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ARS Home » Plains Area » Kerrville, Texas » Knipling-Bushland U.S. Livestock Insects Research Laboratory » LAPRU » Research » Publications at this Location » Publication #366975
Research Project: Cattle Fever Tick Control and Eradication

Location: Livestock Arthropod Pests Research

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

Author
item DUPUIS, JULIAN - Non ARS Employee
item RUIZ, RAUL - Animal And Plant Health Inspection Service (APHIS)
item BARR, NORMAN - Animal And Plant Health Inspection Service (APHIS)
item Thomas, Donald
item Geib, Scott

Submitted to: Evolutionary Applications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/23/2019
Publication Date: 5/31/2019
Citation: Dupuis, J., Ruiz, R., Barr, N., Thomas, D.B., Geib, S.M. 2019. Range-wide population genomics of the Mexican fruit fly: Toward development of pathway analysis tools. Evolutionary Applications. 12(8):1641-1660. https://doi.org/10.1111/eva.12824.
DOI: https://doi.org/10.1111/eva.12824

Interpretive Summary: Invasive pest insects are a threat to agricultural crops and livestock in the USA. Genetic analysis of these pests can indicate the origin and pathway by which these invaders enter the country. The Mexican fruit fly is such a pest, and its incursions into Texas and California represent major threats to fruit crops, especially citrus in those regions. By studying flies from many different foreign countries we were able to identify mutations characteristic of four different regions. Fly populations in Western Mexico, Eastern Mexico (including Texas), Guatemala/Belize/Honduras, and Costa Rica/Panama, are genetically distinguishable. We developed a diagnostic test based on these genetic differences. We then demonstrated the reliability of this diagnostic test on a set of 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. This methodology presents a highly applied use of genomic techniques and can be implemented for any group of invading pests.

Technical Abstract: Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to both 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 genome-wide SNPs, we identified four populations across the range of A. ludens, corresponding to West Mexico, East Mexico/Texas, Guatemala/Belize/Honduras, and Costa Rica/Panama, with some intergradation present between clusters, particularly in isthmian Central America. From this population genomics framework, we developed a diagnostic panel of 28 highly-differentiated SNPs that were able to recreate the genome-wide 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.