Matt Johnson

Associate Professor
Google Scholar

I am an Assistant Professor in Biological Sciences at Texas Tech University. My main area of interest is plant phylogenomics– using the relationships among species to reveal the evolution of plant genomes. My research is aimed at one of the central questions of biology: what forces drive the origin and maintenance of biodiversity?

I received my bachelor’s degree from Duke University, and continued at Duke to receive my Ph.D. advised by Jon Shaw. My dissertation “Evolution of mating systems in Sphagnum peatmosses” investigated the influence of ecology and reproductive biology on mating patterns in peatmosses. I also became interested in computer programming, primarily in R and Python.

Following my Ph.D. I worked for the Chicago Botanic Garden as the lead bioinformatician on the Pleurocarpus Moss Tree of Life Project working with Norman Wickett. As part of this project I developed HybPiper for efficient processing of targeted sequence data for phylogenomics, and used transcriptome data to uncover genomic events associated with a major radiation of mosses.

At Texas Tech I envision my lab merging the interests of my Ph.D. (field biology, ecology, phenotype evolution) with my post-doc (bioinformatics, phylogenomics, data visualization) to conduct question-driven science at the interface of ecology, evolution, and genomics.

Outside of academics, I enjoy watching sports (college basketball, baseball, and pro football), playing tennis and video games, and cooking. Inside of academics, it’s too dark to read.


Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes

homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

Including Phylogenetic Conservatism of Shortgrass Prairie Restoration Desired Species Does Not Improve Species Germination Predictions

Landscapes of Linalool

Are Palmer’s Elm-Leaf Goldenrod and the Smooth Elm-Leaf Goldenrod Real? The Angiosperms353 Kit Provides Within-Species Signal in Solidago ulmifolia s. l.

On the Potential for Angiosperms353 for Population Genomics

Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants

Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering

Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus

Practical considerations for plant phylogenomics

Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High- Throughput Sequencing Reads Using Target Enrichment

Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)

A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta)

Evidence for genetic erosion of a California native tree, Platanus racemosa, via recent, ongoing introgressive hybridization with an introduced ornamental species

Evolution of niche preference in Sphagnum peat mosses


Post-Doc Opportunity


JSE Award

Another New Lab Milestone


Haley's First Paper

Bryum argenteum DNA extraction

Botany 2019 Report


Seed Experiment

TTU URC 2019

Phylogenomics PostDoc

Targeted Sequencing of Herbarium Specimens

First Trip to GUMO

Zach Presents at URC

HybPiper v1.3

Seeking Graduate Students

Welcome to Mossmatters At Texas Tech

Designing HybSeq Probes from a large sequence alignment

Introducing HybPiper

Touring a Peatland Restoration Site