About

Just as Theodosius Dobzhansky said that, “Nothing makes sense except in light of evolution”, similarly nothing in evolution makes sense except in light of DNA.  Understanding evolution starts with understanding the ways in which evolution manifests at the level of nucleotides, genes and genomes. As a scientist, I am interested in studying evolution using genomic tools. In particular, I am interested in the mechanisms that drive speciation and adaptation in plants, and investigating these through the lens of phylogenomics, comparative genomics, population genetics, and conservation genomics. 

In 2016, I completed my Master’s degree in Plant Biology and Conservation at Northwestern University/The Chicago Botanic Garden with The Skogen Lab. My thesis project was focused on answering questions about the evolution of Oenothera sect. Calylophus, a historically confusing group of plants, using targeted enrichment (“hybseq”), extensive population sampling, and summary coalescent methods. More information about my research is available here. Currently, my co-authors and I are preparing this work for publication (expected october 2020), I am working on an updated treatment of Oenothera sect. Calylophus, and I am employed as a data analyst/ecologist with the National Park Service, Chihuahuan Desert Network. I use programs such as SQL, Python, R, and ArcGISpro to analyze a broad set of data related to long term monitoring of native and invasive plant populations in the Southwest United States using statistical approaches such as Generalized Linear Mixed Models (GLMM’s). More information about my professional activities is available here.

Curriculum Vitae

Education

In ProgressPh.D.Plant and Microbial Biology
University of Minnesota, St Paul, MN
Ya Yang (advisor)
2016M.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)
2010B.A.Political Science Major | Biology Minor | Anthropology/Sociology Minor Kalamazoo College, Kalamazoo, MI

Publications

In PrepBenjamin 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 

2020Cooper, B., Analysis and Trends of Invasive Plants at Amistad National Recreation Area. National Park Service, Southwest Network Collaboration Science Seminar (via zoom).
2019BOTANY 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.
2016Thesis Presentation, The Chicago Botanic Garden, Glencoe, IL
Revealing patterns of evolution in the sundrops (Oenothera sect. Calylophus: Onagraceae) using targeted enrichment.
2016BOTANY 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

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

Teaching Experience

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

Additional Professional Experience

2016-2021Data Analyst/Ecologist
The Tucson Audubon Society, Tucson, AZ – contractor to: National Park Service, Chihuahuan Desert Network, Las Cruces, NM
2015-2016Research Assistant
Herendeen Lab, Chicago Botanic Garden, Evanston, IL
Extracted, cleaned, idenified and sorted charcoalified plant fossils based on morphological characters using dissecting scope.
2011-2014Field 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. 
2010-2011Vegetation/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
2010Piping 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-presentBotanical Society of America
2015-presentAmerican Society of Plant Taxonomists

Research

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.

Contact

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