Matthew Parks, Ph.D.

• Ph.D., Botany and Plant Pathology, Oregon State University
• Master of Science, Botany, University of Idaho
• Bachelor of Science, Biology, Washington University in St. Louis

Matthew Parks, Ph.D., is an evolutionary biologist with an emphasis in phylogenomics and microbial communities. He uses large, genome-scale and metabarcoding datasets generated from next-generation sequencing platforms (Illumina, PacBio) to address research questions relating to evolutionary history and microbial community assemblage and function. The Parks lab is currently focused mainly on metabarcoding analyses of varied microbial communities, including the 'gunk' that grows on external surfaces of turtle shells, unseen microbes inhabiting lichen symbioses and within river and lake sediments.

Dr. Parks previous research is similarly varied, including experience in applying plastome-, transcriptome-, and genome-scale datasets to resolve challenging phylogenetic relationships, in sequencing, assembly and analysis of ancient DNA fragments from preserved Adelie penguin subfossils collected in Antarctica, and searching for evidence of lateral gene transfer between a diatom species and closely associated bacteria.

Dr. Parks is excited to be a part of the UCO community, and he is happy to share research opportunities with dedicated undergraduate students. Having the opportunity to work with and train the next generation of scientists is one of the most exciting and rewarding aspects of his job.

• Principles of Biology (BIO1204)
• Genetics (BIO3303)
• Genetics Lab (BIO3311)
• Python for Bioinformatics (Independent Study, BIO4930)

Selected publications (*indicates UCO undergraduate, **indicates collaborating UCO faculty):

Parks M, Hendryx E**, Taylor A**. 2020. Cross-disciplinary study of stream litter accumulation: an affordable, transformative, and scalable undergraduate research experience. Interdisciplinary Journal of Environmental and Seicne Education 17(3):32245.

Parks M, Kedy C*, Skalla C*. 2020. Consistent patterns in 16S and 18S microbial diversity from the shells of the common and widespread red-eared slider turtle (Trachemy scripta). PLOS ONE 15:302444789.

Guillory W, Onyshchenko A, Ruck E, Parks M, Nakov T, Wickett N, Alverson A. 2018. Recurrent loss, horizontal transfer, and the obscure origins of mitochondrial introns in diatoms (Bacillariophyta). Genome Biology and Evolution 10:1504-1515.

Parks M, Nakov T, Wickett NJ, Alverson AJ. 2017. Phylogenomics reveals a history of recurrent genome duplication in diatoms (Bacillariophyta). American Journal of Botany 105:330-347.

Parks M, Wickett NJ, Alverson AJ. 2017. Signal, uncertainty, and conflict in phylogenomic data for a diverse lineage of microbial eukaryotes (diatoms, Bacillariophyta). Molecular Biology and Evolution, msx268, https://doi.org/10.1093/molbev/msx268.

Gernandt, DS, Holman G, Campbell C, Parks M, Mathews S, Raubeson LA, Liston A, Stockey RA, Rothwell GW. 2016. Phylogenetics of extant and fossil Pinaceae: methods for increasing topological stability. Botany 94(9):863-884.

Govindarajulu R, Parks M, Tennessen J, Liston A, Ashman T-L. 2015. Comparison of nuclear, plastid and mitochondrial phylogenies and the origin of wild octoploid strawberry species. American Journal of Botany 102(4):1-11.

Parks M, Subramanian S, Baroni C, Salvatore MC, Zhang G, Millar CD, Lambert D. 2015. Ancient population genomics and the study of evolution. Philosophical Transactions of the Royal Society, 370:20130381.

Alexander A, Steel D, Slikas B, Hoekzema K, Carraher C, Parks M, Cronn R, Baker CS. 2013. Low diversity in the mitogenome of sperm whales revealed by next-generation sequencing. Genome Biology and Evolution, 5(1):113-29.

Salamone I, Govindarajulu R, Falk S, Parks M, Liston A, Ashman T-L. 2013. Bioclimatic, ecological and phenotypic intermediacy and high genetic admixture in a natural hybrid of octoploid strawberries. American Journal of Botany, 100(5):939-950.

Parks M, Liston A, Cronn R. 2012. Separating the wheat from the chaff: Mitigating the effects of noise in a plastome phylogenomic data set. BMC Evolutionary Biology 12:100.

Cronn R, Knaus B, Liston A, Maughan J, Parks M, Syring J, Udall J. 2012. Targeted enrichment strategies for next-generation plant biology. American Journal of Botany 99(2):291-311.

Straub S, Parks M, Weitemier K, Fishbein M, Cronn R, Liston A. 2012. Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. American Journal of Botany 99(2):349-364.

Handy SM, Parks M, Rader JI, Diachenko GW, Callahan J, Liston A, Deeds JR. 2011. Genetic Identification of Pine Nuts Obtained from Consumers Experiencing Dysgeusia. Journal of Agricultural and Food Chemistry 59(20):10995-11002.

Straub S, Fishbein M, Livshultz T, Foster Z, Parks M, Weitemeier K, Cronn C, Liston A. 2011. Building a Model: Developing Genomic Resources for Common Milkweed (Asclepias syriaca) with Low Coverage Genome Sequencing. BMC Genomics 12:211.

Whittall JB, Syring J, Parks M, Buenrostro J, Dick C, Liston A Cronn R. 2010. Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines. Molecular Ecology 19 Suppl 1:100-114.

Parks M, Cronn R, Liston A. 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biology 7:84.

Cronn RC, Liston A, Parks M, Gernandt D, Shen R, Mockler T. 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Research 36(19):e122.