I am a mycologist and bioinformatician. My research largely focuses on using genomics methods to complement ecological research. I am particularly interested in how anthropogenic disturbance affects biological diversity.
My involvement with the Biomonitoring 2.0 project involved using metabarcoding, high throughput sequencing of signature barcode DNA sequences, to detect soil organisms such as bacteria, fungi, and plants. In this study pristine soils were compared with soils potentially impacted by the petroleum industry downstream from the Alberta oil sands. My focus was on species assignment methods, using simulation studies to assess the performance of existing tools, and adapting them for use with the project.
Previous research experience includes analyzing metabarcoding, shotgun metagenomic, and transcriptome datasets obtained from pure cultures as well as from mixed environmental samples like water, soil, and Malaise traps. Experience in the field and in the lab has piqued my interest in the effect of methodological bias. As a result I spend a lot of time considering how molecular methods can be integrated with traditional ecological methods and how these results should be interpreted.
Nilsson, R.H., Tedersoo, L., Ryberg, M., Kristiansson, E., Hartmann, M., Unterseher, M., Porter, T.M., Bengtsson-Palme, J., Walker, D.M., de Souza, F., Gamper, H.A., Larsson, E., Larsson, K.-H., Koljalg, U., Edgar, R., Abarenkov, K. (2015) A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts. Microbes and Environments, 50: 145-150.
Nilsson, R.H. and 58 others (2014) Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Diversity, 67:11-19.
Porter, T.M., Gibson, J., Shokralla, S., Baird, D., Golding, G.B., Hajibabaei, M. (2014) Rapid and accurate taxonomic classification of insect (Class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naive Bayesian classifier. Molecular Ecology Resources, 14: 929-942.
Porter, T.M., Golding, G.B., King, C., Froese, D., Zazula, G., and Poinar, H.N. (2013) Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility. Molecular Ecology Resources, 13: 798-810.
Porter, T.M. and Golding, G.B. (2012) Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error. PLoS ONE, 7(4): e35749.
Porter, T.M. and Golding, G.B. (2011) Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons? New Phytologist, 192: 775-782.
Porter, T.M., Skillman, J.E., and Moncalvo, J.M. (2008) Fruiting body and soil rDNA detects complementary assemblage of Agaricomycotina (Basidiomycota, Fungi) in a hemlock-dominated forest plot in southern Ontario. Molecular Ecology, 17: 3037-3050.
Porter, T.M., Schadt, C., Rizvi, L., Martin, A.P., Schmidt S.K., Scott-Denton, L., Vilgalys, R., and Moncalvo, J.M. (2008) Widespread occurrence and phylogenetic placement of a soil clone group (Ascomycota, Fungi) adds a prominant new branch to the tree of life. Molecular Phylogenetics and Evolution, 46: 635-644.