Benjamin Cooper

Education

In Progress	Ph.D.	Plant and Microbial Biology University of Minnesota, St Paul, MN Ya Yang (advisor)
2016	M.S.	Plant Biology and Conservation Northwestern University and the Chicago Botanic Garden, Evanston, IL Revealing patterns of evolution in the sundrops (Oenothera sect. Calylophus: Onagraceae) using targeted enrichment Krissa Skogen (advisor)
2010	B.A.	Political Science Major | Biology Minor | Anthropology/Sociology Minor Kalamazoo College, Kalamazoo, MI

Publications

In Prep

Benjamin J. Cooper, Michael J. Moore, Norman A. Douglas, Warren L. Wagner, Matthew G. Johnson, Rick P. Overson, Angela J. McDonnell, Krissa A. Skogen, Norman J. Wickett. In Prep (Estimated submission date October, 2020; available upon request). Target enrichment and extensive population sampling help untangle the recent, rapid radiation of Oenothera sect. Calylophus (Onagraceae).

Presentations and Published Abstracts 

2020	Cooper, B., Analysis and Trends of Invasive Plants at Amistad National Recreation Area. National Park Service, Southwest Network Collaboration Science Seminar (via zoom).
2019	BOTANY annual conference, Phylogenomics Section, Tucson, AZ Cooper, B.*, M. Moore, N. Wickett, W. Wagner, M. Johnson, R. Overson and K. Skogen. The power of population sampling, “splash-zone” introns, and summary coalescent methods in targeted enrichment: untangling species relationships inOenothera sect. Calylophus (Onagraceae) using targeted enrichment.
2016	Thesis Presentation, The Chicago Botanic Garden, Glencoe, IL Revealing patterns of evolution in the sundrops (Oenothera sect. Calylophus: Onagraceae) using targeted enrichment.
2016	BOTANY annual conference, Cooley Award Section, Savannah, GA Cooper, B.*, M. Moore, N. Wickett, R. Overson, M. Johnson, and K. Skogen. Using target enrichment methods to resolve the phylogeny of Oenothera sect. Calylophus (Onagraceae) with 322 nuclear loci.

Grants/Honors/Awards

2020	The National Park Service, Service Award Monetary award for leadership during the novel corona virus (COVID-19) pandemic
2016	American Society of Plant Taxonomists Graduate Student Research Award. $850
2016	New Mexico Native Plant Society Research Award. $750
2015 & 2016	Northwestern University PBC Graduate Student Research Award. $1500
2015	Society of Herbarium Curators Student Research Grant. $500
2014	The Shaw Fellowship, Northwestern University/Chicago botanic Garden. $38,000
2014	The National Park Service, Service Award Monetary award for excellence in service
2012	The National Park Service, Service Award Monetary award for superior service
2011	The National Park Service, Service Award Star Award
2009	Kalamazoo College Climate Fellowship. $1500
2007	Kalamazoo College Anthropology/Sociology Annual Departmental Award for Excellence in Anthropology/Sociology

Spring 2016	Teaching Assistant, Northwestern University, Evanston, IL Bio-Chem School of Professional Studies
Winter 2016	Teaching Assistant, Northwestern University, Evanston, IL Cell Biology School of Professional Studies
Fall 2015	Teaching Assistant, Northwestern University, Evanston, IL Physiology School of Professional Studies
Spring 2015	Teaching Assistant, Northwestern University, Evanston, IL Bio-Chem School of Professional Studies

Additional Professional Experience

2016-2021	Data Analyst/Ecologist The Tucson Audubon Society, Tucson, AZ – contractor to: National Park Service, Chihuahuan Desert Network, Las Cruces, NM
2015-2016	Research Assistant Herendeen Lab, Chicago Botanic Garden, Evanston, IL Extracted, cleaned, idenified and sorted charcoalified plant fossils based on morphological characters using dissecting scope.
2011-2014	Field Botanist/Crew Lead Vegetation and Soils Inventory and Monitoring Program, National Park Service, Chihuahuan Desert Network, Las Cruces, NM Lead/supervised interdisciplinary field crew consisting of two paid employees and one intern in sampling upland vegetation and soils following established protocols for sampling cover, frequency, and composition; Identified plants to species using dichotomous keys; Collected, identified, and managed plant specimens according to established methods including updating plant logs, paper datasheets and electronic databases; Designed and developed customized Arcpad applications in Microsoft Java Script for field data collection on handheld GPS units/data loggers.
2010-2011	Vegetation/Springs Intern, The Student Conservation Association, National Park Service, Chihuahuan Desert Network, Las Cruces, NM Conducted sampling of arid land springs according to established protocols
2010	Piping Plover Intern, National Park Service, Sleeping Bear Dunes National Lakeshore, Empire, MI Monitored the federally endangered Great Lakes Piping Plover; Worked on various other projects in the National Lakeshore including a park bee survey, loon survey, beaver survey, water quality testing and Emerald Ash Borer survey.

Professional Memberships

2015-present	Botanical Society of America
2015-present	American Society of Plant Taxonomists

Target enrichment and extensive population sampling help untangle the recent, rapid radiation of Oenothera sect. Calylophus (Onagraceae).

With the development of high through-put sequencing and high performance computing, the use of targeted sequencing methods such as target enrichment combined with summary coalescent phylogenetic methods and genome-scale tests for admixture have arisen as effective approaches for reconstructing species histories in spite of multiple taxonomically confounding processes associated with rapid or recent radiaiton such as incomplete lineage sorting and past or continued gene flow. Yet these methods have only recently become widely available.

My research applies this approach to a historically recalcitrant groups of organisms with near population level sampling. Oenothera sect. Calylophus is a group of 13 recognized taxa in the Evening Primrose family (Onagraceae) with an interesting evolutionary history that includes independent origins of bee pollination, edaphic endemism, and permanent translocation heterozygosity. However, like other groups that radiated relatively recently, taxon boundaries within sect. Calylophus have remained challenging despite being well-circumscribed using traditional methods.

In this study, we used target enrichment, “splash zone” flanking non-coding regions, summary coalescent methods, genome-scale tests for gene flow, with traditional morphometric analysis to reconstruct a phylogenetic hypothesis, test taxon boundaries, and resolve the evolutionary history of Oenothera sect. Calylophus.

Importantly, because sect. Calylophus is a well-circumscribed clade with a relatively restricted geographic range in the northern Chihuahuan Desert of North America, we were able to comprehensively sample across the range of geographic and morphological diversity in the group with near-population level sampling. This approach (robust taxon sampling, target enrichment, using over 200 genes and associated “splash-zone” flanking non-coding regions, and summary coalescent analysis) recovered strong support for species relationships.

Videos

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Here is an older video about the Resource Inventory & Monitoring program in Big Bend National Park (from Ron Bend on Vimeo) from my days as a crew lead for the National Park Service.

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