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

Abstract

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.

Genetic and Ecological Relationships of Anastrepha ludens (Diptera: Tephritidae) Populations in Southern Mexico

“…The results of the present study reveal important new information about genetic variation in populations of A. ludens in the Sococusco region of Chiapas, Southern Mexico, including evidence for a lack of structuring of populations in this region due to host plants or geography. Previous work by Dupuis et al [ 6 ], covering a wide geographic range of A. ludens populations from Western to Eastern Mexico (including samples from Texas), recognized four broadly defined population groups [ 6 ]. In another study, Ruiz-Arce et al [ 24 ] observed genetic differentiation between Mexican populations separated by the Isthmus of Tehuantepec.…”

“…Using double-digest restriction site-associated DNA sequences (ddRAD-Seq), a study considering samples across the range distribution of the species (Texas, Mexico and Central America) produced He values between 0.126–0.150 (specifically, for samples from Chiapas, the He value was 0.147). In this same study, slightly higher values ranging from 0.162–0.227 were obtained using single nucleotide polymorphisms (SNP) markers [ 6 ].…”

“…Previous studies of A. ludens have revealed that this species has high levels of genetic variation and population structuring consistent with the presence of four subpopulations. The subpopulations occur within a distribution range corresponding to: (1) Western Mexico, (2) Eastern Mexico/Texas, (3) Guatemala/Belize/Honduras and (4) Costa Rica/Panama [ 6 ]. The Mexican populations in particular have been shown to exhibit moderate population structuring at a broad geographic scale [ 23 ], along with a stronger structuring at a narrower geographic scale [ 24 , 25 ].…”

“…In Mexico, Anastrepha ludens (Loew) (Diptera: Tephritidae), also known as the Mexican fruit fly, is one of the main pests of cultivated fruit trees, and this species has been the subject of several monitoring and control programs [2]. Currently, this species significantly impacts the production and marketing of several cultivated fruits, including oranges (Citrus sinensis L) and mangoes (Mangifera indica L.) [3,4] in Mexico as well other countries in Central America [5,6].…”

Disjunction between canola distribution and the genetic structure of its recently described pest, the canola flower midge (Contarinia brassicola)

“…2017). Additionally, these SNP‐based datasets can have multifaceted uses in applied pest management settings, such as contextualizing migration routes (Liu, Mori, et al., 2019; Liu, Chen, et al., 2019), providing rapid pathway analysis tools for recurrently invading pests (Picq et al, 2017, Dupuis et al., 2019), and improving existing management tools such as sterile insect technique (Sim et al., 2017).…”