Global Invasion History of the Agricultural Pest Butterfly Pieris Rapae Revealed with Genomics and Citizen Science
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Global invasion history of the agricultural pest butterfly Pieris rapae revealed with genomics and citizen science Sean F. Ryana,b,1, Eric Lombaertc, Anne Espesetd, Roger Vilae, Gerard Talaverae,f,g, Vlad Dinca˘ h, Meredith M. Doellmani, Mark A. Renshawj, Matthew W. Engi, Emily A. Hornettk,l, Yiyuan Lii, Michael E. Pfrenderi,m, and DeWayne Shoemakera,1 aDepartment of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996; bEcological and Biological Sciences Practice, Exponent, Inc., Menlo Park, CA 94025; cInstitut Sophia Agrobiotech, Centre de Recherches de Sophia-Antipolis, Université Côte d’Azur, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, 06 903 Sophia Antipolis, France; dDepartment of Biology, University of Nevada, Reno, NV 89557; eDepartment of Animal Biodiversity and Evolution, Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas and Universitat Pompeu Fabra, Barcelona, 08003 Spain; fDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; gMuseum of Comparative Zoology, Harvard University, Cambridge, MA 02138; hDepartment of Ecology and Genetics, University of Oulu, Oulu, 90014 Finland; iDepartment of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556; jShrimp Department, Oceanic Institute, Hawai’i Pacific University, Waimanalo, HI 96795; kDepartment of Evolution, Ecology and Behaviour, University of Liverpool, L69 7ZB Liverpool, United Kingdom; lDepartment of Vector Biology, Liverpool School of Tropical Medicine, L3 5QA Liverpool, United Kingdom; and mEnvironmental Change Initiative, University of Notre Dame, South Bend, IN 46556 Edited by Peter Kareiva, University of California, Los Angeles, CA, and approved August 19, 2019 (received for review May 2, 2019) The small cabbage white butterfly, Pieris rapae, is a major agricul- Unraveling a species’ invasion history often requires sampling tural pest of cruciferous crops and has been introduced to every across large spatial and temporal scales, which can be challenging continent except South America and Antarctica as a result of hu- and costly, particularly for many invasive species found on multiple man activities. In an effort to reconstruct the near-global invasion continents. Citizen science—research in which the public plays a history of P. rapae, we developed a citizen science project, the role in project development, data collection, or discovery and “Pieris Project,” and successfully amassed thousands of specimens which is subject to the same system of peer review as conventional EVOLUTION from 32 countries worldwide. We then generated and analyzed science—is a potentially powerful means to overcome some of nuclear (double-digest restriction site-associated DNA fragment pro- these challenges. A major strength of citizen science is that it can cedure [ddRAD]) and mitochondrial DNA sequence data for these greatly enhance the scale and scope of science and its impact samples to reconstruct and compare different global invasion his- on society (6). Consequently, there are now thousands of citizen tory scenarios. Our results bolster historical accounts of the global science projects worldwide (https://scistarter.org/), although they spread and timing of P. rapae introductions. We provide molecular evidence supporting the hypothesis that the ongoing divergence of theEuropeanandAsiansubspeciesofP. rapae (∼1,200 y B.P.) coin- Significance cides with the diversification of brassicaceous crops and the devel- opment of human trade routes such as the Silk Route (Silk Road). Over the last few thousand years, the seemingly inconspicuous The further spread of P. rapae over the last ∼160 y was facilitated cabbage white butterfly, Pieris rapae, has become one of the by human movement and trade, resulting in an almost linear series most abundant and destructive butterflies in the world. Here, of at least 4 founding events, with each introduced population go- we assessed variation at thousands of genetic markers from ing through a severe bottleneck and serving as the source for the butterflies collected across 32 countries by over 150 volunteer next introduction. Management efforts of this agricultural pest scientists and citizens to reconstruct the global spread of this may need to consider the current existence of multiple geneti- agricultural pest. Our results suggest this butterfly spread out cally distinct populations. Finally, the international success of the from eastern Europe to occupy every continent except South Pieris Project demonstrates the power of the public to aid scien- America and Antarctica, with the timing of many of these events tists in collections-based research addressing important questions coinciding with human activities—migration, trade, and the de- in invasion biology, and in ecology and evolutionary biology more velopment of crop cultivars that serve as food plants for the broadly. butterfly larvae. Interestingly, many of these invasions were hugely successful despite repeated losses of genetic diversity. invasive | agricultural pest | genomics | citizen science | approximate Bayesian computation Author contributions: S.F.R. designed research; S.F.R. performed research; S.F.R., A.E., R.V., G.T., V.D., M.M.D., M.A.R., E.A.H., M.E.P., and D.S. contributed new reagents/analytic tools; S.F.R. and E.L. analyzed data; and S.F.R., E.L., A.E., R.V., G.T., V.D., M.M.D., M.A.R., nvasive species—species spread to places beyond their natural M.W.E., E.A.H., Y.L., M.E.P., and D.S. wrote the paper. Irange, where they generate a negative impact [e.g., extirpate or The authors declare no conflict of interest. displace native fauna, spread disease, destroy agricultural crops This article is a PNAS Direct Submission. (1)]—continue to increase in number, with no signs of saturation Published under the PNAS license. (2). The spread of invasive species often is driven by (human) Data deposition: Demultiplexed double-digest restriction site-associated DNA fragment migration, global trade, and transportation networks (3), and, in procedure sequencing reads generated in this study are available through the National Center for Biotechnology Information’s Sequence Read Archive associated with Bioproject some cases, domestication of wild plants and animals (4). A critical PRJNA542919. All gene cytochrome c oxidase subunit 1 (COI) sequences were deposited in and often first step to mitigating the spread and impacts of invasive the Barcode of Life Database under the project “Pieris rapae Global Invasion History [PRA]” species is to understand their invasion history, including assessing and in the GenBank database (BankIt2244911: accession nos. MN181608 to MN182331). All metadata and scripts associated with analyses in this study have been deposited on GitHub source populations, routes of spread, number of independent in- (https://github.com/citscisean/PierisrapaeInvasionHistory). vasions, and the effects of genetic bottlenecks, among other factors. 1To whom correspondence may be addressed. Email: [email protected] or dewayne. Such detailed knowledge is crucial from an applied perspective [email protected]. (e.g., developing an effective biological control program) as well as This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. for addressing basic questions associated with the invasion process 1073/pnas.1907492116/-/DCSupplemental. (e.g., genetic changes, adaptation to novel environments) (5). www.pnas.org/cgi/doi/10.1073/pnas.1907492116 PNAS Latest Articles | 1of10 Downloaded by guest on September 27, 2021 are not always described as such (7). Yet, still very few involve 751 individuals (559 of these individuals were also used to generate agricultural pests (8), and nearly all rely on observations (e.g., ddRADseq data) and supplemented these sequences with 251 ad- sightings, photographs), limiting their capacity to address some ditional sequences from various online databases (total individuals fundamental questions in ecology and evolution, for example, with COI sequence = 1,002; Fig. 1B). those requiring physical material for molecular analyses. Pieris rapae, the small cabbage white butterfly, is arguably one of Global Patterns of Autosomal Genetic Differentiation and Diversity. the world’s most widespread and abundant pest butterflies. Cat- We filtered the ddRADseq data for autosomal markers and found erpillars of this species are a serious agricultural pest of crops in evidence for at least 7 genetically distinct clusters (ADMIXTURE the Brassicaceae family (e.g., cabbage, canola, bok choy, turnips) lowest cross-validation error: 0.25 for subpopulations [K] = 7) (9). This butterfly is believed to have originated in Europe and to (Fig. 2A). These genetic clusters largely correspond to the have subsequently undergone a range expansion into Asia several continental regions sampled, and we refer to them henceforth as thousand years ago as a result of domestication and trade of its populations, named based on their sampling region: Europe, host plants (10, 11). The Europe and Asia populations recognized North Africa, Asia (west/east; including Crete, Georgia, China, today are believed to represent separate subspecies—P. rapae Taiwan, Japan, and South Korea), Siberia, North America (east), rapae and P. rapae crucivora, respectively. North America (west), and Australia/New Zealand (Fig. 2E). The This butterfly has been introduced to many other parts of the greatest genetic differentiation