Vinson Doyle

Fungal systematics and population genetics; fungal taxonomy; plant-associated fungi; bioinformatics; statistical phylogenomics; phylogenetic methods

The pace at which fungal systematics has changed in recent years is directly related to the deluge of molecular sequence data and the methodological advances for analyzing these data. These advancements have led to the development of new tools to address a broad swath of interesting, fundamental, and previously intractable biological questions. As a more stable classification system for fungi emerges and the advancement in data collection and analysis continue, we are able to address fundamental questions related to the ecological and genetic factors that influence variation in life history traits among plant-associated fungi.  My principal interest is leveraging these technical and methodological advances to illuminate the processes that have shaped plant-associated fungal diversity. In this context, my research is both empirical and methodological.

The empirical side of my research is focused on developing a better understanding of fungal diversity, particularly understanding the diversity and species divergence of endophytic, epiphytic, and plant pathogenic fungi. Molecular systematics, population genetics, and classical taxonomy are essential parts of my research in fungal evolution. Fundamental to understanding how various biotic and abiotic factors influence the evolutionary trajectory of plant-associated fungi is a robust understanding of their evolutionary history (phylogeny). This side of my research relies heavily on fieldwork to collect the vast fungal diversity that can be found associated with agricultural and wild host plant species as well as lab and computational work to gain insight into their evolutionary history.

My interest in methodological phylogenetics research has emerged from a reliance on accurate phylogenetic inferences in order to address questions relating to fungal evolution. While expanding the size of molecular datasets has generally produced stronger confidence in phylogenetic hypotheses, there are many instances where systematic bias can mislead our analysis despite strong support for a given hypothesis. I am interested in understanding what assumptions made during phylogenetic analysis can produce biased results, how we can identify when we are being misled, and how we can avoid these pitfalls.

Khodadi, F., Gonzalez, J., Martin, P., Giroux, E., Bilodeau, G., Peter, K., Doyle, V.P., Acimovic, S. 2020. Identification and characterization of Colletotrichum species causing apple bitter rot in New York and description of C. noveboracense sp. nov. Sci Rep 10, 11043 (2020). https://doi.org/10.1038/s41598-020-66761-9

Sautua, F., V.P. Doyle, *J. Searight, M. Scandiani, M. Carmona. 2020. Cercospora cf. nicotianae is a causal agent of Cercospora Leaf Blight of soybean. European Journal of Plant Pathology. doi: 10.1007/s10658-020-01969-z

**Vieira, W.A.S., Bezerra, P.A., da Silva, A.C., Veloso, J.S., Camara, M.P.S., Doyle, V.P. 2020. Optimal markers for the identification of Colletotrichum species. Molecular Phylogenetics and Evolution 143:106694. doi: https://doi.org/10.1016/j.ympev.2019.106694

Prasanna, A.N., D. Gerber, T. Kijpornyongpan, M.C. Aime, V.P. Doyle, L.G. Nagy. 2020. Model choice, missing data and taxon sampling impact phylogenomic inference of deep Basidiomycota relationships. Systematic Biology 69:17-37. doi: 10.1093/sysbio/syz029 (5 Year Impact Factor: 14.501)

Hudson, O., M. Buchholz, V. P. Doyle, M.A. Sundue. 2019. Multilocus Phylogeny of Acrospermaceae: new epibiotic species and placement of Gonatophragmium, Pseudovirgaria, and Phaeodactylium anamorphs. Mycologia 111:6, 1041-1055, doi: 10.1080/00275514.2019.1668905 (5 Year Impact Factor: 2.833)

Sautua, F., S.A. Gonzalez, V.P. Doyle, M.F. Berretta, M. Gordó, M.M. Scandiani, M.L. Rivarola, P. Fernandez, M.A. Carmona 2019. Draft genome sequence of Cercospora kikuchii, a species associated with Cercospora leaf blight in Argentina. Data in Brief 27: 104693. doi: 10.1016/j.dib.2019.104693

Almeida, T. de, Coelho, I., de Vasconcelos, L.S., Pontes, M.A., Vieira, W., Camara, M., Doyle, V.P., Laranjeira, D. 2019. First report of Diaporthe kongii causing foot rot on sweet potato in Brazil. Plant Disease 104:284. doi: 10.1094/PDIS-04-19-0868-PDN

Prasanna, A.N., D. Gerber, Teeratas Kijpornyongpan, M. Catherine Aime, V. P. Doyle, Laszlo G. Nagy. 2019. Model choice, missing data and taxon sampling impact phylogenomic inference of deep Basidiomycota relationships. Systematic Biology syz029. Online ahead of print. https://doi.org/10.1093/sysbio/syz029

Doyle, V.P., **Tonry, H.T., Amsden, B., Beale, J., Dixon, E., Li, H., Szarka, D., Ward, N. Gauthier. 2019. First report of Cercospora cf. flagellaris on industrial hemp (Cannabis indica x sativa) in Kentucky. Plant Disease https://doi.org/10.1094/PDIS-01-19-0135-PDN

Clark, C.A., V. P. Doyle, A.Q. Villordon, J.C. Gregorie. 2018. First report of Pythium root rot on aeroponically grown sweet potato caused by Pythium myriotylum in Louisiana. Plant Disease https://doi.org/10.1094/PDIS-05-18-0865-PDN.

Garcia-Aroca, T., Doyle, V.P., Singh, R., Price, T., Collins, K. 2018. First Report of Curvularia Leaf Spot of Corn, Caused by Curvularia lunata, in the United States. Plant Health Progress 19:140-142.

Veloso, J.S., Câmara, M.P.S., Lima, W.G., Michereff, S.J., Doyle, V.P. 2018. Why species delimitation matters for fungal ecology: Colletotrichum diversity on wild and cultivated cashew in Brazil. Fungal Biology 122:677-691.

Vieira, W.A.S., W.G. Lima, E.S. Nascimento, S.J. Michereff, M.P. S. Câmara, V.P. Doyle. 2018. The impact of phenotypic and molecular data on the inference of Colleotrichum diversity associated with Musa. Mycologia 16:1-23. doi: 10.1080/00275514.2017.1418577.

Sharma, S., A. Z. Zaccaron, J.B. Ridenour, Tom Allen, Kassie Conner, Vinson P. Doyle, Trey Price, Edward Sikora, Raghuwinder Singh, Terry Spurlock, Maria Tomaso-Peterson, Tessie Wilkerson, and Burt H. Bluhm. 2018. Draft genome sequence of Xylaria sp., the causal agent of taproot decline of soybean in Southern United States. Data in Brief 17:129–133.

Reid, C.S., V.P. Doyle, R. Carter, Y. Vargas-Rodriguea, L.E. Urbatsch. 2017. Molecular systematics of targeted flat sedges (Cyperus, Cyperaceae) of the Americas. Plant Ecology and Evolution 150 (3): 343–357, 2017 https://doi.org/10.5091/plecevo.2017.1262

Singh, R. and Doyle, V.P. 2017. Boxwood dieback caused by Colletotrichum theobromicola: a diagnostic guide. Plant Health Progress 18:174-180.

Albu, S., S. Sandeep, B. Bluhm, P. Price, R. Schneider, V.P. Doyle. 2017. Draft Genome Sequence of Cercospora cf. sigesbeckiae, a causal agent of Cercospora Leaf Blight on soybean. Genome Announcements 2017 Sep; 5(36): e00708-17.

Allen, T., B. Bluhm, K. Conner, V.P. Doyle, T. Price, E. Sikora, R. Singh, T. Spurlock, M. Tomaso-Peterson, T. Wilkerson. 2017. First Report of Taproot Decline of Soybean, Caused by a Species of Xylaria, in the Southern United States. Plant Health Progress 18:35-40.

Albu S., P.P. Price, V.P. Doyle, B. Padgett, R.W. Schneider. 2016. The G143A Mutation is Responsible for Strobilurin Fungicide Resistance in Cercospora Leaf Blight and Purple Seed Stain Pathogens of Louisiana Soybean. Plant Health Progress, 17(3): 197.

Albu, S., R.W. Schneider, P.P. Price, V.P. Doyle. 2016. Cercospora cf. flagellaris and C. cf. sigesbeckiae are associated with Cercospora leaf blight and purple seed stain on soybean in North America. Phytopathology, 106(11): 1376-1385.

Doyle, Vinson P., Young R.E., Naylor G.J.P., Brown J.M. 2015. Can We Identify Genes with Increased Phylogenetic Reliability? Systematic Biology, 64: 824-837

Doyle, Vinson P., Andersen, J., Nelson, B., and Brown, J. 2014. Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission  cluster. Molecular Phylogenetics and Evolution, 75:126-137.

Doyle, Vinson P., Oudemans, P., Rehner, S., Litt, A. 2013.  Habitat and host indicate lineage identity in Colletotrichum gloeosporioides s.l. from wild and agricultural landscapes in North America. PLoS ONE 8(5): e62394. doi:10.1371/journal.pone.0062394.

Doyle, Vinson P., 2012. Colletotrichum gloeosporioides s.l. in North America: sex, host, and habitat-mediated diversity in a plant-associated ascomycete. City University of New York, ProQuest, UMI Dissertations Publishing, 2012. 3541889. http://search.proquest.com/docview/1115277829?accountid=12154

Wheeler, Q.D., S. Knapp, D. W. Stevenson, J. Stevenson, S. D. Blum, B. M. Boom, G. G. Borisy, J. L. Buizer, M. R. De Carvalho, A. Cibrian, M. J. Donoghue, V. Doyle, E. M. Gerson, C. H. Graham, P. Graves, S. J. Graves, R. P. Guralnick, A. L. Hamilton, J. Hanken, W. Law,D. L. Lipscomb, T. E. Lovejoy, H. Miller, J. S. Miller, S. Naeem, M. J. Novacek, L. M. Page, N. I. Platnick, H. Porter-Morgan, P. H. Raven, M. A. Solis, A. G. Valdecasas, S. Van Der Leeuw, A. Vasco, N. Vermeulen, J. Vogel, R. L. Walls, E. O. Wilson, and J. B. Woolley. 2012. Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity. Systematics and Biodiversity, 10(1): 1–20.

Constantelos, Chris, Doyle, Vinson P., Litt, Amy and Oudemans, Peter V. 2011.  First Report of Gliocephalotrichum bulbilium Causing Cranberry Fruit Rot in New Jersey and Massachusetts. Plant Disease, Volume 95, Number 5: 618-619.