Range-wide population genomics of the Mexican fruit fly: Toward development of pathway analysis tools

Julian R. Dupuis, Raul Ruiz-Arce, Norman B. Barr, Donald B. Thomas, Scott M. Geib

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to understand invasion dynamics and inform regulatory management through pathway analysis. In the southern United States, the Mexican fruit fly Anastrepha ludens is such a pest, and its incursions into Texas and California represent major threats to the agricultural systems of those regions. We developed a draft genome assembly for A. ludens, conducted range-wide population genomics using restriction site-associated DNA sequencing, and then developed and demonstrated a panel of highly differentiated diagnostic SNPs for source determination of intercepted flies in this system. Using 2,081 genomewide SNPs, we identified four populations across the range of A. ludens, corresponding to western Mexico, eastern Mexico/Texas, Guatemala/Belize/Honduras, and Costa Rica/Panama, with some intergradation present between clusters, particularly in Central America. From this population genomics framework, we developed a diagnostic panel of 28 highly differentiated SNPs that were able to recreate the genomewide population structure in this species. We demonstrated this panel on a set of test specimens, including specimens intercepted as part of regular trapping surveillance in Texas and California, and we were able to predict populations of origin for these specimens. This methodology presents a highly applied use of genomic techniques and can be implemented in any group of recurrently invading pests.

Original languageEnglish
Pages (from-to)1641-1660
Number of pages20
JournalEvolutionary Applications
Issue number8
StatePublished - 2019

Bibliographical note

Funding Information:
ddRAD sequencing libraries were prepared at the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) Daniel K. Inouye US PBARC Genomics facility by Nicole Yoneishi and Angela Kauwe, and sequencing was conducted at the Vincent J. Coates Genomics Sequencing Laboratory at University of California at Berkeley, supported by National Institutes of Health S10 Instrumentation Grants S10RR029668 and S10RR027303. Whole-genome sequencing (fragment and mate-pair) libraries were constructed and sequenced at BGI. We thank Pedro Rendón (USDA Animal and Plant Health Inspection Service (APHIS) International Services) for providing flies from the San Miguel Petapa rearing facility, Sandra N. Leal and Lupita Gracia (USDA Animal and Plant Health Inspection Service, Plant Protection and Quarantine (APHIS-PPQ)) for providing intercepted flies, Hugh Conway (USDA-APHIS-PPQ) for information on the Willacy strain, and Bruce McPheron (Ohio State University) and USDA-APHIS technicians for collecting specimens. Funding for this project was provided by USDA-APHIS Farm Bill Section 10007 Projects “Diagnostic Resources to Support Fruit Fly Exclusion and Eradication, 2012–2014” and “Genomic approaches to fruit fly exclusion and pathway analysis, 2015–2016” to USDA-APHIS, USDA-ARS, and UH Manoa (Projects 3.0251.02 and 3.01251.03 (FY 2014), 3.0256.01 and 3.0256.02 (FY 2015), and 3.0392.02 and 3.0392.03 (FY 2016)). Figures were prepared using R (R Core Team,) and Inkscape v0.91 (The Inkscape Team,). USDA is an equal opportunity employer. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. Figures were prepared using R (R Core Team,) and Inkscape v0.91 (The Inkscape Team,).

Publisher Copyright:
© 2019 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd


  • Anastrepha
  • Fluidigm
  • Tephritidae
  • agricultural pest
  • ddRAD
  • pathway analysis
  • source determination

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Agricultural and Biological Sciences (all)


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