Population genetics and migration pathways of the Mediterranean fruit fly Ceratitis capitata inferred with coalescent methods

Invasion History and Dispersion Dynamics of the Mediterranean Fruit Fly in the Balkan Peninsula

The Mediterranean fruit fly (medfly), Ceratitis capitata (Wiedemann 1824; Diptera, Tephritidae), is considered one of the most important pests, infesting more than 300 species of fresh fruit and vegetables worldwide. The medfly is an important invasive species, which has spread from the eastern part of sub-Saharan Africa to all of the world's continents in recent centuries. Currently, the medfly is expanding its geographical range to cooler, temperate areas of the world, including northern areas of Mediterranean countries and continental areas of Central Europe. We collected and analysed all the available information, including in historical records, on the phenology of the medfly in the Balkan Peninsula, to map and understand the path of invasion and spread dynamics on the northern Mediterranean coast and in Central Europe. The medfly was first recorded in the Balkan Peninsula in 1915, in the Aegean area on the island of Aigina, followed by a few records on its presence in the Peloponnese in the early 1930s and throughout the Adriatic coastal area in the 1950s; it was first detected on the Croatian coast in 1947. By 2010, the medfly had been detected along the entire Ionian coast, while the first record of its presence on the Balkan coast of the Black Sea was made in 2005. Since 2000 to date, there has been a significant increase in the frequency of medfly detections in the interior of the Balkan Peninsula, including occasional detections in areas with unfavourable climatic conditions for overwintering, which seems to be favourable for reproduction during the summer and lead to significant infestation of late ripening fruits (late summer and autumn). In the last 20 years, the medfly has spread to more northerly areas (43 to 45 degrees latitude) and has been detected at higher altitudes (>200 to 600 m). Along the Balkan Peninsula, the infestation of fruits from 25 host plant species, from 14 genera and 10 plant families, has been reported. Considering the extremely high invasiveness of the medfly and its wide distribution in several Balkan regions with different climatic conditions, we can assume that it is adapting to new climatic conditions and infesting new host plants.

Global invasion history with climate-related allele frequency shifts in the invasive Mediterranean fruit fly (Diptera, Tephritidae: Ceratitis capitata)

The Mediterranean fruit fly (Ceratitis capitata) is a globally invasive species and an economically significant pest of fruit crops. Understanding the evolutionary history and local climatic adaptation of this species is crucial for developing effective pest management strategies. We conducted a comprehensive investigation using whole genome sequencing to explore (i) the invasion history of C. capitata with an emphasis on historical admixture and (ii) local climatic adaptation across African, European, Central, and South American populations of C. capitata. Our results suggest a stepwise colonization of C. capitata in Europe and Latin America in which Mediterranean and Central American populations share an ancestral lineage. Conversely, South American invasion history is more complex, and our results partly suggest an old secondary invasion into South America from Europe or a colonization of South America directly from Africa, followed by admixture with an European lineage. Throughout its invasive range, C. capitata is challenged with diverse climatic regimes. A genome wide association study identified a relationship between allele frequency changes and specific bioclimatic variables. Notably, we observed a significant allele frequency shift related to adaptation to cold stress (BIO6), highlighting the species' ability to rapidly adapt to seasonal variations in colder climates.

Unveiling biogeographic patterns in the worldwide distributed Ceratitis capitata (medfly) using populations genomics and microbiome composition

Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean medfly, Ceratitis capitata, is one of the most damaging representatives of a group of rapidly expanding species in the Tephritidae family, due to their wide host range and high invasiveness potential. Here, we used restriction site-associated DNA sequencing (RADseq) to investigate the population genomic structure and phylogeographic history of medflies collected from six sampling sites, including Africa (South Africa), the Mediterranean (Spain, Greece), Latin America (Guatemala, Brazil) and Australia. A total of 1,907 single nucleotide polymorphisms (SNPs) were used to identify two genetic clusters separating native and introduced ranges, consistent with previous findings. In the introduced range, all individuals were assigned to one genetic cluster except for those in Brazil, which showed introgression of an additional genetic cluster that also appeared in South Africa, and which could not be previously identified using microsatellite markers. Moreover, we assessed the microbial composition variations in medfly populations from selected sampling sites using amplicon sequencing of the 16S ribosomal RNA (V4 region). Microbiome composition and structure were highly similar across geographic regions and host plants, and only the Brazilian specimens showed increased diversity levels and a unique composition of its microbiome compared to other sampling sites. The unique SNP patterns and microbiome features in the Brazilian specimens could point to a direct migration route from Africa with subsequent adaptation of the microbiota to the specific conditions present in Brazil. These findings significantly improve our understanding of the evolutionary history of the global medfly invasions and their adaptation to newly colonised environments.

Looking at the big picture: worldwide population structure and range expansion of the cosmopolitan pest Ceratitis capitata (Diptera, Tephritidae)

The Mediterranean fruit fly, Ceratitis capitata (Weidemann), is considered one of the most significant tephritid pest species worldwide and is an exotic species in most of its range. Here, we investigated polymorphism at 14 microsatellite loci for a total of 126 populations of C. capitata from six geographical regions, applying network theory and cluster analyses. Analyses revealed nine distinct modules for the Central American region and one in each of the remaining five regions. Bayesian cluster analysis revealed that the highest level of genetic partitioning corresponds with the presence of 3 well-defined genetic clusters. Our results confirm the African origin for Mediterranean populations based on genetic diversity and suggest a direct invasion of C. capitata from the Mediterranean to Central-America. South American populations show links with Central-America, but also exhibit indications of direct admixture with the European cluster. Additionally, the network analysis proposes a South American origin for the Madeiran and Hawaiian flies. Cluster analysis corroborates the hypothesis of a Mediterranean origin for Australian samples. Our work provides novel insights regarding the migration history of Medfly worldwide.

Genetic structure and symbiotic profile of worldwide natural populations of the Mediterranean fruit fly, Ceratitis capitata

BACKGROUND

The Mediterranean fruit fly, Ceratitis capitata, is a cosmopolitan agricultural pest of worldwide economic importance and a model for the development of the Sterile Insect Technique (SIT) for fruit flies of the Tephritidae family (Diptera). SIT relies on the effective mating of laboratory-reared strains and natural populations, and therefore requires an efficient mass-rearing system that will allow for the production of high-quality males. Adaptation of wild flies to an artificial laboratory environment can be accompanied by negative effects on several life history traits through changes in their genetic diversity and symbiotic communities. Such changes may lead to reduced biological quality and mating competitiveness in respect to the wild populations. Profiling wild populations can help understand, and maybe reverse, deleterious effects accompanying laboratory domestication thus providing insects that can efficiently and effectively support SIT application.

RESULTS

In the present study, we analyzed both the genetic structure and gut symbiotic communities of natural medfly populations of worldwide distribution, including Europe, Africa, Australia, and the Americas. The genetic structure of 408 individuals from 15 distinct populations was analyzed with a set of commonly used microsatellite markers. The symbiotic communities of a subset of 265 individuals from 11 populations were analyzed using the 16S rRNA gene-based amplicon sequencing of single individuals (adults). Genetic differentiation was detected among geographically distant populations while adults originated from neighboring areas were genetically closer. Alpha and beta diversity of bacterial communities pointed to an overall reduced symbiotic diversity and the influence of the geographic location on the bacterial profile.

CONCLUSIONS

Our analysis revealed differences both in the genetic profile and the structure of gut symbiotic communities of medfly natural populations. The genetic analysis expanded our knowledge to populations not analyzed before and our results were in accordance with the existing scenarios regarding this species expansion and colonization pathways. At the same time, the bacterial communities from different natural medfly populations have been characterized, thus broadening our knowledge on the microbiota of the species across its range. Genetic and symbiotic differences between natural and laboratory populations must be considered when designing AW-IPM approaches with a SIT component, since they may impact mating compatibility and mating competitiveness of the laboratory-reared males. In parallel, enrichment from wild populations and/or symbiotic supplementation could increase rearing productivity, biological quality, and mating competitiveness of SIT-important laboratory strains.

Female-to-male sex conversion in Ceratitis capitata by CRISPR/Cas9 HDR-induced point mutations in the sex determination gene transformer-2

The Sterile Insect Technique (SIT) is based on the mass release of sterilized male insects to reduce the pest population size via infertile mating. Critical for all SIT programs is a conditional sexing strain to enable the cost-effective production of male-only populations. Compared to current female-elimination strategies based on killing or sex sorting, generating male-only offspring via sex conversion would be economically beneficial by doubling the male output. Temperature-sensitive mutations known from the D. melanogaster transformer-2 gene (tra2^ts) induce sex conversion at restrictive temperatures, while regular breeding of mutant strains is possible at permissive temperatures. Since tra2 is a conserved sex determination gene in many Diptera, including the major agricultural pest Ceratitis capitata, it is a promising candidate for the creation of a conditional sex conversion strategy in this Tephritid. Here, CRISPR/Cas9 homology-directed repair was used to induce the D. melanogaster-specific tra2^ts SNPs in Cctra2. 100% female to male conversion was successfully achieved in flies homozygous for the tra2^ts2 mutation. However, it was not possible, to identify a permissive temperature for the mutation allowing the rearing of a tra2^ts2 homozygous line, as lowering the temperature below 18.5 °C interferes with regular breeding of the flies.

Worldwide Phylogeography of Ceratitis capitata (Diptera: Tephritidae) Using Mitochondrial DNA

The Mediterranean fruit fly, Ceratitis capitata (Weidemann), is one of the most economically important tephritid species worldwide. It has spread across six geographic regions as a result of successful invasions and continues to cause substantial losses to agricultural communities. Our study examined 1,864 flies originating from 150 localities, using mitochondrial DNA sequencing methods. We tested for population structure and revealed the genetic diversity for 1,592 specimens gathered from 144 wild fly collections from 46 countries representing the entire geographic range for this species. We also include in this study 272 Sterile Insect Technique (SIT) specimens from four SIT facilities. We recovered 202 haplotypes from the current sampling and updated previously published work to reveal a total of 231 haplotypes for this pest. These data show population structure at and below the regional level for these collections, shedding light on the current demographics for this species. We observed four common haplotypes, seen among 62% of the samples sequenced that have worldwide distribution. Three haplotypes were seen in SIT flies, with one seen as the predominant haplotype. Our work showed that two of the haplotypes were private to SIT flies, not present among wild fly collections. However, a third haplotype common among wild fly collections was also seen in one SIT facility but at a low frequency based on the current sampling. We provide guidance on the interpretation of these methods for the source estimation of current and future infestations.