Affiliated Department

Biology

Scholarly and creative works

• Article in Refereed Journal

  Ubiquity and diversity of Basidiobolus across amphibian species inhabiting an urbanization gradient

  Mycologia
  2025
  Madison R Hincher, Jasper P Carleton, Sara J Wheeler, Manning DelCogliano, Kaitlyn Mathis, Javier F Tabima
• Article in Refereed Journal

  Impacts on the microbial fungal communities across water, sediment, and amphibian hosts across an urbanization gradient waterway in Worcester, Massachusetts

  bioRxiv
  2025
  Sara Jean Wheeler, Manning DelCogliano, Brennan Hare, Alexander James Bradshaw, Madison Rae Hincher, Jasper Perseus Carleton, Philip J Bergmann, Nathan A Ahlgren, Javier Felipe Tabima
• Article in Refereed Journal

  Unraveling the Genomic and Phylogenetic Complexity of the understudied microfungus Basidiobolus: Insights from 19 Newly Sequenced Genomes

  bioRxiv
  2025
  Jasper Perseus Carleton, Alexander James Bradshaw, Liam Patrick Cleary, Madison R Hincher, Kathryn E Bushley, Javier Felipe Tabima
• Article in Refereed Journal

  Ubiquity and diversity of Basidiobolus across amphibian species inhabiting an urbanization gradient

  Mycologia
  February

  2025
  Madison R Hincher, Jasper P Carleton, Sarah J Wheeler, Manning Delcogliano, Kaitlyn A. Mathis, Javier F Tabima Restrepo
• Article in Refereed Journal

  Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria

  Msphere
  2024

  Vol. 9

  Issue #3
  Lluvia Vargas-Gast’elum, Alexander S Romer, Marjan Ghotbi, Jason W Dallas, N Reed Alexander, Kylie C Moe, Kerry L McPhail, George F Neuhaus, Leila Shadmani, Joseph W Spatafora, others
• Article in Refereed Journal

  Climatic variability, spatial heterogeneity and the presence of multiple hosts drive the population structure of the pathogen Phytophthora ramorum and the epidemiology of Sudden Oak Death

  Ecography
  2024

  Vol. 2024

  Issue #10
  Melina Kozanitas, Brian J Knaus, Javier F Tabima, Niklaus J Gr"unwald, Matteo Garbelotto
• Article in Refereed Journal

  Population-level immunologic variation in wild threespine stickleback (Gasterosteus aculeatus)

  Fish & Shellfish Immunology
  2024

  Vol. 149
  Anika M Wohlleben, Javier F Tabima, N’eva P Meyer, Natalie C Steinel
• Article in Refereed Journal

  Suillus hypogaeus: First record of a truffle Suillus

  Mycologia
  2024

  Vol. 116

  Issue #5
  P’aez, Pi~na, Kyle A Gervers, Jessica A Martin, Javier F Tabima, Daniel L Luoma, Joseph W Spatafora
• Papers Published – Conference Proceedings

  A TALE of how a segmented worm makes its nerve cord: Capitella teleta and cell fate specification
  INTEGRATIVE AND COMPARATIVE BIOLOGY

  2024

  Vol. 64
  Johnny Davila-Sandoval, Javier Tabima, Neva Meyer
• Article in Refereed Journal

  Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer

  Molecular Plant-Microbe Interactions
  2023

  Vol. 36

  Issue #1
  Brent A Kronmiller, Nicolas Feau, Danyu Shen, Javier F Tabima, Shahin S Ali, Andrew D Armitage, Felipe Arredondo, Bryan A Bailey, Stephanie R Bollmann, Angela Dale, others
• Article in Refereed Journal

  First report of Pyricularia oryzae causing gray leaf spot of perennial ryegrass (Lolium perenne L.) in Oregon

  Plant Health Progress
  2023

  Issue #ja
  Emily Braithwaite, Ruying Wang, Alexander Robert Kowalewski, Javier Tabima, Todd N Temple, Hannah M Rivedal
• Article in Refereed Journal

  First Report of Pyricularia oryzae Causing Gray Leaf Spot of Perennial Ryegrass (Lolium perenne) in Oregon

  Plant Health Progress
  2023

  Vol. 24

  Issue #3
  E Braithwaite, R Wang, A Kowalewski, J F Tabima, T N Temple, H M Rivedal
• Article in Refereed Journal

  The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing

  NAR Genomics and Bioinformatics
  2023

  Vol. 5

  Issue #2
  Robert A Drewell, Tayla C Cormier, Jacob L Steenwyk, James St Denis, Javier F Tabima, Jacqueline M Dresch, Denis A Larochelle
• Article in Refereed Journal

  Rapid new diagnostic LAMP (loop-mediated isothermal amplification) assays to distinguish among the four lineages of Phytophthora ramorum

  Plant Disease
  2023

  Vol. 107

  Issue #11
  Kelsey L Sondreli, Javier F Tabima, Jared M LeBoldus
• Article in Refereed Journal

  Exploring Gene Expression Patterns and Evolutionary Responses in Host-Parasite inteactions: Insights from the Schistocephalus solidus–Threespine stickleback System

  bioRxiv
  2023
  Anika M Wohlleben, Javier F Tabima, N’eva P Meyer, Natalie C Steinel
• Article in Refereed Journal

  Secreted effector proteins of poplar leaf spot and stem canker pathogen Sphaerulina musiva manipulate plant immunity and contribute to virulence in diverse ways

  Molecular Plant-Microbe Interactions
  2023

  Vol. 36

  Issue #12
  Yao Zhao, Xinyue Zheng, Javier F Tabima, Sheng Zhu, Kelsey L Sondreli, Hope Hundley, Diane Bauer, Kerrie Barry, Yaxin Zhang, Jeremy Schmutz, others
• Presentations

  Fungal species and populations in a genomic perspective

  University of Georgia Plant Pathology Seminar series

  University of Georgia
  April

  2023
  Sponsored by University of Georgia
  Javier F Tabima Restrepo
• Presentations

  Fungal and oomycete populations and the boundaries of species

  Seminar Series: University of Richmond

  University of Richmond, VA
  February

  2023
  Sponsored by University of Richmond, VA
  Javier F Tabima Restrepo
• Article in Refereed Journal

  Evolution and epidemiology of global populations of nursery-associated Agrobacterium

  Ecological genetics
  2022

  Vol. 20
  Alexandra Weisberg, II, Edward Davis, Javier Tabima, Melodie Putnam, Marilyn Miller, Michael Belcher, Niklaus Gr"unwald, Walt Ream, Erh-Min Lai, Chih-Horng Kuo, others
• Article in Refereed Journal

  Identity and pathogenicity of fungi associated with root, crown, and vascular symptoms related to winter squash yield decline

  Plant disease
  2022

  Vol. 106

  Issue #6
  Hannah M Rivedal, Javier F Tabima, Alexandra G Stone, Kenneth B Johnson
• Article in Refereed Journal

  Genetic diversity and aggressiveness of Fusarium virguliforme isolates across the midwestern United States

  Phytopathologytextregistered
  2022

  Vol. 112

  Issue #6
  Rodrigo A Olarte, Rebecca Hall, Javier F Tabima, Dean Malvick, Kathryn Bushley
• Article in Refereed Journal

  Tolypocladamide H and the proposed tolypocladamide NRPS in Tolypocladium species

  Journal of Natural Products
  2022

  Vol. 85

  Issue #5
  Richard M Tehan, Rheannon R Blount, Ryan L Goold, Daphne R Mattos, Nicolas R Spatafora, Javier F Tabima, Romina Gazis, Chengshu Wang, Jane E Ishmael, Joseph W Spatafora, others
• Article in Refereed Journal

  Genome Sequence of the Estuarine Synechococcus sp. Strain NB0720_010

  Microbiology Resource Announcements
  2022

  Vol. 11

  Issue #8
  Campbell A MacKenzie, Marcia F Marston, Javier F Tabima, Nathan A Ahlgren
• Article in Refereed Journal

  Tolypocladamide H and the Proposed Tolypocladamide NRPS in Tolypocladium Species

  Journal of Natural Products
  Richard M. Tehan, Rheannon R. Blount, Ryan L. Goold, Daphne R. Mattos, Nicolas R. Spatafora, Javier F. Tabima, Romina Gazis, Chengshu Wang, Jane E. Ishmael, Joseph W. Spatafora, Kerry L. McPhail
• Presentations

  Swedish University of Agricultural Sciences (SLU, Sveriges lantbruksuniversitet)

  Invited Seminar Series

  Murfreesboro, Tennessee
  February

  2022
  Sponsored by Middle Tennessee State University
  Javier F Tabima Restrepo
• Presentations

  Fungal and oomycete populations and the boundaries of species

  Seminar Series: Plant Pathology department

  Penn State University
  October

  2022
  Sponsored by Penn State University
  Javier F Tabima Restrepo
• Article in Refereed Journal

  Genome Sequence of Estuarine Synechococcus sp. NB0720_010

  Microbiology Resource Announcements
  2022
  Campbell McKenzie, Javier F Tabima Restrepo, Nathan A Ahlgren
• Article in Refereed Journal

  Molecular phylogenomics and population structure of Phytophthora pluvialis

  Phytopathology
  2021

  Vol. 111

  Issue #1
  Javier F Tabima, Lilah Gonen, Mireia G’omez-Gallego, Preeti Panda, Niklaus J Gr"unwald, Everett M Hansen, Rebecca McDougal, Jared M LeBoldus, Nari M Williams
• Article in Refereed Journal

  The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility

  BMC microbiology
  2021

  Vol. 21

  Issue #1
  Nathaly Benavides, Alejandro Alvarez, Mario L Arrieta-Ortiz, Luis Miguel Rodriguez-R, David Botero, Javier Felipe Tabima, Luisa Castiblanco, Cesar Trujillo, Silvia Restrepo, Adriana Bernal
• Article in Refereed Journal

  Identity and pathogenicity of fungi associated with root, crown and vascular symptoms related to winter squash yield decline

  Plant Disease
  2021

  Issue #ja
  Hannah M Rivedal, Javier Felipe Tabima, Alexandra G Stone, Ken Johnson
• Article in Refereed Journal

  Genetic diversity and aggressiveness of Fusarium virguliforme isolates across the Midwestern United States

  Phytopathology
  2021

  Issue #ja
  Rodrigo A Olarte, Rebecca Hall, Javier Tabima, Dean Malvick, Kathryn Bushley
• Article in Refereed Journal

  The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility

  BMC microbiology
  2021

  Vol. 21
  Benavides, Montenegro, B, Alejandro Alvarez, Mario L Arrieta-Ortiz, Luis Miguel Rodriguez-R, David Botero, Javier Felipe Tabima, Luisa Castiblanco, Cesar Trujillo, Silvia Restrepo, Adriana Bernal
• Article in Refereed Journal

  QTL analysis of adult plant resistance to stripe rust in a winter wheat recombinant inbred population

  Plants
  2021

  Vol. 10

  Issue #3
  Kali M Brandt, Xianming Chen, Javier F Tabima, Deven R See, Kelly J Vining, Robert S Zemetra
• Article in Refereed Journal

  Data from: Mitotic recombination and rapid genome evolution in the invasive forest pathogen Phytophthora ramorumm

  2021
  Angela L Dale, Nicolas Feau, Sydney E Everhart, Braham Dhillon, Barbara Wong, Julie Sheppard, Guillaume J Bilodeau, Avneet Brar, Javier F Tabima, Danyu Shen, others
• Article in Refereed Journal

  Spatial genetic structure of the insect-vectored conifer pathogen Leptographium wageneri suggests long distance gene flow among Douglas-fir plantations in western Oregon

  Frontiers in Forests and Global Change
  2021

  Vol. 4
  Patrick I Bennett, Javier F Tabima, Anna L Leon, John Browning, Michael J Wingfield, Jared M LeBoldus
• Article in Refereed Journal

  The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility

  2021
  David Botero, Javier Felipe Tabima, Luisa Castiblanco, Cesar Trujillo, Silvia Restrepo, Adriana Bernal
• Article in Refereed Journal

  QTL Analysis of Adult Plant Resistance to Stripe Rust in a Winter Wheat Recombinant Inbred Population

  Plants
  March

  2021

  Vol. 10

  Issue #3
  Kali M Brandt, Xianming Chen, Javier F Tabima Restrepo, Deven R See, Kelly J Vining, Robert S Zemetra
• Presentations

  The intricacies of the genome of a small, gut associated fungus: Basidiobolus (Basidiobolaceae, Zoopagomycota)

  Winter Bioinformatics School

  Bogota, Colombia
  November

  2021
  Sponsored by Universidad del Rosario
  Javier F Tabima Restrepo
• Presentations

  The intricacies of the genome of a small, gut associated fungus: Basidiobolus (Basidiobolaceae, Zoopagomycota)

  Invited Seminar Series

  Uppsala, Sweden
  November

  2021
  Sponsored by Swedish University of Agricultural Sciences (SLU, Sveriges lantbruksuniversitet)
  Javier F Tabima Restrepo
• Article in Refereed Journal

  Pathogenicity and phylogenetic relationships of fungi associated with root, crown and vascular symptoms related to winter squash yield decline

  Plant Disease
  Hannah M Rivedal, Alexandra G Stone, Javier F Tabima, Kenneth B Johnson
• Article in Refereed Journal

  “Spatial genetic structure of the insect-vectored conifer pathogen Leptographium wageneri suggests long distance gene flow among Douglas-fir plantations in western Oregon

  Frontiers in Forests and Global Change
  Spring

  2021
  Patrick Bennett, Javier F Tabima Restrepo, Anna Leon, John Browning, Michael John Wingfield, Jared Michael LeBoldus
• Article in Refereed Journal

  Unexpected conservation and global transmission of agrobacterial virulence plasmids

  Science
  2020

  Vol. 368

  Issue #6495
  Alexandra J Weisberg, Edward W Davis, Javier Tabima, Michael S Belcher, Marilyn Miller, Chih-Horng Kuo, Joyce E Loper, Niklaus J Gr\"unwald, Melodie L Putnam, Jeff H Chang
• Article in Refereed Journal

  Genome-wide increased copy number is associated with emergence of dominant clones of the Irish potato famine pathogen Phytophthora infestans

  MBio
  2020

  Vol. 11

  Issue #3
  Brian J Knaus, Javier F Tabima, Shankar K Shakya, Howard S Judelson, Niklaus J Gr\"unwald
• Article in Refereed Journal

  Molecular phylogenomics and population structure of Phytophthora pluvialis

  Phytopathology
  2020

  Issue #ja
  Javier Tabima, Lilah Gonen, Mireia G\’omez-Gallego, Preeti Panda, Niklaus J Gr\"unwald, Rebecca McDougal, Everett Hansen, Jared Leboldus, Nari M Williams
• Article in Refereed Journal

  Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving

  G3 (Bethesda, Md.), 10 (9)
  2020
  Javier F Tabima, Ian A Trautman, Ying Chang
• Article in Refereed Journal

  Short title: Amazonian Cordyceps of Orthopterida Entomopathogens of Amazonian stick insects and locusts are members of the Beauveria species complex (Cordyceps sensu stricto) Tatiana Sanjuan Laboratorio de Taxonom’ia y Ecolog’ia de Hongos, Universidad de Antioquia, calle 67 No. 53–

  Javier Tabima, Silvia Restrepo, Thomas Laessoe, Joseph W Spatafora, Ana Esperanza Franco-Molano
• Article in Refereed Journal

  From genomes to forest management–tackling invasive Phytophthora species in the era of genomics

  Canadian Journal of Plant Pathology
  2020

  Vol. 42

  Issue #1
  S Keri"o, H A Daniels, M G’omez-Gallego, J F Tabima, R R Lenz, K L Sondreli, NJ Gr"unwald, N Williams, R Mcdougal, J M LeBoldus
• Article in Refereed Journal

  Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva

  Molecular Plant-Microbe Interactions
  2020

  Vol. 33

  Issue #2
  J F Tabima, K L Sondreli, S Keri"o, N Feau, M L Sakalidis, R C Hamelin, J M LeBoldus
• Article in Refereed Journal

  Genomic investigation of the strawberry pathogen Phytophthora fragariae indicates pathogenicity is associated with transcriptional variation in three key races

  Frontiers in Microbiology
  2020

  Vol. 11
  Thomas M Adams, Andrew D Armitage, Maria K Sobczyk, Helen J Bates, Javier F Tabima, Brent A Kronmiller, Brett M Tyler, Niklaus J Gr"unwald, Jim M Dunwell, Charlotte F Nellist, others
• Article in Refereed Journal

  Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus

  G3
  2020
  Javier Felipe Tabima, Ian Trautman, Ying Chang, Yan Wang, Stephen Mondo, Asaf Salamov, Igor Grigoriev, Jason Stajich, Joseph Spatafora
• Article in Refereed Journal

  effectR: An expandable R package to predict candidate RxLR and CRN effectors in oomycetes using motif searches

  Molecular Plant-Microbe Interactions
  2019

  Vol. 32

  Issue #9
  Javier F Tabima, Niklaus J Gr"unwald
• Article in Refereed Journal

  Mitotic recombination and rapid genome evolution in the invasive forest pathogen Phytophthora ramorum

  MBio
  2019

  Vol. 10

  Issue #2
  Angela L Dale, Nicolas Feau, Sydney E Everhart, Braham Dhillon, Barbara Wong, Julie Sheppard, Guillaume J Bilodeau, Avneet Brar, Javier F Tabima, Danyu Shen, others
• Article in Refereed Journal

  Genome-wide increased copy number is associated with emergence of super-fit clones of the Irish potato famine pathogen Phytophthora infestans

  BioRxiv
  2019
  Brian J Knaus, Javier F Tabima, Shankar K Shakya, Howard S Judelson, Niklaus J Gr"unwald
• Article in Refereed Journal

  Designing a Socio-Cultural Approach for Teaching and Learning Computational Thinking

  Nordic Journal of Digital Literacy
  2019

  Vol. 15

  Issue #02
  Francisco Buitrago-Fl’orez, Giovanna Danies, Javier Tabima, Silvia Restrepo, Carola Hern’andez
• Other Scholarly or Creative Work

  Mitotic recombination and rapid genome evolution in the invasive forest pathogen Phytophthora ramorum. MBio 10: e02452-18

  A L Dale, N Feau, S E Everhart, B Dhillon, B Wong, J Sheppard, G J Bilodeau, A Brar, J F Tabima, D Shen, others
• Article in Refereed Journal

  Genetic diversity of Phytophthora pluvialis, a pathogen of conifers, in New Zealand and the west coast of the United States of America

  Plant Pathology
  2018

  Vol. 67

  Issue #5
  S Brar, J F Tabima, R L McDougal, P-Y Dupont, N Feau, R C Hamelin, P Panda, J M LeBoldus, NJ Gr"unwald, E M Hansen, others
• Article in Refereed Journal

  Phytophthora betacei, a new species within Phytophthora clade 1c causing late blight on Solanum betaceum in Colombia

  Persoonia: Molecular Phylogeny and Evolution of Fungi
  2018

  Vol. 41
  M F Mideros, D A Turissini, N Guayaz’an, H Ibarra-Avila, G Danies, M C’ardenas, K Myers, J Tabima, E M Goss, A Bernal, others
• Article in Refereed Journal

  Populations of Phytophthora rubi show little differentiation and high rates of migration among states in the Western United States

  Molecular Plant-Microbe Interactions
  2018

  Vol. 31

  Issue #6
  Javier F Tabima, Michael D Coffey, Inga A Zazada, Niklaus J Gr"unwald
• Article in Refereed Journal

  Evolution of the US biological select agent Rathayibacter toxicus

  MBio
  2018

  Vol. 9

  Issue #4
  Edward W Davis, Javier F Tabima, Alexandra J Weisberg, Lucas Dantas Lopes, Michele S Wiseman, Michael S Wiseman, Tal Pupko, Michael S Belcher, Aaron J Sechler, Matt A Tancos, others
• Papers Published – Conference Proceedings

  Copy number variation appears increased in clonal lineages over sexual lineages of Phytophthora infestans
  International Congress of Plant Pathology (ICPP) 2018: Plant Health in A Global Economy

  2018
  Brian J Knaus, Javier Tabima, Shankar Shakya, Howard S Judelson, Niklaus J Grunwald
• Article in Refereed Journal

  effectR: An expandable R package to predict candidate effectors

  BioRxiv
  2018
  Javier F Tabima, Niklaus J Gr"unwald
• Article in Refereed Journal

  Whole genome sequences of the raspberry and strawberry pathogens Phytophthora rubi and P. fragariae

  Molecular Plant-Microbe Interactions
  2017

  Vol. 30

  Issue #10
  Javier F Tabima, Brent A Kronmiller, Caroline M Press, Brett M Tyler, Inga A Zasada, Niklaus J Gr"unwald
• Papers Published – Conference Proceedings

  Population Genomics in R
  2017 APS Annual Meeting

  2017
  Niklaus Grunwald, Steve Klosterman, Brian J Knaus, Javier Tabima
• Article in Refereed Journal

  SNP-based differentiation of Phytophthora infestans clonal lineages using locked nucleic acid probes and high-resolution melt analysis

  Plant Disease
  2016

  Vol. 100

  Issue #7
  Zachariah R Hansen, Brian J Knaus, Javier F Tabima, Caroline M Press, Howard S Judelson, Niklaus J Gr"unwald, Christine D Smart
• Article in Refereed Journal

  Loop-mediated isothermal amplification for detection of the tomato and potato late blight pathogen, P hytophthora infestans

  Journal of Applied Microbiology
  2016

  Vol. 120

  Issue #4
  Z R Hansen, B J Knaus, J F Tabima, C M Press, H S Judelson, NJ Gr"unwald, Christine D Smart
• Article in Refereed Journal

  Evolutionary history of the group formerly known as protists using a phylogenomics approach

  Revista de la Academia Colombiana de Ciencias Exactas, F’isicas y Naturales
  2016

  Vol. 40

  Issue #154
  Silvia Restrepo, Juan Enciso, Javier Tabima, Diego Mauricio Ria~no-Pach’on
• Article in Refereed Journal

  Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria

  PeerJ
  2016

  Vol. 4
  II, Davis, Alexandra J Weisberg, Javier F Tabima, Niklaus J Grunwald, Jeff H Chang
• Article in Refereed Journal

  Microbe-ID: an open source toolbox for microbial genotyping and species identification

  PeerJ
  2016

  Vol. 4
  Javier F Tabima, Sydney E Everhart, Meredith M Larsen, Alexandra J Weisberg, Zhian N Kamvar, Matthew A Tancos, Christine D Smart, Jeff H Chang, Niklaus J Gr"unwald
• Article in Refereed Journal

  Genomic analyses of dominant US clonal lineages of Phytophthora infestans reveals a shared common ancestry for clonal lineages US11 and US18 and a lack of recently shared ancestry among all other US lineages

  Phytopathology
  2016

  Vol. 106

  Issue #11
  B J Knaus, J F Tabima, C E Davis, H S Judelson, NJ Gr"unwald
• Article in Refereed Journal

  A Covert Operation by a Plant Pathogen

  Cell host & microbe
  2016

  Vol. 20

  Issue #4
  Jeff H Chang, Javier F Tabima
• Article in Refereed Journal

  Ecological speciation within the Phytophthora genus

  bioRxiv
  2016
  Maria F Mideros, David A Turissini, Natalia Guayazan, Giovanna Danies, Martha Cardenas, Kevin Myers, Javier Tabima, Erica M Goss, Adriana Bernal, Luz E Lagos, others
• Papers Published – Conference Proceedings

  What is a clone? Rethinking the ancestry of US clonal lineages of Phytophthora infestans using whole genome sequences
  PHYTOPATHOLOGY

  2016

  Vol. 106

  Issue #12
  B Knaus, J Tabima, Z Kamvar, C Davis, H Judelson, N Grunwald
• Papers Published – Conference Proceedings

  Searching for genomic signatures of host jumping onto raspberry and strawberry in two Phytophthora sister taxa
  PHYTOPATHOLOGY

  2016

  Vol. 106

  Issue #12
  J Tabima, B Kronmiller, B Knaus, C Press, I Zasada, B Tyler, N Grunwald, D Shen
• Article in Refereed Journal

  Five new species of entomopathogenic fungi from the Amazon and evolution of neotropical Ophiocordyceps

  Fungal Biology
  2015

  Vol. 119

  Issue #10
  Tatiana I Sanjuan, Ana E Franco-Molano, Ryan M Kepler, Joseph W Spatafora, Javier Tabima, A’ida M Vasco-Palacios, Silvia Restrepo
• Chapters In Books

  
  Chapter: Application of genome studies of coffee rust

  Published by Springer, Cham

  2014
  Marco Cristancho, William Giraldo, David Botero, Javier Tabima, Diana Ortiz, Alejandro Peralta, ‘Alvaro Gait’an, Silvia Restrepo, Diego Ria~no
• Article in Refereed Journal

  Entomopathogens of Amazonian stick insects and locusts are members of the Beauveria species complex (Cordyceps sensu stricto)

  Mycologia
  2014

  Vol. 106

  Issue #2
  Tatiana Sanjuan, Javier Tabima, Silvia Restrepo, Thomas Laessoe, Joseph W Spatafora, Ana Esperanza Franco-Molano
• Article in Refereed Journal

  Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

  PeerJ
  2014

  Vol. 2
  Zhian N Kamvar, Javier F Tabima, Niklaus J Gr"unwald
• Article in Refereed Journal

  The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes

  Proceedings of the National Academy of Sciences
  2014

  Vol. 111

  Issue #24
  Erica M Goss, Javier F Tabima, David EL Cooke, Silvia Restrepo, William E Fry, Gregory A Forbes, Valerie J Fieland, Martha Cardenas, Niklaus J Gr"unwald
• Article in Refereed Journal

  Pathogenicity, fungicide resistance, and genetic variability of Phytophthora rubi isolates from raspberry (Rubus idaeus) in the western United States

  Plant Disease
  2014

  Vol. 98

  Issue #12
  Jane E Stewart, Duncan Kroese, Javier F Tabima, Meredith M Larsen, Valerie J Fieland, Caroline M Press, Inga A Zasada, Niklaus J Gr"unwald
• Article in Refereed Journal

  Speciation in fungal and oomycete plant pathogens

  Annual review of phytopathology
  2014

  Vol. 52
  Silvia Restrepo, Javier F Tabima, Maria F Mideros, Niklaus J Gr"unwald, Daniel R Matute
• Chapters In Books

  
  Chapter: Phytophthora ramorum

  Published by Springer, Berlin, Heidelberg

  2014
  Sydney E Everhart, Javier F Tabima, Niklaus J Gr"unwald
• Article in Refereed Journal

  Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales

  Frontiers in plant science
  2014

  Vol. 5
  Marco A Cristancho, David Octavio Botero-Rozo, William Giraldo, Javier Tabima, Diego Mauricio Ria~no-Pach’on, Carolina Escobar, Yomara Rozo, Luis F Rivera, Andr’es Dur’an, Silvia Restrepo, others
• Other Scholarly or Creative Work

  Polyphasic characterization of Colletotrichum sp. Isolates from tree tomato and mango crops in Cundinamarca and Tolima, Colombia

  Mendoza, Calder’on, others
• Papers Published – Conference Proceedings

  Identification of pathogenesis-related proteins in the coffee rust, Hemileia vastatrix.
  25th International Conference on Coffee Science, ASIC 2014, Armenia, Colombia, 8-13 September 2014

  2014
  M Cristancho, W Giraldo, J Tabima, D Botero, D Ria~no, S Restrepo, A Gait’an, others
• Article in Refereed Journal

  Poppr: an R package for genetic analysis of populations with clonal or partially clonal reproduction

  2014
  Zhian N Kamvar, Javier F Tabima, Niklaus J Gr"unwald
• Article in Refereed Journal

  Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction.

  PeerJ
  March

  2014
  Z N Kamvar, J F Tabima, NJ Gr"unwald
• Article in Refereed Journal

  Seborrheic dermatitis: predisposing factors and ITS2 secondary structure for Malassezia phylogenic analysis

  Medical Mycology
  2013

  Vol. 51

  Issue #8
  Yulien Amado, Anelvi Pati~no-Uzc’ategui, Maria C Garc’ia, Javier Tabima, Adriana Motta, Martha C’ardenas, Adriana Bernal, Silvia Restrepo, Adriana Celis
• Article in Refereed Journal

  Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. manihotis strain CIO151

  PloS one
  2013

  Vol. 8

  Issue #11
  Mario L Arrieta-Ortiz, Luis M Rodr’iguez-R, Alvaro L Perez-Quintero, Lucie Poulin, Ana C D’iaz, Nathalia Arias Rojas, Cesar Trujillo, Mariana Restrepo Benavides, Rebecca Bart, Jens Boch, others
• Article in Refereed Journal

  The poppr R package for genetic analysis of populations with mixed (clonal/sexual) reproduction

  Phytopathology
  2013

  Vol. 103

  Issue #6
  Zhian N Kamvar, J F Tabima, Niklaus J Gr"unwald
• Article in Refereed Journal

  Defining species boundaries in the genus Phytophthora: the case of Phytophthora andina A response to ‘Phytophthora andina sp. nov., a newly identified heterothallic pathogen of solanaceous hosts in the Andean highlands’(Oliva et al., 2010)

  Plant Pathology
  2012

  Vol. 61

  Issue #2
  M C’ardenas, J Tabima, W E Fry, NJ Gr"unwald, A Bernal, S Restrepo
• Article in Refereed Journal

  Phytophthora infestans population structure: A worldwide scale

  Acta Biol’ogica Colombiana
  2012

  Vol. 17

  Issue #2
  Martha Cardenas, Giovanna Danies, Javier Tabima, Adriana Bernal, Silvia Restrepo
• Papers Published – Conference Proceedings

  The dynamics of evolution in Phytopththora infestans as told by phylogeographical approaches
  PHYTOPATHOLOGY

  2012

  Vol. 102

  Issue #7
  J Tabima, M Mideros, A Bernal, P Jimenez, D Riano-Pachon, N Grunwald, S Restrepo
• Papers Published – Conference Proceedings

  Morphological characterization of Colletotrichum species isolated from mango and tree tomato in Cundinamarca and Tolima, Colombia
  Phytopathology

  2012

  Vol. 102

  Issue #7
  C Calder’on, M C’ardenas, S Restrepo, P Jim’enez
• Article in Refereed Journal

  Fusarium species associated to onychomycoses in Colombia.

  F1000Research
  2012

  Vol. 3
  Marcela Guevara, Angela Mu~noz, Yulien Amado, Laura Bocanegra, Leticia Sopo, Adriana Motta, Maria Garc’ia, Javier Tabima, Silvia Restrepo, Adriana Celis
• Article in Refereed Journal

  Phylogeography and molecular epidemiology of Papaya ringspot virus

  Virus research
  2011

  Vol. 159

  Issue #2
  XA Olarte Castillo, G Fermin, J Tabima, Y Rojas, P F Tennant, M Fuchs, R Sierra, A J Bernal, S Restrepo
• Article in Refereed Journal

  Virulence gene expression in Malassezia spp from individuals with seborrheic dermatitis

  Journal of investigative dermatology
  2011

  Vol. 131
  MfLipl Mg13326
• Article in Refereed Journal

  First report of Phytophthora infestans causing late blight on Solanum viarum in Colombia

  Plant Disease
  2011

  Vol. 95

  Issue #7
  ME C’ardenas, E Medina, J Tabima, A Vargas, C Lopera, A Bernal, S Restrepo
• Article in Refereed Journal

  Dissecting the function of the DNMT2-homolog (DNMA) in Dictyostelium discoideum

  Genetics
  Zaza Gelasvili, Denis A Larochelle, Jacqueline M. Dresch, Maddie Hincher, Javier F Tabima Restrepo, Robert Drewell

Awards and grants

• CAREER: Unraveling the Diversity, Evolution, and Origin of Novel Secondary Metabolism in Commensal Microscopic Filamentous Fungi.

  National Science Foundation

• Conference: Society Prioritizes Our Recruitment of Every Scholar (SPORES): A mentoring program with the goal of diversifying, advancing, and promoting future mycologists.

  National Science Foundation

• NOTICE OF SUBMISSION Application for the Faculty Development Grant Submitted by: Faculty Name: Faculty Rank and Department: Number of Years at Clark: Title of Project: Effective Dates: Total Funds Requested: From: To: Date Submitted: It is understood that there is no continuing University commitment beyond the termination date of this grant. Signatures: Applicant: Department Chair: Date: Date: Please submit your proposal and the signed submission form via email to FacultyDevelopmentFunds@clarku.edu Please use the filename format: yourlastnameFD2 .pdf. Clark Help Desk is available to help with bundling the form and proposal into a single pdf file. Population Genetics of the invasive European Fire ant within New England Faculty Development Fund proposal Dr. Kaitlyn Mathis, Assistant Professor, Biology Department, Dr. Javier Tabima, Assistant Professor, Biology Department Project overview and background Invasive ants can play a major role in ecosystems at multiple trophic levels leading to disruptions in local communities and major impacts to biodiversity [1-3]. Myrmica rubra is an invasive ant introduced to the US at the Arnold Arboretum (Boston, MA) in the early 1900’s and widely considered a pest species due to its painful sting, aggressive behavior, and high population densities where it is present [4]. Furthermore, presence of M. rubra in its invaded range can displace food resources for other arthropods and alter hemipteran and plant communities [5-7]. Thus, these invasive ants have been negatively associated with native ant and arboreal arthropod presence in the invasion range [8]. Although M. rubra is relatively widespread throughout its native range in Eurasia, from the Black sea to the Arctic Circle, the invaded range is much more patchy and narrow. M. rubra are currently found in northeastern North America (parts of Maine, Massachusetts, New Hampshire, New York, Rhode Island, and Vermont), and more recently (within the last 20 years) in parts of eastern Canada (including New Brunswick, Nova Scotia, Ontario, and Quebec) [9], as well as a small population in the pacific northwest (Washington) [10]. Movement of these ants from Eurasia to North America has been presumed to be through soils of trade-ship ballast or ornamental plant pots [4, 11]. However, it is currently unknown how the M. rubra range has expanded after invasion. In the native range, M. rubra disperses colonies via budding new nests from existing colonies or through nuptial flights where mated queens can reach new habitat patches [12, 13], yet previous work speculates that both budding events and nuptial flights occur relatively rarely in the invasive range because M. rubra colony sizes do not reach the size to suggest frequent budding events, and infestations often end abruptly when similar habitat is bisected by roads/streams [14]. This project proposes to compare the population genetics of colonies within the native and invasive ranges of M. rubra to better understand the origin of invasion for populations within the invasion range, how genetic diversity has changed after invasion, and how M. rubra has expanded within the invasion range. An understanding of these dynamics will allow us to better predict how the invasion range may change in the future, and thus where M. rubra may impact ecosystems. Objectives and research plan To examine the population genetics of the invasive ant, Myrmica rubra, throughout native and invasive ranges, our objectives are to determine whether (1) a single invasion event is responsible for the current US populations of M. rubra, (2) the native populations of M. rubra have more genetic diversity than the invaded populations, and (3) M. rubra moves through small or large-scale dispersal in its invaded range. To address these questions, we will collect 13 M. rubra ant colonies from 7 populations throughout their native and invasive ranges (at sites near Boston, Toronto, Quebec City, Montreal, Halifax, Seattle, and in Finland). Individuals from colonies within the northeastern US will be collected in the summer of 2024. Individuals from colonies in the pacific northwest have already been collected (Summer 2023), and individuals from colonies within Europe will be sent by our collaborator Dr. Heikki Helanterrä at the University of Oulu in Finland. Our sites were chosen to represent locations where the ant was first introduced, sites at the edges of its current range, and sites within the native range. To examine the population genetics of M. rubra, a single adult worker per colony will be subjected to genomic DNA high molecular weight (HMW) extraction with the goal of performing restriction amplification and digestion sequencing (RADSeq) [15] using Illumina short read sequencing (SRS). A total of 91 adults will be collected. The genomic sequencing for RADseq will be performed by Floragenex Inc. Approximately 60,000 – 100,000 loci and and 1000 – 3000+ SNPs are expected to be obtained for all 91 samples. The RADseq results will be processed using STACKS v.2.6.6 [16]. The results from STACKS will be used to test the hypothesis of multiple independent versus single invasion from Europe to the Americas, and to determine the major route of genetic connectivity of the MA samples with other colonies from the known range of the species. Faculty development As new faculty members our goals are twofold. We seek to establish a new project working in a local ecosystem and a new collaboration within the Biology Department at Clark. This project is a natural extension of and builds a collaborative bridge across our shared research interests in ecology. Kaitlyn Mathis has previously studied the ecology and evolution of invasive ant species including Myrmica rubra, and Javier Tabima has an extensive background examining the population genetics of a wide range of organisms. Funds from this research grant would give us the ability generate exploratory data that would allow us to ask a wide range of questions about the ecology and evolution of invasive species and assist in securing additional funding from external granting agencies. Previous Faculty development grant outcomes 2020 FDF: Kate Mathis was co-awarded a Faculty Development Grant with Dr. Nathan Ahlgren in to study how urbanization, host species, and caste impact acorn nesting ant gut microbiomes. Daley O’Keefe, a PhD student in the Mathis lab has also led a presentation at the Ecological Society of America conference in Portland, Oregon in summer of 2023. Anna Le is a master’s student that will be completing her thesis in the summer of 2024 which include results from this project. Two student co-authored manuscripts are also currently in the final stages before being submitted to scientific journals. 2023 FDF: The results of the FDF to Javier Tabima were used to successfully submit a NSF BRC-BIO grant on Dec 2023 which is still under review. In addition, the preliminary results from the 2024 FDF were used to obtain a Department of Energy/Joint Genome Institute Community Science Program Award. Two master’s student theses have resulted based on the results from this fund. The project is on the closing stages and the results are being written in a manuscript for publication at a scientific journal. 2022 Academic innovation fund: The results of the academic innovation fund obtained by Prof. Javier Tabima with Prof. Nathan Ahlgren and Prof. Philip Bergman have yielded the preliminary results for this proposal. One master’s student thesis is based on the results from this fund, that has led to the discovery of Basidiobolus in MA. The project is still ongoing as comparative assays of microbial communities across urban protected ecosystems are still being analyzed. 2022 FDF to Javier Tabima with Rob Drewell and Denis Larochelle: The results from this FDF have led to the publication of a manuscript of this project to Nucleic Acid, Genes and Genomes. Broader impacts for Clark and local communities This project will provide students the opportunity to participate in hands on, interdisciplinary research. Student’s researchers will learn field collection techniques, insect identification, molecular techniques, and data analysis. Shared lab meetings will expose Tabima’s and Mathis’ students to ideas beyond the primary topics studied in each individual lab. Students will also learn how to communicate their research findings in several ways. Our students will present at Clark Fest, at the Biology Department Student Symposium (Bumpus), and assist in the preparation of a manuscript of our findings for an academic journal. Budget This budget represents information from a recent quote by Floragenex to sequence 91 samples. While Prof. Tabima and Prof. Mathis have startup funds, this project would pilot a new research collaboration between these labs. RADseq: 91 Samples, PstI, Sp 2x150bp Service Quantity Unit Price Subtotal SBG / ddRAD Library Prep – 95 Plex 91 35.00 3185.00 Library QA/QC 1 125.00 125.00 Sequencing Management Fee 1 400.00 400.00 Illumina NovaSeq 6000 Sp 2x150bp 1 3200.00 3200.00 Data Management Fee 1 500.00 500.00 TOTAL 7410.00 References 1. Porter, S. D. & Savignano, D. A. Invasion of Polygyne Fire Ants Decimates Native Ants and Disrupts Arthropod Community. Ecology 71: 2095–2106 (1990). 2. O’Dowd, D. J., Green, P. T. & Lake, P. S. Invasional ‘meltdown’ on an oceanic island. Ecology Letters 6: 812–817 (2003). 3. Holway, D. A., Lach, L., Suarez, A. V., Tsutsui, N. D. & Case, T. J. The Causes and Consequences of Ant Invasions. Annu. Rev. Ecol. Syst. 33: 181–233 (2002). 4. Groden, E., Drummond, F. A., Garnas, J. & Franceour, A. Distribution of an Invasive Ant, Myrmica rubra (Hymenoptera: Formicidae), in Maine. ec 98: 1774–1784 (2005). 5. Garnas, J., Groden, E. & Drummond, F. A. Mechanisms of Competitive Displacement of Native Ant Fauna by Invading Myrmica rubra (Hymenoptera: Formicidae) Populations. environ entomol 43: 1496–1506 (2014). 6. McPhee, K., Garnas, J., Drummond, F. & Groden, E. Homopterans and an Invasive Red Ant, Myrmica rubra (L.), in Maine. Environ Entomol 41: 59–71 (2012). 7. Prior, K. M., Robinson, J. M., Meadley Dunphy, S. A. & Frederickson, M. E. Mutualism between co-introduced species facilitates invasion and alters plant community structure. Proc. R. Soc. B. 282: 20142846 (2015). 8. Naumann, K. & Higgins, R. J. The European fire ant (Hymenoptera: Formicidae) as an invasive species: impact on local ant species and other epigaeic arthropods. Can Entomol 147: 592–601 (2015). 9. Wetterer, J. K. & Radchenko, A. G. Worldwide spread of the ruby ant, Myrmica rubra (Hymenoptera: Formicidae). Myrmecological News 14: 87–96. 10. Warren, R. J. et al. Myrmica rubra microhabitat selection and putative ecological impact. Ecological Entomology 44: 239–248 (2019). 11. Hicks, B. J., Pilgrim, B. L. & Marshall, H. D. Origins and genetic composition of the European fire ant (Hymenoptera: Formicidae) in Newfoundland, Canada. Can Entomol 146: 457–464 (2014). 12. Elmes, G. W. & Petal, J. Queen Number as an Adaptable Trait: Evidence from Wild Populations of Two Red Ant Species (Genus myrmica). The Journal of Animal Ecology 59: 675 (1990). 13. Boomsma, J. J. & Leusink, A. Weather conditions during nuptial flights of four European ant species. Oecologia 50: 236–241 (1981). 14. Chen, W. & Adams, E. S. The Distribution and Habitat Affinities of the Invasive Ant Myrmica rubra (Hymenoptera: Formicidae) in Southern New England. Environmental Entomology 47: 527–534 (2018). 15. Davey, J. W. & Blaxter, M. L. RADSeq: next-generation population genetics. Briefings in Functional Genomics 9: 416–423 (2010). 16. Rochette, N. C., Rivera‐Colón, A. G. & Catchen, J. M. Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics. Molecular Ecology 28: 4737–4754 (2019). Kaitlyn Mathis, PhD Assistant Professor of Ecology Department of Biology, Clark University 234 Lasry Center for Bioscience Worcester, MA 01610 508-793-7514, kmathis@clarku.edu Website: katemathis.org EDUCATION Ph.D. Environmental Science, Policy and Management, University of California- Berkeley Advisor: Dr. Neil Tsutsui // Thesis: Behavioral and chemical ecology of ants (Hymenoptera, Formicidae) and their natural enemies in dynamic coffee agroecosystems. B.A. Insect Ecology and Biochemistry, Hampshire College 2015 2008 PROFESSIONAL EXPERIENCE Assistant Professor, Department of Biology, Clark University 2018-present NIH Postdoctoral Excellence in Research and Teaching (PERT) Fellow 2015-2018 Department of Ecology and Evolutionary Biology, University of Arizona. Collaboration with Judith Bronstein Ph.D. Candidate: Under Dr. Neil Tsutsui, Dept. of ESPM, UC Berkeley, Berkeley, CA Synthetic Chemist: Under Dr. Thomas Horn, Kalinex Inc., User of Lawrence Berkeley National Lab, Berkeley, CA Undergraduate Researcher: Under Dr. Stacy Philpott, Environmental Studies Department, UC Santa Cruz, Santa Cruz, CA 2009-2015 2008-2009 2007-2008 Undergraduate Researcher: Under Dr. Brian Schultz, Department of Natural Science, Hampshire College, Amherst, MA 2007 Mosquito Control Biological Aide: 2006 Delaware Department of Natural Resources and Environmental Control, Milford, DE TEACHING Philosophy Whether mentoring an individual student or teaching in a lecture hall filled to the brim, my teaching objectives are similar. I aim to cultivate excitement and passion for the sciences while also making concepts understandable and applicable. My goals as an educator are to (1) bring wonder and enthusiasm for the material to the classroom, (2) use inquiry-based active learning to promote critical thinking, and (3) focus on the fundamentals while providing real world context to the information I impart. Courses Taught BIOL 106: Intro to Biostatistics, Clark University Course director and instructor for lecture and lab based undergraduate course. The course is an introduction to mathematical and statistical methods that are most useful to biologists. S23: 37 students; S21: 36 students; S20: 36 students; F18: 24 students BIOL 216/316: Ecology, Clark University Course director and instructor for lecture and lab based undergraduate and graduate course. Course overviews ecology as a discipline with emphasis on explaining and predicting the distribution and abundance of organisms, how ecological communities are composed and why they vary in time and space. BIOL 216 BIOL 316 F22: 21 students; F21: 18 students; F20: 27 students; F19: 32 students; S19: 29 students F22: 5 students; F21: 6 students F20: 4 students; F19: 3 students; S19: 2 students BIOL 276/376: Biology of Social Insects, Clark University Course director and instructor for mixed format lecture, lab, and discussion undergraduate and graduate course. Course focuses on ecology, evolution and behavior of social insects. BIOL 276 S23: 19 students; S21: 18 students BIOL 376 S23: 2 students; S21: 2 students BIOL 266/366: Chemical Ecology, Clark University Course director and instructor for mixed format lecture, lab, and discussion undergraduate and graduate course. Course focuses on the role of chemical compounds in mediating interactions between organisms. BIOL 266 S20: 14 students BIOL 366 S20: 2 students BIOL 293: Peer Learning Assistant, Clark University Oversee undergraduate students serving as peer learning assistant to BIOL 106: Intro Biostatistics course. S23: 1 student; S20: 1 student BIOL 299/399: Directed Research, Clark University Oversee independent research projects by undergraduates (299) or graduate (399) students. This includes weekly lab meetings to give project updates, discuss research and primary research articles relevant to their projects. BIOL 299 S22: 4 students; F21: 2 students; S21: 3 students; F20: 5 students; S20: 2 students; F19: 6 students; S19: 5 students; F18: 2 students BIOL 399 S22: 1 student; S20: 1 student; F19: 1 student; S19: 1 student BIOL 317: Graduate Research, Clark University Oversee independent research by graduate level students. This includes weekly lab meetings to give project updates, discuss research and primary research articles relevant to their projects. S23: 5 students; S22: 5 students; F22: 5 students; S21: 4 students; F21: 5 students; S20: 2 students; F20: 4 students; S19: 1 student. Summer undergraduate research internships, Clark University Oversee and mentor student research projects. This includes weekly meetings with the students to check in on progress, and teaching the students field and lab techniques. Summer 23: 4 students; Summer 22: 2 students; Summer 21: 2 students; Summer 20: 3 students; Summer 19: 4 students EIS 544: Insect Ecology, University of Arizona Course co-director and instructor for seminar based graduate course. The course overviewed species interactions between insects. F17: 16 graduate students BIO 105: Environmental Biology, Pima Community College. Course director and instructor for a lecture and lab based undergraduate course. This course overviews the fundamentals of ecology and their relevance to human impact on natural ecosystems. Includes ecosystem structure and function, population dynamics, and human impacts on air, water, land, and biodiversity. F16: 28 undergraduate students Graduate Student Instructor Natural History of Insects (ESPM 42). University of California Berkeley. Fall 2014 Introduction to Culture and Natural Resource Management (ESPM 50). University of California, Berkeley. Fall 2010 Guest Lecturer Introduction to Biology (BIOL 102). Clark University, Worcester. Spring 2023 Natural Resource Ecology (RNR 316). University of Arizona, Tucson. Spring 2017 Environmental Biology (Bio 105). Pima Community College, Tucson. Fall 2015 Insect Ecology (ENVS 131). University of California, Santa Cruz Fall 2013, Fall 2014 Basic Animal Behavior Theory (CS 216). Hampshire College. Spring 2008 General Introduction to Ecology (NS 207). Hampshire College. Spring 2008 Other Instructor. Gas Chromatography/Mass Spectrometry Workshop. University of California, Berkeley. Spring 2015 Syllabus Designer. Insect Behavior Lab Section (ESPM 142). University of California, Berkeley. Fall 2011 Publications Corresponding Author *, Undergraduate Students U , Master’s student authors † , Ph.D student authors ‡ Dinell, H., K. Mathis, J. Bronstein (in review) “Biosphere 2 Reexamined: Species Composition Within a Human-Constructed Ecosystem” Southwestern Naturalist. Stevens, D. ‡* , K. Mathis, N. Meyer (in review) “The importance of considering the plastic expression of phenotypes when determining evolutionary relationships” Bioessays. Harris, B. † , D. Stevens ‡ , K. Mathis* (Accepted) “The effect of urbanization and temperature on thermal tolerance, foraging performance, and competition in cavity dwelling ants” Ecology & Evolution. Sankovitz M., M. Rivera, T. Manjarress, K. Mathis (2024) “The role of ant-mediated biological interactions in agroecosystems” Annals of the Entomological Society of America. Saee02. Curry, A. † , D. Stevens ‡ , J. Nelsen‡ , K. Mathis* (2023) “The effects of land use change on ant communities in New England” Insect Conservation & Biodiversity 1-7. Stevens, D. ‡*, M. Graham, C. BardjisU , S. Foster, J. Baker, K. Mathis (2023) “Evolution of chemical-cue-mediated antipredator behavior in threespine stickleback populations experiencing northern pike predation” Biological Invasions 25: 1561-1577. Stevens, D. ‡*, M. Wund, K. Mathis (2023) “Integrating environmental complexity and the plasticity first hypothesis to study responses to human-altered habitats” Animal Behavior 200: 273:284. Anastasio, O. † , K. Mathis*, M. Rivera (2021) “Impacts of invasive ant-hemipteran interactions, edge effects, and habitat complexities on the spatial distribution of ants” Agriculture, Ecosystems & Environment. 310: 107299. Mathis, K.* , J. Bronstein (2020) “Our current understanding of commensalism.” Annual Review of Ecology, Evolution and Systematics 51:167-89. Vandermeer, J.* , I. Armbrecht, A. de la Mora, K. Ennis, G. Fitch, D. Gonthier, Z. Hajian- Forooshani, H. Hsieh, A. Iverson, D. Jackson, S. Jha, E. Jiménez-Soto, G. Lopez- Bautista, A. Larsen, K. Li, H. Liere, A. MacDonald, L. Marin, K. Mathis, I. Monagan, J. R Morris, T. Ong, G. Pardee, I. Rivera-Salinas, C. Vaiyda, K. Williams-Guillen, S. Yitbarek, S. Uno, A. Zemenick, S. Philpott, I. Perfecto (2019) “The community ecology of herbivore regulation in an agroecosystem: lessons from complex systems” Bioscience 69:974-996. Mathis, K. * , N. Tsutsui (2016) “Dead Ant Walking: A beetle predator benefits ants by preferentially consuming parasitized individuals.” Proceedings of the Royal Society: B. 238: 20161281. Mathis, K. * , S. Ramirez, S. Philpott (2016) “Variation in spatial scale of competing polydomous twig-nesting ants in coffee agroecosystems. ” Insectes Sociaux 63: 447- 456. Mathis, K. * , N. Tsutsui. (2016) “Cuticular hydrocarbon cues are used for host acceptance by Pseudacteon spp. phorid flies that attack Azteca sericeasur ants.” Journal of Chemical Ecology 42: 286-293. Mathis, K.* , K. Eldredge (2014) “Descriptions of two new species of Myrmedonota Cameron (Staphylinidae: Aleocharinae) from Mexico with comments on the genus taxonomy and behavior.” Zootaxa 3768(1): 095-100. Mathis, K.* , S. Philpott (2012) “Current Understanding and Future Prospects of Host Selection, Acceptance, Discrimination and Regulation of Phorid Fly Parasitoids that attack Ants” Psyche. 2012: 1-9. Smith, C.*, E. Abouheif, R. Benton, E. Cash, V. Croset, C. Currie, E. Elhaik, C. Elsik, M. J. Favé, V. Fernandes, J. Gadau, J. Gibson, D. Graur, K. Grubbs, D Hagen, M. Helmkampf, J. A. Holley, C. Holt, H. Hu, A. S. I. Viniegra, B. Johnson, R. Johnson, A. Khila, J. Kim, J. Laird, K. Mathis, J. Moeller, M. Munoz-Torres, M. Murphy, R. Nakamura, S. Nigam, R. Overson, J. Placek, R. Rajakumar, J. Reese, H. Robertson, C. Smith, A. Suarez, G. Suen, E. Suhr, S. Tao, C. Torres, E. van Wilgenburg, L. Viljakainen, K. Walden, A. Wild, M. Yandell, J. Yorke, A. Zimin, N. Tsutsui. (2011) “The Draft Genome of the Globally Widespread and Invasive Argentine ant (Linepithema humile)” Proceedings of the National Academy of Sciences of the United States of America. 108: 5673-5678. Smith, C.*, C. Smith, H. Robertson, M. Helmkampf, A. Zimin, M. Yandell, C. Holt, H. Hu, E. Abouheif, R. Benton, E. Cash, V. Croset, C. Currie, E. Elhaik, C. Elsik, M. J. Favé, V. Fernandes, J. Gibson, D. Graur, W. Gronenberg, K. Grubbs, D. Hagen, A. S. I. Viniegra, B. Johnson, R. Johnson, A. Khila, J. Kim, K. Mathis, M. Muñoz-Torres, M. Murphy, J. Mustard, R. Nakamura, O. Niehuis, S. Nigam, R. Overson, J. Placek, R. Rajakumar, J. Reese, G. Suen, S. Tao, C. Torres, N. Tsutsui, L. Viljakainen, F. Wolschin, J. Gadau. (2011) “A draft genome of the red harvester ant Pogonomyrmex barbatus” Proceedings of the National Academy of Sciences of the United States of America. 108: 5667-5672. Mathis, K.* , S. Philpott, R. Moreira. (2011) “Parasite lost: Chemical and visual cues used by Pseudacteon in search of Azteca instabilis” Journal of Insect Behavior. 24: 186-199. Presentations at Professional Meetings Mathis K., B. Harris†, D. Stevens‡. The effect of urbanization on thermal tolerance, foraging performance, and competition in cavity-dwelling ants. Ecological Society of America Conference, Portland, OR, 2023 Nelsen, J. ‡, A. Curry†, D. Stevens‡ , K. Mathis. Comparing ant communities across rural-urban landscapes in Massachusetts. Ecological Society of America Conference, Portland, OR, 2023 O’Keefe, D. ‡, K. Pela U, K. Crowley†, N. Ahlgren, K. Mathis Sympatric North American acorn- nesting ant species possess distinct gut-microbiomes. Ecological Society of America Conference, Portland, OR, 2023 Mathis K., B. Harris † , D. Stevens ‡ . The effect of urbanization on thermal tolerance, foraging performance, and competition in acorn nesting ants. Entomological Society of America Eastern Branch Meeting, Providence, RI, 2023 Nelsen, J. ‡ , A. Curry † , D. Stevens ‡ , K. Mathis. The effects of urban land use change on ant communities in New England. Entomological Society of America Eastern Branch Meeting, Providence, RI, 2023. Stevens D. ‡ , M. Wund, K. Mathis. Assessing the role of phenotypic plasticity in the evolutionary responses to human disturbance. The 58th Annual Conference of the Animal Behavior Society, Virtual Meeting. Invited presentation. 2021. Stevens D. ‡ , M. Wund, K. Mathis. Differences between threespine stickleback populations hides any signs of adaptation in response to an invasive predator, northern pike. The Annual Meeting of the Ecological Society of America, Virtual Meeting, 2021. Manjarress T., M. Rivera, K. Mathis. The ecology of ants in agroecosystems. Entomological Society of America. Online, 2021. Bronstein J., K. Mathis. Ecology and Evolution of commensalism. American Society of Naturalists Meeting, Asilomar, CA, 2020. Mathis K. The role of ant seed dispersers and predators in woody plant encroachment of arid grasslands. Entomological Society of America, St. Louis, MO, 2019. Mathis K. Dominant ground foraging ants impact ant-plant protection mutualisms in peach orchards. Entomological Society of America, Denver, CO, 2017. Mathis K., S. Ramirez, S. Philpott. Variation in spatial scale of competing polydomous twig-nesting ants in coffee agroecosystems. International Congress of Entomology, Orlando, FL, 2016. Mathis K., N. Tsutsui. Dead ant walking: A beetle predator uses parasitoid host location cues to selectively prey on parasitized ants. American Society of Naturalists Meeting, Asilomar, CA. 2016. Mathis K., N. Tsutsui. Defensive Strategies of Azteca Ants against Phorid Fly Parasitism International Union for the Study of Social Insects Conference, Cairns, QLD, Australia. 2014. Mathis K., N. Tsutsui. Phorid fly parasitoid host preference in Azteca ants in coffee agroecosystems. Ecological Society of America, Sacramento, CA. 2014. Mathis K., N Tsutsui. Predators for the Greater Good: The role of an ant associated beetle in Azteca ant-phorid fly interactions. Entomological Society of America Conference, Austin, TX. 2013. Mathis K. The Rules of Attraction: Host Location and Acceptance of the ant, Azteca instabilis, by their Phorid Fly Parasitoids. XX Simposio de Mirmecologia, Petropolis, Brazil. 2011. INVITED TALKS Mathis, K. Small but mighty: ant-plant interactions in human-managed ecosystems. Ware River Nature Club. Rutland, MA. 2023 Mathis, K. Small but mighty: ant-plant interactions in human-managed ecosystems. Keynote for Tri Beta Induction Ceremony. The College of New Jersey. Trenton, NJ. 2023 Mathis, K. Ants-plant interactions in Citrus and Peach. Festscrift: Symposium in honor of Ivette Perfecto. University of Michigan, Ann Arbor, MI, 2023. Mathis, K. Ecological complexity and ant-plant interactions in human-managed ecosystems. College of the Holy Cross, Worcester, MA. 2022. Mathis, K. Ecological complexity and ant-plant protection mutualisms in agroecosystems. Amherst College Biology Department Seminar, Amherst, MA. 2019. Mathis, K. Chemical and community ecology of ant interactions in agroecosystems. Clark University Chemistry Department Seminar, Worcester, MA, 2018. Mathis, K. Ecological Complexity and ant-plant protection mutualisms in agroecosystems. Clark University Biology Department Seminar, Worcester, MA, 2018. Mathis, K. Ant-plant protection mutualisms in complex agroecosystems. University of Maryland EEB Department Seminar, College Park, MD, 2017. Mathis, K. Insect plant interactions in agroecosystems. McDaniel College Biology Department Seminar, Westminster, MD, 2017. Mathis, K. Azteca ants and natural enemies in coffee agroecosystems. Entomology Department Seminar, University of Arizona, Tucson, AZ. 2015. Grants and Fellowships 2023 Clark Grant Incentive Award Unfunded 2022 Northeast Sustainable Agriculture Research & Education (SARE) Grant Unfunded 2021 Northeast Sustainable Agriculture Research & Education (SARE) Grant 2020 Faculty Development Fund Award ($6123) 2018-2019 AAUW American Postdoctoral Fellowship, Declined. 2015-2018 NIH Postdoctoral Excellence in Research and Teaching Fellowship, University of Arizona Center for Insect Science ($147,000) 2014 2011-2014 2014 2014 2010-2014 2011-2013 2013 2012 2012 ESPM Continuing Graduate Student Fellowship, UC Berkeley ($9,162) Graduate Research Fellowship, National Science Foundation ($94,000) ESPM Travel Grant, UC Berkeley ($2,000) Travel Grant, International Union for the Study of Social Insects ($2,500) Margaret C. Walker Fund Grant, UC Berkeley ($1,000 per year) UC Mexus Dissertation Research Grant, University of California ($11,852) Julius H. Freitag Memorial Award, UC Berkeley ($1,000) Van den Bosch Research Award, UC Berkeley ($10,000) Robert L. Usinger Memorial Award, UC Berkeley ($1,000) 2011 2010, 2011 2010 2007 2004-2008 Student Awards Edna and Yoshinori “Joe” Tanada Fellowship, UC Berkeley ($1,000) ESPM Summer Grant, UC Berkeley ($3,000 per year) ESPM Travel Grant, UC Berkeley ($1,000) Ray Coppinger Research Grant, Hampshire College ($2,000) Science Scholarship, Hampshire College ($4,000 per year) 2023 2023 2023 2022 2022 2021 2021 2021 2020 2020 2019 2019 2019 Elise Beier: Weiller Fellowship ($4000) Gwen Grabarek: Penn Fellowship ($4000) Fengying Guo: SURE Fellowship ($3500) Anna Le: LEEP Award and SURE Fellowship ($3500) Christina Martin: Hastings Fellowship ($3500) Amelia Curry: Lyerla Fellowship, Clark ($3500) Brooke Harris: Hastings Fellowship, Clark ($3500) Josh Canning: SURP Fellowship, Clark ($3000) Emily Maynard: LEEP Award, Clark ($2500) Bailey Ross: Steinbrecher Fellowship, Clark ($3000) Hannah Cooper: LEEP Award, Clark ($2500) Brooke Harris: SURE Fellowship, Clark ($2500) Josh Canning: SURE Fellowship, Clark ($2500) Miscellaneous Awards 2021 2020 Outstanding graduate mentoring/advising award, Clark University Nominated for Outstanding undergraduate teacher of the year award, Clark University Community and University Service University Service: Herban Gardeners Club Advisor, Clark University 2023-present Chief HR Officer Search Committee, Clark University 2023 New Science Facility Strategic Planning Committee, Clark University 2022-2023 College Board Member, Clark University, 2019-2021 Departmental Service: Department Seminar Series Coordinator, 2020-present Graduate Studies Committee Member, 2020-2021, 2022-present Evolutionary Biology Faculty Search Committee Member, 2020 Development of Diversity, Equity and Inclusion Advocate Positions, 2020 Development of Student DEI Advisory Council, 2020 Communications Committee Member, 2018-2020 Litsky Chair Committee Member, 2020 Visiting Lecturer Search Committee Member, 2019 Society Service and Memberships: Ecological Society of America (ESA) International Union for the Study of Social Insects (IUSSI) Entomological Society of America (ESA) American Society of Naturalists (ASN) Ad hoc Review of Manuscripts: Ecology & Evolution (2024), Sociobiology (2023), Journal of Chemical Ecology (2023), Agricultural and Forest Entomology (2022), Naturwissenschaften (2021), Journal of Insect Behavior (2020, 2021), Chemoecology (2020), Insectes Sociaux (2018, 2019, 2020); Basic and Applied Ecology (2019, 2020), Biology Letters (2019), Environmental Entomology (2018), Bulletin of Entomological Research (2018); Frontiers in Zoology (2017); PeerJ (2017); Biotropica (2016); Apidologie (2016); Ecology and Evolution (2016); Biological Invasions (2014); Ecology (2014); Biological Control (2014); Journal of Insect Science (2013) Journal Section Editor: Sociobiology (2023) Panel Services & Selection Committees: LEEP Fellowship Panelist, Clark University, Spring 2021 and Spring 2022 Heller Agroecology Research Grant Judge, University of California, Santa Cruz, 2014-2020 Poster Judge, Graduate Student Multidisciplinary Conference, Clark University Spring 2019 Postdoctoral Representative, PERT Advisory Board, 2017-2018 Center for Insect Science Travel Grant Judge, University of Arizona, 2015 ESPM 201C Starter Grant Panel, University of California, Berkeley, 2012 Outreach Participated in Academic Fair for Clarktoberfest Admissions Outreach. 2023 Participated in Davis Maine Scholars Event. 2022, 2023 Participated in Destination Clark Event. 2022 Participated in Faculty Interviews for Admissions Outreach. 2020 Participated in STEM panel for Clarktoberfest Admissions Outreach. 2020 Participated in Research and Study Abroad Webinar for Clark Admissions Outreach. 2020 Participated in filmed interviews with my lab on local research for Clark Admissions Outreach https://clarknow.clarku.edu/2019/11/07/clark-students-get-their-hands- dirty-with-ant-research/. 2019 Organized two Reddit AMAs for Biology Department Admissions Outreach. 2019 https://www.reddit.com/r/ClarkU/comments/avsegy/we_are_biology_f aculty_at_clark_university_ask_us/ “From Garden Peonies to a Career Studying Ant-Plant Interactions” Entomology Today https://entomologytoday.org/2018/05/31/kate-mathis-standout-early- career-professional-garden-peonies-career-studying-ant-plant- interactions/ . 2018. Volunteer: Arizona Insect Festival. 2015-2017 Media Interview. Forschung aktuell: German National Public Radio, August 16, 2016 “Parasitic flies, zombified ants, predator beetles – insect drama on Mexican coffee plantations. The Conversation. https://theconversation.com/parasitic- flies-zombified-ants-predator-beetles-insect-drama-on-mexican-coffee- plantations-63692 . 2016 Volunteer: Cal Day, Entomological Student Organization. 2012-2014 Guest Presentations on Insects: 2nd Grade Class, Malcolm X Elementary School, Oakland, CA. 2013 Artist in Residence: Entomological Student Organization. 2011-2014. Career Development and Pedagogical Training Participant. Write winning grant proposals NSF Focus Workshop. Clark University (January 11-13th). 2023 Participant. Teaching in Different Modalities Course. Clark University (July 6-August 16th). 2020 Participant. Professional Grant Development Workshop. Grant Training Center, Online (May 28-29th) 2020 Panelist. Young Professionals Lunch and Learn. Entomological Society of America Conference. St Louis, Missouri. 2019 Participant. Process Oriented Guided Inquiry Learning Pedagogy Workshop. Tucson, Arizona (Oct2-3rd). 2017 Participant. Institutional research and academic career development award (IRACDA) Conference. Birmingham, Alabama. (June 4-6th). 2017 Organizer. Institutional research and academic career development award (IRACDA) Conference. Tucson, Arizona. (June 12-14th). 2016 Participant. Active Learning Pedagogy Workshop (February 25-26th) 2016 Participant. Institutional research and academic career development award (IRACDA) Conference. San Diego, California. (June 14-16th). 2015 Student Mentoring Clark University 14 undergraduate research projects: Elise Beier (2022-present), Fengying Guo (2022-present), Gwen Grabarek (2022-2023), Anna Le (2021-2023), Christina Martin (2021-2022), Emily Maynard (2019-2021), Joshua Canning (2019-2021), Brooke Harris (2019-2020), Amelia Curry (2018-2020), Bailey Ross (2019-2020), Hannah Cooper (2019-2020), Katerina Pela (2019-2020), Daniel Cohn (2019), Kelsey Perry (2018-2019) Three Ph.D. students: Joe Nelsen (2021-present), Daley O’Keefe (2021-present), Dale Stevens (2018-2022). Seven Master’s students: Anna Le (2023-present), Josh Canning (2021-2023), Christina Martin (2021-2023), Amelia Curry (2020-2022), Brooke Harris (2020-2022), Christina Kopacz (2020- 2021), Olivia Anastasio (2018-2020). Five PhD thesis committees in Biology: Samia Riaz (2023-present), Prasanth Prabhu (2019- present), Liam Cleary (2022-present), Anika Wollenburg (2020-2022), Amy Cheu (2019-2023). Twelve Master’s thesis committees in Biology and Chemistry: Jasper Carlton (2023-present), Emma McClellan (2023-present), Sarah Wheeler (2023-present), Maddie Hincher (2022-2023), Katie Crowley (2021-2022), Isabel Tonelli (2020-2021), Christina Barjis (2019-2020), Jivanna Mason (2019-2020), Linnea Menin (2019-2021), Young Sun Lee (2019-2020), Samantha Reed (2019-2020), Wynn Haimer (2018-2019). University of Arizona 9 undergraduate research projects: Heather Ellison (2015-2018), Nicolette Potts (2017-2018), Kalen Krause (2017), Abby Wang (2017), Karen Wang (2016-2017), John Bosak (2016), Sarah Evans (2016), Niels Schmidt-Crans (2016), Nicolas Alexandre (2015). One Tucson Highschool Student project: Kristina Marikos (2017). One Ecology and Evolutionary Biology Master’s thesis committee: Hannah Dinell (2017-2019). University of California – Berkeley 7 undergraduate research projects: Leila Ramanculova (2014-2015), Hiromi Murata (2013- 2015), Savannah Carnes (2013-2015), Blake Caracci (2013-2015), Shelley Pneh (2013-2014), Kimberley Chen (2012), Nicholas Sykora (2012). Javier Felipe Tabima R., Ph.D. Assistant Professor Department of Biology, Clark University. 15 Maywood Street, Worcester, MA 01610 jtabima@clarku.edu, (541)740-3768 Education: 2018 2010 2008 Research Interests Ph.D. Botany and Plant Pathology. Oregon State University. Corvallis, OR. M.Sc. Biological Sciences. Universidad de los Andes. Bogotá, Colombia. B.Sc. Biology. Universidad de los Andes. Bogotá, Colombia. Evolutionary Genomics Genomics, Bioinformatics, and Molecular Biology Phylogenetics and Population genomics Fungal Biology Development of tools for genomics in R, BASH and PERL (github.com/Tabima) Research Experience: Department of Biology, Clark University. Assistant Professor. Evolution, genomics, and population genomics of fungal species: Biology, diversity and genomics of the genus Basidiobolus Department of Botany and Plant Pathology, Oregon State University. Postdoctoral scholar. Evolution, genomics, and population genomics of fungal species: Identification and evolution of secondary metabolites in Zygomycota Two-year appointment: 2018-2020 Postdoctoral mentor: Joseph Spatafora, Ph.D Department of Botany and Plant Pathology, Oregon State University. Postdoctoral scholar. Genomics of Septoria musiva: Using genomics tools for the identification of population genetics, expression profiles and GWAS in plant-patogen interactions. Two-year appointment: 2018-2020 Postdoctoral mentor: Jared LeBoldus, Ph.D. Department of Botany and Plant Pathology, Oregon State University. Doctoral dissertation: Comparative genomics and population genomics of Phytophthora rubi and P. fragariae. 2013 – 2017. USDA-HCRL, Corvallis, OR. Research assistantship: Host speciation of sister Phytophthora species using genomics, population genetics and phylogenetics. 2012 – 2013. Laboratory of Mycology and Phytopathology (LAMFU), Universidad de los Andes, Bogotá, Colombia. Research assistant in molecular evolution of fungi, bacteria and oomycetes. Phylogenetics and population genetics of plant and human pathogens (Cordyceps spp., Malassezia spp., Colletothricum spp., Phytophthora spp.). 2010 – 2013. Biological Computing and Evolution group, Universidad de los Andes, Bogotá, Colombia. Research assistant in the development of pipelines computational biology and genomics: Applications of high-throughput computing in the biological sciences. 2010 – 2013 Universidad de los Andes. Masters Thesis: Adaptive radiation in Eastern Pacific sea fans. Reticulate evolution and hybridization in corals of the genus Pacifigorgia. 2008-2010 Professional Experience: Reviewer. G3. Genetics Society of America. 2021 – Today Reviewer. Plant Health. American Phytopathological Society. 2020 – Today Reviewer. MPMI. American Phytopathological Society. 2020 – Today Reviewer. PeerJ. 2019 – Today Reviewer. Diversity. MDPI. 2019 – Today Reviewer. Annals of Applied Biology. Association of Applied Biologists. 2019 – Today Reviewer. Mycologia. Mycological Society of America. 2017 – Today Reviewer. Phytopathology. American Phytopathological Society. 2015 – Today Reviewer. Plant Disease. American Phytopathological Society. 2015 – Today DeLil Nasser award reviewer. Genetics Society of America. 2021- Today Outreach and Equity Committee. Mycological Society of America. Secretary. 2022 – Today Poster Judge for Postdoctoral Comparative and Functional Genomics. 21 Fungal Genetics conference. Genetics Society of America. 2022 ZyGoLife Consortium. Consortium to study the genomics and evolution of Zygomycota species. 2018 – Today Phytophthora Genus Sequencing Consortium. Consortium to understand the genomics and evolution of multiple species of the devastating plant pathogen genus Phytophthora. 2013 – Today USDA-HCRL, Corvallis, OR. Evolution, genomics and population dynamics of Phytophthora species, with emphasis in pathogen centers of origin and worldwide dispersal 2012 – 2013. Colombian Center for Genomics and Bioinformatics of Extreme Environments (GEBIX), Bogotá, Colombia. Metagenomics on extreme environments. Barcoding analysis and diversity in extreme soils. 2011-2012 Researcher at CENICAFE (Research center of coffee, National federation of Coffee Growers). Chinchiná, Colombia. Genomics and transcriptomics of Hemilea vastatrix (Coffee Rust). 2011 – 2012 Teaching Experience: Main Instructor. MBB101/BIOL123: Introduction to Bioinformatics. Clark University, Worcester, MA. Fall, 2020; Fall, 2021; Fall, 2022 Main Instructor. BIOL120: Quantitative Methods for the Biological Sciences. Clark University, Worcester, MA. Fall, 2022 Main Instructor. BIOL209: The Genome Project. Clark University, Worcester, MA. Spring, 2020; Spring 2022 Main Instructor. BIOL265: Population Genetics (Seminar). Clark University, Worcester, MA. Fall, 2021 Guest Lecturer. Oomycete and Slime Mold biology. Mycology. Oregon State University, Corvallis, OR. Fall, 2019 Guest Lecturer. Genomics and molecular evolution. Ecosystem Genomics course. Oregon State University, Corvallis, OR. Spring, 2019 Guest Lecturer. Genomics and molecular evolution. Ecosystem Genomics course. Oregon State University, Corvallis, OR. Spring, 2019 Guest Lecturer. Oomycete and Slime Mold biology. Mycology. Oregon State University, Corvallis, OR. Fall, 2018 Instructor. Workshop in Population Genetics in R. American Phytopathological Society annual meeting. San Antonio, TX. 2017. Special Assistant Instructor. Special Topics: Techniques in Genotyping-By-Sequencing. Graduate course (MCB 599). Oregon State University, Corvallis, OR. Spring, 2016 Teaching assistant. Introductory Plant Pathology. Undegraduate/Graduate course (BOT 350/550). Oregon State University, Corvallis, OR. Fall, 2016 Instructor. Summer Oomycete Bioinformatics Training Workshop. Virginia Tech University, Blacksburg, VA. 2015 Invited instructor. Genomics and molecular evolution. Industry course. Corporation Center for Research in Palm Oil (CENIPALMA). Bogotá, Colombia. 2011 Laboratory teacher. Systematics and phylogenetics. Undergrad course, Universidad de los Andes, Bogotá, Colombia. 2009 – 2011. Teaching assistant. Genomics and Bioinformatics. Graduate course, Universidad de los Andes, Bogotá, Colombia. 2010 – 2012 Invited teacher. Section of molecular evolution: Mycology. Undergrad course, Universidad de los Andes, Bogotá, Colombia. 2009 – 2012 Leading organizer. Tutorial of genomics and evolutionary methods in plant pathogens. Undergrad course, Universidad de los Andes, Bogotá, Colombia. 2009 – 2011 Posters and presentations: Invited Seminar “Evolutionary Genomics of fungi: Fungal and oomycete populations and the boundaries of species in the scope of genomics”. University of Georgia. April 2023 Invited Seminar “Evolutionary Genomics of fungi: Fungal and oomycete populations and the boundaries of species in the scope of genomics”. University of Richmond. March 2023 Invited Seminar “Evolutionary Genomics of fungi: Fungal and oomycete populations and the boundaries of species in the scope of genomics”. Penn State University. February 2023 Invited Seminar “The intricacies of the genome of a small, gut associated fungus: Basidiobolus (Basidiobolaceae, Zoopagomycota)”. Tecnologico de Monterrey, Monterrey, Mexico. August 2022 Invited Seminar “The intricacies of the genome of a small, gut associated fungus: Basidiobolus (Basidiobolaceae, Zoopagomycota)”. Winter Genomics School, Universidad del Rosario, Bogota, Colombia. November 2021 Invited Seminar “The intricacies of the genome of a small, gut associated fungus: Basidiobolus (Basidiobolaceae, Zoopagomycota)”. Swedish University of Agricultural Sciences (SLU, Sveriges lantbruksuniversitet). November 2021 Invited Seminar “The intricacies of the genome of a small, gut associated fungus: Basidiobolus (Basidiobolaceae, Zoopagomycota)”. Middle Tenessee State University. February 2021 Poster Seminar “A novel natural product reservoir: secondary metabolite extracts from a zygomycete, Basidiobolus meristosporus, show selective antibacterial activity.” Meeting of the Mycological Society of America, 2021. Presented by Ian Trautman. Oral Presentation “Prediction and identification of secondary metabolism production in the cosmopolitan gut-associated zygomycete Basidiobolus (Basidiobolaceae, Zoopagomycota)”. Meeting of the Mycological Society of America, 2019. Poster Presentation “Population genomic analyses reveal human-mediated transport, and differences in virulence of Sphaerulina musiva among poplar plantations in North America”. Meeting of the Mycological Society of America, 2019. Oral Presentation “Prediction and identification of secondary metabolism production in the cosmopolitan gut-associated zygomycete Basidiobolus (Basidiobolaceae, Zoopagomycota)”. Fungal Genetics Conference. 2019. Poster Presentation “Prediction and identification of secondary metabolism production in the cosmopolitan gut-associated zygomycete Basidiobolus (Basidiobolaceae, Zoopagomycota)”. Fungal Genetics Conference. 2019. BEST POSTDOCTORAL POSTER POPULATION AND EVOLUTIONARY GENETICS SESSION. Poster Presentation “Population genomic analyses reveal human-mediated transport, and differences in virulence of Sphaerulina musiva among poplar plantations in North America”. Fungal Genetics Conference. 2019. Oral Presentation “Population dynamics of Phytophthora rubi indicate high rates of migration between states and nurseries in the Western United States”. American Phytopathological Society annual meeting. 2017. Oral Presentation “Population dynamics of Phytophthora rubi indicate high rates of migration between states and nurseries in the Western United States”. Oomycete Genomics Network Meeting. 2017. Invited Oral Presentation “Searching for genomic signatures of host jumping onto raspberry and strawberry in two Phytophthora sister taxa”. American Phytopathological Society meeting. 2016. Representing APS Pacific Division. Special session: “Plant Pathologist of the Future” Oral Presentation “Searching for genomic signatures of host jumping onto raspberry and strawberry in two Phytophthora sister taxa”. American Phytopathological Society meeting. 2015. FIRST PRIZE WINNER. APS Pacific Division Oral competition Poster presentation. “A best practices pipeline for GBS variant calling in population genomic studies”. Center for genomic and Biocomputing research Fall conference, Oregon State University. 2015 Poster presentation. “Genomic signatures of host jumping to raspberry and strawberry in two ancestrally related Phytophthora pathogens”. Center for genomic and Biocomputing research Fall conference, Oregon State University. 2014 Poster presentation. “Phytophthora-ID 2.0: Novel open source tools for Phytophthora species and genotype identification”. Center for genomic and Biocomputing research Fall conference, Oregon State University. 2014 Poster presentation. “The origin of Phytophthora infestans using phylogeographical methods”. American Phytopathological Society meeting, Providence, RI. 2014 Oral Presentation “Phylogeographical history of the late blight disease oomycete: Phytophthora infestans.”. First Colombian Computational Congress, Bogotá, Colombia. 2012. FIRST PRIZE WINNER Awards and Recognitions Faculty Development Funds award. 2023. Clark University. ($5,261) Faculty Academic Innovation Fund award. Using the study of urban impacts on water quality, frogs, and microbial communities in Worcester waterways to integrate student research, classroom learning, and local STEM outreach. (With Prof. Nathan Ahlgren and Prof. Philip Bergmann). 2022. Clark University. ($20,000) Faculty Development Funds award. Investigating epigenetic nucleic acid methylation in Dictyostelium slime mold. (With Prof. Robert Drewell and Prof. Denis Larochelle). 2022. Clark University. ($10,000) Start-up funds. Biology Department, Clark University. 2020 ($250,000) Best Postdoctoral Poster. 2019. Fungal Genetics Conference, Population and Evolutionary Genetics Session. CAS Savery Outstanding Doctoral Student Award. 2017. College of Agricultural Sciences, Oregon State University Lenore Bayley Fellow (2016-2017, $4000). Oregon State University. Travel Award ($500). American Phytopathological Society Foundation travel award to assist the American Phytopathological Society. San Antonio, Texas. 2017 Anita Summers Travel Award. 2017. ($1000). Botany and Plant Pathology Department. College of Agricultural Sciences. Oregon State University Anita Summers Travel Award. 2016. ($1000). Botany and Plant Pathology Department. College of Agricultural Sciences. Oregon State University Larry Moore Travel Award. 2016. ($500). Botany and Plant Pathology Department. College of Agricultural Sciences. Oregon State University Invited Oral Presentation “Searching for genomic signatures of host jumping onto raspberry and strawberry in two Phytophthora sister taxa”. American Phytopathological Society meeting. 2016. Representing APS Pacific Division. Special session: “Plant Pathologist of the Future” Representative of CAS graduate students at 2016 Board of Trustees dinner. Oregon State University, 2016. CAS Registry of Distinguished Students. College of Agricultural Sciences. Oregon State University. 2016 Representative of the College of Agriculture on the 2016 Board of Trustees meeting. Oregon State University. 2016 Plant Pathologists of the Future: Showcasing the Top Graduate Students from APS Division Meetings. American Phytopathological Society. 2016 First prize. Oral Presentation “Searching for genomic signatures of host jumping onto raspberry and strawberry in two Phytophthora sister taxa”. American Phytopathological Society meeting. Pacific Division. Travel Award ($500). American Phytopathological Society Foundation travel award to assist the American Phytopathological Society. Pasadena, California. 2015 Travel Award ($500). American Phytopathological Society Pacific division to assist the American Phytopathological Society. Pasadena, California. 2015 Travel Award ($1200). Oomycete Workshop on genomics. Virginia Tech, Virginia. 2014 First prize. Oral Presentation “Phylogeographical history of the late blight disease oomycete: Phytophthora infestans.”. First Colombian Computational Congress, 2012. Travel Award ($500). Open Science Grid Summer School. University of Wisconsin, Madison. 2011 Research award, Graduate School Startup grant. (Ph. D., $10.000) Universidad de los Andes, Bogota, Colombia. 2012 Research award, Graduate School Startup grant (Masters, $10.000). Universidad de los Andes, Bogota, Colombia. 2010 Awards to Students: Jasper Carleton ’24. Research award, The Edwin A. Weiller Summer Fellowship Program in the Sciences ($5,000). Clark University, 2023 Emily Newman ’24. Research award, SURP (Summer Undergraduate Research Experience, $3,000). Clark University, 2023 Brianna Bodner ’24. Research award, SURP (Summer Undergraduate Research Experience, $3,000). . Clark University, 2023 Jasper Carleton ’24. Research award, SURP (Summer Undergraduate Research Experience, $3,000). Clark University, 2022 Sara Wheeler ’24. Research award, SURP (Summer Undergraduate Research Experience, $3,000). Clark University, 2022 Maddison Hincher ’22. Research award, SURP (Summer Undergraduate Research Experience, $3,000). Clark University, 2021 Cameron McIlvenna ’22. Research award, SURP (Summer Undergraduate Research Experience, $3,000). Clark University, 2021 Riddhima Pathak ’22. The Edwin A. Weiller Summer Fellowship Program in the Sciences ($3,000). Clark University, 2021 Professional memberships: Genetics Society of America (2018 -Present) Mycological Society of America (2018 -Present) American Phytopathological Society (2012- Present) – Organizer: Special session in “Disease management in the genomic era”. APS Annual Meeting 2016. Society for the Study of Evolution (2014 -Present) Peer-reviewed Publications: Papers in preparation Trautman, I., Tehan, R. M., Tabima, J. F., Spatafora, J. W., McPhail K. L. A novel natural product reservoir: secondary metabolite extracts from a zygomycete, Basidiobolus meristosporus, show selective antibacterial activity. In prep. Hincher, M., Wheeler, S., Carleton, J. P., Devan-Song, A., and Tabima, J.F. First report of Basidiobolus species isolated from gastrointestinal tracts of amphibians in New England. In Prep. Papers in revision Kelsey L. Søndreli, Javier F. Tabima, and Jared M. LeBoldus. A rapid new diagnostic tool, LAMP (Loop-mediated Isothermal Amplification), to detect the four lineages of Phytophthora ramorum. Submitted, in revisions. Plant Disease – I performed orthologous gene identification, genomic assays and primer creation for the manuscript. I helped write the paper and reviewed the drafts and final manuscript. As Assistant Professor at Clark University Robert A Drewell, Tayla C Cormier, Jacob L Steenwyk, James St Denis, Javier F Tabima, Jacqueline M Dresch, Denis A Larochelle, The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing, NAR Genomics and Bioinformatics, Volume 5, Issue 2, June 2023, lqad035, https://doi.org/10.1093/nargab/lqad035 Braithwaite, E., Wang, R., Kowalewski, A.R., Tabima, J., Temple, T.N. and Rivedal, H.M., 2023. First report of Pyricularia oryzae causing gray leaf spot of perennial ryegrass (Lolium perenne L.) in Oregon. Plant Health Progress, (ja). Weisberg, A., Davis II, E., Tabima, J., Putnam, M., Miller, M., Belcher, M., Grünwald, N., Ream, W., Lai, E.M., Kuo, C.H. and Loper, J., 2022. Evolution and epidemiology of global populations of nursery-associated Agrobacterium. Ecological genetics, 20, pp.26-27. Brent A. Kronmiller, Nicolas Feau, Danyu Shen, Javier F. Tabima, et al. Comparative genomic analysis of 31 <i>Phytophthora</i> genomes reveal genome plasticity and horizontal gene transfer. Accepted with minor revisions. Molecular Plant-Microbe Interactions, 36(1), pp.26-46. – I performed orthologous gene identification, phylogenomic and evolutionary assays for the manuscript. I helped write the paper and reviewed the drafts and final manuscript. MacKenzie, C.A., Marston, M.F., Tabima, J.F. and Ahlgren, N.A., 2022. Genome Sequence of the Estuarine Synechococcus sp. Strain NB0720_010. Microbiology Resource Announcements, pp.e00151-22. – I was in charge of sequencing the genome, assembling and annotating the genome (this was the reference genome for the BIOL209 course) as well as funding the sequencing efforts. In addition, I advised MacKenzie in the writing of the paper and reviewed the drafts and final manuscript. Tehan, R.M., Blount, R.R., Goold, R.L., Mattos, D.R., Spatafora, N.R., Tabima, J.F., Gazis, R., Wang, C., Ishmael, J.E., Spatafora, J.W. and McPhail, K.L., 2022. Tolypocladamide H and the Proposed Tolypocladamide NRPS in Tolypocladium Species. Journal of Natural Products. – I processed the data and did correlation analyses between RNA expression and LCMSMS profiles to test the hypothesis of secondary metabolite production in Tolypocladium. In addition, I helped write the paper and reviewed the drafts and final manuscript. Olarte, R.A., Hall, R., Tabima, J., Malvick, D. and Bushley, K., 2021. Genetic diversity and aggressiveness of Fusarium virguliforme isolates across the Midwestern United States. Phytopathology, Early Online View – I performed some population genetics analyses and advised Olarte about population genetics methods and theory. I helped write the paper and reviewed the drafts and final manuscript. Rivedal, H.M., Tabima, J.F., Stone, A.G. and Johnson, K.B., 2022. Identity and Pathogenicity of Fungi Associated with Root, Crown, and Vascular Symptoms Related to Winter Squash Yield Decline. Plant Disease, 106(6), pp.1660-1668. – I performed phylogenetic analyses and advised Rivedal on systematics, phylogenetics and bioinformatic methods of species identification in fungi. I helped write the paper and reviewed the drafts and final manuscript. Benavides, N., Alvarez, A., Arrieta-Ortiz, M. L., Rodriguez-R, L. M., Botero, D., Tabima, J. F., Bernal, A. (2021). The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility. BMC Microbiology, 21(1), 1–12. – I performed orthologous gene identification, phylogenomics and evolutionary assays for the manuscript. I helped write the paper and reviewed the drafts and final manuscript. Bennett, P.I., Tabima, J.F., Leon, A.L., Browning, J., Wingfield, M.J. and LeBoldus, J.M., 2021. Spatial genetic structure of the insect-vectored conifer pathogen Leptographium wageneri suggests long distance gene flow among Douglas-fir plantations in western Oregon. Frontiers in Forests and Global Change. 4: 695981., 4, p.695981. – I performed the mating assays for the manuscript, as well as trained and wrote the code used by Bennett for his bioinformatic and population genetic assays. I helped write the paper and reviewed the drafts and provided revisions for final manuscript. Tabima, J. F., Gonen, L., Gomez-Gallego, M., Panda, P., Grunwald, N. J., Hansen, E. M., LeBoldus, J., Williams, N. M. (2021). Molecular phylogenomics and population structure of Phytophthora pluvialis. Phytopathology, 111(1), 108–115. – I performed all experiments, assays and metrics for this manuscript. I also write the paper, added all corrections and submitted the final manuscript. Brandt, K. M., Chen, X., Tabima, J. F., See, D. R., Vining, K. J., & Zemetra, R. S. (2021). QTL Analysis of Adult Plant Resistance to Stripe Rust in a Winter Wheat Recombinant Inbred Population. Plants, 10(3), 572.https://doi.org/10.3390/plants10030572. – I performed the initial bioinformatic assays for the detection of QTLs trained Brandt for the subsequent analyses. I helped write the paper and reviewed the drafts and provided revisions for final manuscript. Before Clark University Tabima, J. F., Trautman, I. A., Chang, Y., Wang, Y., Mondo, S., Kuo, A., Salamov, A., Grigoriev, I. V., Stajich, J. E., & Spatafora, J. W. (2020). Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus. G3 (Bethesda, Md.), g3.401516.2020. Advance online publication. https://doi.org/10.1534/g3.120.401516 Tabima J. F., Sondreli, K.L., Keriö, S., Feau, N., Sakalidis, M.L., Hamelin, R.C., and LeBoldus, J.M. Population genomic analyses reveal human-mediated transport, and differences in virulence of Sphaerulina musiva among poplar plantations in North America. (2020). Molecular Plant Microbe Interactions. Weisberg, A.J., Davis, E.W., Tabima, J., Belcher, M.S., Miller, M., Kuo, C.H., Loper, J.E., Grünwald, N.J., Putnam, M.L. and Chang, J.H., (2020). Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science, 368(6495). Knaus, B.J., Tabima, J.F., Shakya, S.K., Judelson, H.S. and Grünwald, N.J., (2020). Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen Phytophthora infestans. Mbio, 11(3). Adams, T.M., Armitage, A.D., Sobczyk, M.K., Bates, H.J., Tabima, J.F., Kronmiller, B.A., Tyler, B.M., Grünwald, N.J., Dunwell, J.M., Nellist, C.F. and Harrison, R.J., (2020). Genomic investigation of the strawberry pathogen Phytophthora fragariae indicates pathogenicity is associated with transcriptional variation in three key races. Frontiers in Microbiology, 11, p.490. Tabima J.F., Grünwald NJ. (2019). effectR: An expandable R package to predict candidate RxLR and CRN effectors in oomycetes using motif searches. Molecular Plant-Microbe Interactions. DOI: 10.1094/MPMI-10-18-0279-TA Buitrago-Flórez, F., Danies, G., Tabima, J., Restrepo, S. and Hernández, C., 2019. Designing a Socio- Cultural Approach for Teaching and Learning Computational Thinking. Nordic Journal of Digital Literacy, 15(02), pp.106-124. Keriö, S., Daniels, H.A., Gomez-Gollego, M., Tabima, J.F., Lenz, R.R., Søndreli, K.L., Grünwald, N.J., Williams, N. and McDougal, R., LeBoldus, J.M. (2019). From genomes to forest management–tackling invasive Phytophthora species in the era of genomics. Canadian Journal of Plant Pathology. DOI: 10.1080/07060661.2019.1626910 Dale, A.L., Feau, N., Everhart, S.E., Dhillon, B., Wong, B., Sheppard, J., Bilodeau, G.J., Brar, A., Tabima, J.F., Shen, D. and Brasier, C.M., (2019). Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum. mBio, 10(2), pp. e02452-18. Brar, S., Tabima, J.F., McDougal, R.L., Dupont, P‐Y., Feau, N., Hamelin, R.C., Panda, P., LeBoldus, J.M., Grünwald, N.J., Hansen, E.M. (2018). Genetic diversity of Phytophthora pluvialis, a pathogen of conifers, in New Zealand and the west coast of the United States of America. Plant Pathology 67: (5) 1131-1139. Davis, Edward W, Tabima, J.F., Weisberg, Alexandra J, Lopes, L. D., Wiseman, M. S, Pupko, T., Belcher, M. S., Sechler, A. J., Tancos, M. A. (2018). Evolution of the US Biological Select Agent Rathayibacter toxicus. mBio 9(4)e01280-18. Tabima, J.F., Coffey, M., Zasada, I., Grünwald, N.J. (2018). Populations of Phytophthora rubi show little differentiation and high rates of migration among states in the Western United States. Molecular Plant Microbe Interactions. 31(6):614-622. Tabima, J.F., Kronmiller, B., Press, C., Tyler, B.M., Zasada, I., Grünwald, N.J. (2017). Whole genome sequences of the raspberry and strawberry pathogens Phytophthora rubi and P. fragariae. Molecular Plant Microbe Interactions. 30(10):767-769. Tabima, J.F., Everhart, S.E., Larsen, M. M. , Weisberg, A.J., Kamvar, Z.N., Tancos, M.A., Smart, C.D., Chang, J.H., Grünwald, N.J. (2016). Microbe-ID: an open source toolbox for microbial genotyping and species identification. PeerJ 4:e2279 Mideros, M.F., Turissini, D.A., Guayazán, N., Ibarra-Avila, H., Danies, G., Cárdenas, M., Myers, K., Tabima, J., Goss, E.M., Bernal, A. and Lagos, L.E. (2018). Phytophthora betacei, a new species within Phytophthora clade 1c causing late blight on Solanum betaceum in Colombia. Persoonia-Molecular Phylogeny and Evolution of Fungi, 41:39-55. Chang, J. H., & Tabima, J. F. (2016). A Covert Operation by a Plant Pathogen. Cell host & microbe. 20(4):413-415. Davis II, E.W., Weisberg, A.J., Tabima, J.F., Grunwald, N.J. and Chang, J.H. (2016). Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria. PeerJ. 4:e2222. Restrepo, S., Enciso, J., Tabima, J. and Riaño-Pachón, D.M. (2016). Evolutionary history of the group formerly known as protists using a phylogenomics approach. Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales/ 40(154):147-160. Knaus, B.J., Tabima, J.F., Davis, C.E., Judelson, H.S., and Grünwald, N.J. (2016). Genomic analyses of dominant US clonal lineages of Phytophthora infestans reveals a shared common ancestry for clonal lineages US11 and US18 and a lack of recently shared ancestry among all other US lineages. Phytopathology 106:1393- 1403. Hansen, Z.R., Knaus, B.J., Tabima, J.F., Press, C.M., Judelson, H.S., Grünwald, N.J., and Smart, C.D. (2016). SNP-Based Differentiation of Phytophthora infestans Clonal Lineages Using Locked Nucleic Acid Probes and High-Resolution Melt Analysis. Plant Disease. 100:1297-1306. Hansen, Z. R., Knaus, B.J., Tabima, J.F., Press, C.M., Judelson, H.S., Grünwald, N.J., and Smart, C.D. (2016). Loop-mediated isothermal amplification for detection of the tomato and potato late blight pathogen, Phytophthora infestans. Journal of applied microbiology. 120:1010-1020. Sanjuan, T.I., Franco-Molano, A.E., Kepler, R.M., Spatafora, J.W., Tabima, J., Vasco-Palacios, A.M. and Restrepo, S., 2015. Five new species of entomopathogenic fungi from the Amazon and evolution of neotropical Ophiocordyceps. Fungal Biology. 119(10):901-916. Stewart, J.E., Kroese, D., Tabima, J.F., Larsen, M.M., Fieland, V.J., Press, C.M., Zasada, I.A. and Grünwald, N.J., 2014. Pathogenicity, Fungicide Resistance, and Genetic Variability of Phytophthora rubi Isolates from Raspberry (Rubus idaeus) in the Western United States. Plant Disease. 98(12):1702- 1708. Restrepo, S., Tabima, J.F., Mideros, M.F., Grünwald, N.J., and Matute, D.R. (2014). Speciation in fungal and oomycete plant pathogens. Annual Review of Phytopathology. 52:289–316 Goss, E.M., Tabima, J.F., Cooke, D.E., Restrepo, S., Fry, W.E., Forbes, G.A., Fieland, V.J., Cardenas, M., and Grünwald, N.J. (2014). The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes. Proceedings of the National Academy of Sciences. 111, 8791– 8796 Kamvar, Z.N., Tabima, J.F., and Grünwald, N.J. (2014). Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ. 2:e281 Sanjuan, T., Tabima, J., Restrepo, S., Laessøe, T., Spatafora, J.W., and Franco-Molano, A.E. (2014). Entomopathogens of Amazonian stick insects and locusts are members of the Beauveria species complex (Cordyceps sensu stricto). Mycologia 106:260–275 Cristancho, M.A., Botero-Rozo, D.O., Giraldo, W., Tabima, J., Riaño-Pachón, D.M., Escobar, C., Rozo, Y., Rivera, L.F., Durán, A., Restrepo, S., et al. (2014). Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales. Frontiers in Plant Science. 5 Amado, Y., Patiño-Uzcátegui, A., de García, M.C.C., Tabima, J., Motta, A., Cárdenas, M., Bernal, A., Restrepo, S., and Celis, A. (2013). Seborrheic dermatitis: predisposing factors and ITS2 secondary structure for Malassezia phylogenic analysis. Medical Mycology 51, 868–875 Arrieta-Ortiz, M.L., Rodríguez-R, L.M., Pérez-Quintero, Á.L., Poulin, L., Díaz, A.C., Rojas, N.A., Trujillo, C., Benavides, M.R., Bart, R., Boch, J., Tabima, J. et al. (2013). Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. manihotis strain CIO151. PloS One 8, e79704 Cárdenas, M., Tabima, J., Fry, W., Grünwald, N., Bernal, A., and Restrepo, S. (2012). Defining species boundaries in the genus Phytophthora: the case of Phytophthora andina A response to “Phytophthora andina sp. nov., a newly identified heterothallic pathogen of solanaceous hosts in the Andean highlands”(Oliva et al., 2010). Plant Pathology 61, 215–220 Cárdenas, M., Danies, G., Tabima, J., Bernal, A., and Restrepo, S. (2012). Phytophthora infestans Population Structure: A Worldwide Scale. Acta Biológica Colombiana 17, 227–240 Cárdenas, M., Medina, E., Tabima, J., Vargas, A., Lopera, C., Bernal, A., and Restrepo, S. (2011). First report of Phytophthora infestans causing late blight on Solanum viarum in Colombia. Plant Disease 95, 875–875 Olarte Castillo, X.A., Fermin, G., Tabima, J., Rojas, Y., Tennant, P.F., Fuchs, M., Sierra, R., Bernal, A.J., and Restrepo, S. (2011). Phylogeography and molecular epidemiology of Papaya ringspot virus. Virus Research 159, 132–140 Patino-Uzcategui, A., Amado, Y., Cepero de Garcia, M., Chaves, D., Tabima, J., Motta, A., Cardenas, M., Bernal, A., Restrepo, S., and Celis, A. (2011). Virulence Gene Expression in Malassezia spp from Individuals with Seborrheic Dermatitis. J Invest Dermatol 131, 2134–2136 Book Chapters: Everhart, S. E., Tabima, J. F., & Grünwald, N. J. (2014). Phytophthora ramorum. In Genomics of Plant-Associated Fungi and Oomycetes: Dicot Pathogens (pp. 159-174). Springer Berlin Heidelberg Cristancho, M., Giraldo, W., Botero, D., Tabima, J., Ortiz, D., Peralta, A., & Riaño, D. 2014. Application of Genome Studies of Coffee Rust. In Advances in Computational Biology (pp. 133- 139). Springer, Switzerland Leadership Diversity and Equality committee. (2022-Now). Mycological Society of America. Faculty Adviser: Future Latinxs in STEM student group (2020- Now). Clark University Faculty Adviser: SPOC (Science-Fiction People of Clark) student group (2020- Now). Clark University Outreach and Communications committee. (2020-Now). Biology Department. Clark University. Diversity and Equality committee. (2019-2020). Department of Botany and Plant Pathology. Oregon State University. Biology Graduate Student Symposium. (2018). Faculty advisor. Evolutionary ecology committee, American Phytopathological Society. Organizer of 2016 symposium: “Disease management in the genomics era”. (2016) Biology Graduate Student Symposium. (2017). Vice-president Biology Graduate Student Symposium. (2016). Vice-president Biology Graduate Student Symposium. (2015). Botany and Plant Pathology delegate Botany and Plant Pathology Graduate Student Association, Oregon State University. Position: Vice president (2014 – 2015) Association of Latin American Students (ALAS), Oregon State University. Position: Board member (2012 – 2016), Senior advisor (2014- 2017), Co-Chair (2012 – 2015) Undergrad thesis advisor (2012). “Use of avirulence markers to study genetic diversity in Phytophthora infestans” Student: Daniela Castiblanco. Universidad de los Andes, Bogotá, Colombia. Undergrad thesis advisor (2012). “Evolutionary history of the kingdom protista using a Phylogenomical approach” Student: Juan D. Enciso. Universidad de los Andes, Bogotá, Colombia. Thesis published: Restrepo, S., Enciso, J., Tabima, J., & Riaño-Pachón, D. (2016). Evolutionary history of the group formerly known as protists using a phylogenomics approach. Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales, 40(154), 147-160. doi:http://dx.doi.org/10.18257/raccefyn.277 Outreach Diversity and Equality committee. (2022-Now). Mycological Society of America. RecWoo and Clark STEM camps (2020 – Now). Creation of a community partnership between the Biology Department and the Recreation Worcester program of the City of Worcester to create STEM camps in after-hours for the youth at Worcester. Clark University Faculty Adviser: Future Latinxs in STEM student group (2020- Now). Clark University Diversity and Equality committee. (2019-2020). Department of Botany and Plant Pathology. Oregon State University. Biology Graduate Student Symposium. (2018). Faculty advisor. Botany and Plant Pathology Graduate Student Association, Oregon State University. Position: Vice president (2014 – 2015) Association of Latin American Students (ALAS), Oregon State University. Position: Board member (2012 – 2016), Senior advisor (2014- 2017), Co-Chair (2012 – 2015) Courses in Phylogenetics and bioinformatics to the private industry. Bogotá, Colombia. 2010- 2012. (Main instructor) Discovery Days. Botany and Plant Pathology department. (2012 – 2017) Botany and Plant Pathology Bolstering Undergraduate Development and Success program. Mentor (2014-2017)

  Clark University

• JGI CSP New PI: Diversity and evolution of secondary metabolism in a commensal cosmopolitan genus, Basidiobolus.

  Joint Genome Institute

• How the mushroom lost its gills: phylogenomics and population genetics of a morphological innovation in the fungal genus Lentinus

  National Science Foundation

• The Evolutionary Dynamics of a Filamentous Fungal Genus (Basidiobolus) Associated with Amphibian Gastrointestinal Tracts

  National Science Foundation

• How the mushroom lost its gills: phylogenomics and population genetics of a morphological innovation in the fungal genus Lentinus

  National Science Foundation

• Diversity and richness of an understudied Filamentous Fungal Genus (Basidiobolus) Associated with Amphibian Gastrointestinal Tracts.

  Clark University

• Using the study of urban impacts on water quality, frogs, and microbial communities in Worcester waterways to integrate student research, classroom learning, and local STEM outreach.

  Clark University

  Feb. 1, 2022 – Dec. 31, 2022

• The Evolutionary Dynamics of a Filamentous Fungal Genus (Basidiobolus) Associated with Amphibian Gastrointestinal Tracts

  National Science Foundation

• Investigating epigenetic nucleic acid methylation in Dictyostelium slime mold

  Clark University