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della Torre, A.

Publications and source records attributed to della Torre, A..

7 recordsLinked to original sources

Towards Scalable Age-Grading of Aedes albopictus mosquito using Mid-Infrared Spectroscopy and Machine Learning

The age structure and dynamics of mosquito populations are crucial for understanding their ability to spread diseases and assessing the effectiveness of anti-mosquito control measures. However, available methods to age-grade mosquito populations are labour-intensive and imprecise, particularly for Aedes species. We investigated the potential of Mid-Infrared Spectroscopy (MIRS) combined with Supervised Machine Learning (ML) to rapidly and accurately predict the age of adult females and males of the arbovirus vector, Aedes albopictus. First, we demonstrated the ability of MIRS-ML to age male and female mosquitoes reared under laboratory conditions. Second, we optimised the model with adults emerged from wild collected eggs reared under natural conditions in a semi-field facility, to expose them to more realistic ambient conditions. For each sex we developed three ML models based on the resolution of the predicted adult age class: low (9 day interval), medium (6 days) and high resolution (3 days) from 1 to 15 or 33 days for males and females, respectively. The prediction accuracy decreased as the resolution increased. In males, the accuracy dropped from 99% (low) to 93% (medium) and 85.8% (low); in females the high and medium resolution models showed 89.4% and 78.5% accuracy, which decreased to 72.6% for the low resolution. In a simulated vector control intervention, the low-resolution models allowed to detect shifts in the age-structure of Ae. albopictus populations with minimal sampling effort (<100 specimens). Finally, we validated MIRS-ML on two unseen data and reconstructed plausible age structures in 1) laboratory-reared and 2) field-collected Ae. albopictus males and females. Overall, the results represent a first step towards the development of a sound and reproducible MIRS-ML approach for age-grading of Ae. albopictus populations in the wild. AUTHOR SUMMARYKnowing the age of mosquito populations is critical for understanding how effectively they can transmit viruses like dengue, chikungunya, and Zika, as older mosquitoes are more likely to be infectious. Also, comparing ages of mosquito population before and after a control intervention - such as insecticide aerial spraying - may allow to understand the impact of the intervention. However, existing methods to estimate mosquito age are time-consuming and imprecise. In this study, we tested whether a rapid and scalable method based on detection of age-related changes by mid-infrared spectroscopy (MIRS) coupled with machine learning (ML) could accurately estimate the age of Aedes albopictus, the Asian Tiger mosquito, an important arbovirus vector. We trained MIRS-ML models using mosquitoes reared in both laboratory and semi-field conditions to reflect realistic environmental variation. Our models were able to classify mosquito age with high accuracy, especially when grouping individuals into broader age categories. In simulated vector control scenarios, low-resolution models effectively detected shifts in population age structure with minimal sampling effort. We also applied our approach to field-collected mosquitoes that showed plausible age structures, suggesting potential of this approach for real-world surveillance. This method represents a promising, scalable, and non-destructive tool for monitoring mosquito population dynamics and could help monitor control strategies against Aedes-borne diseases.

ecology↗

Aalbo1200: global genetic differentiation and variability of the mosquito Aedes albopictus

The mosquito Aedes albopictus transmits human viruses including dengue and chikungunya and is an extremely successful invasive species expanding into new regions of the world. New tools are needed to complement existing tools to help monitor and control this species. Genomic resources are improving for this species including genome reference sequences, and whole genome sequencing data will help to catalog genetic diversity in this species and further enable genetic analysis. We collected populations of Ae. albopictus from throughout its distribution and generated whole genome sequencing data from population samples. These data will be used to address a number of basic and applied questions for this species. Here, we show genetic differentiation patterns among the tropical and temperate forms, as well as finer scale genetic clustering at the regional and population scale. These data and results will be a valuable resource for further study and tool development for this species.

evolutionary biology↗

Aedes albopictus bionomics in Procida Island, a promising Mediterranean site for the assessment of innovative and community-based integrated pest management methods.

The colonization of Mediterranean Europe and of other temperate regions by Aedes albopictus created in the last decades an unprecedented nuisance problem in highly infested areas, as well as a new public health threat due to the species competence to transmit exotic arboviruses, such as dengue, chikungunya and zika. The Sterile Insect Technique (SIT) and the Incompatible Insect Technique (IIT) are insecticide-free mosquito-control methods relying on mass release of irradiated/manipulated males which are believed to have a potential in complementing existing and only partially effective control tools. Testing and implementing these approaches are challenging and selection of study sites is an instrumental and crucial step. We carried out a 4-year study in Procida Island (Gulf of Naples, Italy) in strict collaboration with local administrators and citizens to estimate: i) the temporal dynamics, spatial distribution, and population size of Ae. albopictus; and ii) the dispersal and survival of irradiated males. Overall, results provide insights on the bionomics of the mosquito in Southern Europe and draw attention to Procida Island as an ideal site to test innovative control programs against Ae. albopictus which may be used in other Mediterranean and temperate areas."

ecology↗

Inversion Genotyping in the Anopheles gambiae Complex Using High-Throughput Array and Sequencing Platforms

Chromosomal inversion polymorphisms have special importance in the Anopheles gambiae complex of malaria vector mosquitoes, due to their role in local adaptation and range expansion. The study of inversions in natural populations is reliant on polytene chromosome analysis by expert cytogeneticists, a process that is limited by the rarity of trained specialists, low throughput, and restrictive sampling requirements. To overcome this barrier, we ascertained tag single nucleotide polymorphisms (SNPs) that are highly correlated with inversion status (inverted or standard orientation). We compared the performance of the tag SNPs using two alternative high throughput molecular genotyping approaches versus traditional cytogenetic karyotyping of the same 960 individual An. gambiae and An. coluzzii mosquitoes sampled from Burkina Faso, West Africa. We show that both molecular approaches yield comparable results, and that either one performs as well or better than cytogenetics in terms of genotyping accuracy. Given the ability of molecular genotyping approaches to be conducted at scale and at relatively low cost without restriction on mosquito sex or developmental stage, molecular genotyping via tag SNPs has the potential to revitalize research into the role of chromosomal inversions in the behavior and ongoing adaptation of An. gambiae and An. coluzzii to environmental heterogeneities.

genomics↗

Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii

Mosquito control remains a central pillar of efforts to reduce malaria burden in sub-Saharan Africa. However, insecticide resistance is entrenched in malaria vector populations, and countries with high malaria burden face a daunting challenge to sustain malaria control with a limited set of surveillance and intervention tools. Here we report on the second phase of a project to build an open resource of high quality data on genome variation among natural populations of the major African malaria vector species Anopheles gambiae and Anopheles coluzzii. We analysed whole genomes of 1,142 individual mosquitoes sampled from the wild in 13 African countries, and a further 234 individuals comprising parents and progeny of 11 lab crosses. The data resource includes high confidence single nucleotide polymorphism (SNP) calls at 57 million variable sites, genome-wide copy number variation (CNV) calls, and haplotypes phased at biallelic SNPs. We used these data to analyse genetic population structure, and characterise genetic diversity within and between populations. We also illustrate the utility of these data by investigating species differences in isolation by distance, genetic variation within proposed gene drive target sequences, and patterns of resistance to pyrethroid insecticides. This data resource provides a foundation for developing new operational systems for molecular surveillance, and for accelerating research and development of new vector control tools.

genomics↗

In silico karyotyping of chromosomally polymorphic malaria mosquitoes in the Anopheles gambiae complex

Chromosomal inversion polymorphisms play an important role in adaptation to environmental heterogeneities. For mosquito species in the Anopheles gambiae complex that are significant vectors of human malaria, paracentric inversion polymorphisms are abundant and are associated with ecologically and epidemiologically important phenotypes. Improved understanding of these traits relies on determining mosquito karyotype, which currently depends upon laborious cytogenetic methods whose application is limited both by the requirement for specialized expertise and for properly preserved adult females at specific gonotrophic stages. To overcome this limitation, we developed sets of tag SNPs inside inversions whose biallelic genotype is strongly correlated with inversion genotype. We leveraged 1,347 fully sequenced An. gambiae and Anopheles coluzzii genomes in the Ag1000G database of natural variation. Beginning with principal components analysis (PCA) of population samples, applied to windows of the genome containing individual chromosomal rearrangements, we classified samples into three inversion genotypes, distinguishing homozygous inverted and homozygous uninverted groups by inclusion of the small subset of specimens in Ag1000G that are associated with cytogenetic metadata. We then assessed the correlation between candidate tag SNP genotypes and PCA-based inversion genotypes in our training sets, selecting those candidates with >80% agreement. Our initial tests both in held-back validation samples from Ag1000G and in data independent of Ag1000G suggest that when used for in silico inversion genotyping of sequenced mosquitoes, these tags perform better than traditional cytogenetics, even for specimens where only a small subset of the tag SNPs can be successfully ascertained.

genomics↗

Fine-mapping complex inversion breakpoints and investigating somatic pairing in the Anopheles gambiae species complex using proximity-ligation sequencing

Chromosomal inversions are fundamental drivers of genome evolution. In the main afro-tropical malaria vector species, belonging to the Anopheles gambiae species complex, inversions play an important role in local adaptation and have a rich history of cytological study. Despite the importance and ubiquity of some chromosomal inversions across the species complex, inversion breakpoints are often challenging to map molecularly due to the presence of large repetitive regions. Here, we develop an approach that uses Hi-C sequencing data to molecularly fine-map the breakpoints of inversions 2Rbc and 2Rd in A. coluzzii. We found that inversion breakpoints occur in large repetitive regions, and strikingly among three inversions analyzed, two breakpoints appear to be reused in two separate inversions. Additionally, we use heterozygous individuals to quantitatively investigate somatic pairing disruption in the regions immediately surrounding inversion breakpoints, and we find that pairing disruption is undetectable beyond approximately 250 Kb from the inversion breakpoints.

evolutionary biology↗