About the blog author:
Dr Christopher (Chris) Irwin Smith is an evolutionary ecologist, a Professor of Biology at Willamette University in Salem, Oregon, and current AGA council member. His research focuses on the pollination biology of yuccas and combines traditional field ecology with molecular genetics and genomics. Chris was a 2022 Fulbright Garcia Robles US Scholar at the National Autonomous University in Mexico City.
Agavoideae Conference and Genotyping By Sequencing Workshop:
Can it really have been a year since we were in Mexico? Time has flown since last year’s bioinformatics workshop at The Institute of Ecology at the National Autonomous University in Mexico City (UNAM). In June of 2022, 28 early career graduate students and advanced undergraduates from throughout the Americas gathered to learn about reduced representation sequencing methods to address population genomic and phylogenomic problems, with a focus on plant genomes. Julian Catchen, from University of Illinois, provided a crash course in fundamental UNIX skills, and detailed, step-by-step lessons in the analysis of RADseq data using the STACKS software. Michael Mckain, from the University of Alabama, provided tutorials on the assembly and annotation of chloroplast genomes using the Fast-Plast software. Jim Leebens-Mack, from the University of Georgia, gave an overview of the use of sequence capture and the Astral software.
As an integral part of the workshop, scientists from the US and Mexico described how these approaches are being used to address evolutionary problems in the Agavoideae. Our speakers included: Luis Eguiarte (Instituto de Ecología at Universidad Nacional Autónoma de México) , Jim Leebens Mack (University of Georgia), Michael McKain (University of Alabama), Maria Magdalena Ayala (Facultad de Estudios Superiores Zaragoza, UNAM), Maria Clara Arteaga Uribe (Centro de Investigación Científica y de Educación Superior de Ensenada), Rob Raguso (Cornell University), Jorge Nieto Sotelo (Instituto de Biología, UNAM), Karolina Heyduk (University of Connecticut), Yuyini Licona-Vera (Instituto de Ecología, UNAM), Andrew Salywon (Desert Botanical Garden), and Fabiola Magallan-Hernandez (Universidad Autónoma de Querétaro).
Students representing seven nations attended the workshop, and collectively they reported that the workshop produced substantial improvements in their computational skills and greater confidence in their abilities to take on large scale analyses of genomic data. In addition, the workshop provided a foundation for future collaboration between scientists in the US and throughout Latin America.
I am exceptionally grateful to our hosts, Luis Eguiarte and Ella Vazquez at Instituto de Ecología, and to the many staff members and technicians that supported the course. Jaime Gasca, Rosa Leon Zayas, Bryan MacNeill, and Malia Santos provided TA support during the workshop. Extra special thanks are due to Erika Aguirre Plantar at Instituto de Ecología, without whose tireless assistance the conference would not have been possible.
Travel funds for students coming from outside of Mexico City, meals, and computational resources for the workshop, as well as palatial accommodations in the historic district of Coyoacán were provided through generous support from the American Genetic Association’s Special Event Award. Travel funding for the instructors was provided by Willamette University. My time in residence at UNAM was funded by the US Fulbright Scholars program and the Comisión México-Estados Unidos para el Intercambio Educativo y Cultural. It is my pleasure to acknowledge this support.