A.J. Shaw, and B. Goffinet. 2019. Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. Nature communications 10: 1485.

Medina, R., M. G. Johnson, Y. Liu, N. J. Wickett, A. J. Shaw, and B. Goffinet. 2019. Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma. Journal of systematics and evolution. doi: 10.1038/s41467-019-09454-w

M.G. Johnson, E.M. Gardner, Y. Liu, R. Medina, B. Goffinet, A.J.Shaw, N.J.C. Zerega, and N.J. Wickett. 2016. “HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment.” Applications in Plant Sciences. 4(7):1600016 doi:10.3732/apps.1600016.

M.G. Johnson, C. Malley, A.J. Shaw, B. Goffinet, and N.J. Wickett. 2016. “A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta).” Molecular Phylogenetics and Evolution. 98:29-40. doi:10.1016/j.ympev.2016.01.008

M.G. Johnson, G. Granath, T. Tahvanainen, R. Pouliot, H. Stenoien, L. Rochefort, H. Rydin, and A.J. Shaw. 2015. “Evolution of niche preference in Sphagnum peat mosses” Evolution. 69(1) 90-103. doi:10.1111/evo.12547

*Undergraduate author