Biology subjects

Besansky, N. J.

Publications and source records attributed to Besansky, N. J..

9 recordsLinked to original sources

bioRxiv2026

Estimation of adult census size from close-kin dyads in the malaria mosquito Anopheles gambiae

Accurate estimates of adult mosquito abundance are central to the design and evaluation of vector control strategies, yet they are difficult to obtain from natural populations. Conventional mark-recapture methods for estimating adult mosquito census size pose logistical and other challenges. A recently developed close-kin mark-recapture (CKMR) approach is a promising alternative. However, application of CKMR has been largely confined to long-lived vertebrates. Validation on empirical data from short-lived, highly fecund insects is lacking. Here, we apply CKMR to a natural population of Anopheles gambiae, the primary African malaria mosquito, sampled from a small island in Lake Victoria, Uganda. Using a high-diversity amplicon panel of genome-wide markers, we genotyped 714 adult mosquitoes collected over a 20-day period. We classified pairs to close-kin categories by implementing probabilistic latent-kinship estimation rather than using a deterministic threshold-based framework. We observe numerous full-sibling pairs but no parent-offspring pairs, a pattern indicative of extreme variance in reproductive success owing to frequent failure of mosquito egg clutches to produce adults. To adapt the CKMR framework to mosquito life history, we explicitly modeled the mosquito life cycle including the possibility of clutch failure. By incorporating probabilities of both parent-offspring and full-sibling relationships, we estimate an adult female census size of 26,887 (95% credible interval: 6,979 - 146,011), and a clutch failure probability of 97.6% (CrI: 91.3 - 99.6%). We use these estimates to calculate the predicted variance in reproductive success and effective population size. Through individual-based simulations we confirm our estimates and the necessity of modeling reproductive variance to explain observed kinship patterns. Our results demonstrate that CKMR can be applied successfully to mosquitoes, provided that appropriate adjustments are made to account for their natural history.

ecology↗

bioRxiv2022

Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria vector

Species distributed across heterogeneous environments often evolve locally adapted ecotypes, but understanding of the genetic mechanisms involved in their formation and maintenance in the face of gene flow is incomplete. In Burkina Faso, the major African malaria mosquito Anopheles funestus comprises two strictly sympatric and morphologically indistinguishable yet karyotypically differentiated forms reported to differ in ecology and behavior. However, knowledge of the genetic basis and environmental determinants of An. funestus diversification was impeded by lack of modern genomic resources. Here, we applied deep whole-genome sequencing and analysis to test the hypothesis that these two forms are ecotypes differentially adapted to breeding in natural swamps versus irrigated rice fields. We demonstrate genome-wide differentiation despite extensive microsympatry, synchronicity, and ongoing hybridization. Demographic inference supports a split only ~1,300 years ago, closely following the massive expansion of domesticated African rice cultivation ~1,850 years ago. Regions of highest divergence, concentrated in chromosomal inversions, were under selection during lineage splitting, consistent with local adaptation. The origin of nearly all variation implicated in adaptation, including chromosomal inversions, substantially predates the ecotype split, suggesting that rapid adaptation was fueled mainly by standing genetic variation. Sharp inversion frequency differences likely facilitated adaptive divergence between ecotypes, both by suppressing recombination between opposing chromosomal orientations of the two ecotypes, and by maximizing recombination within the structurally monomorphic rice ecotype. Our results align with growing evidence from diverse taxa that rapid ecological diversification can arise from evolutionarily old structural genetic variants that modify genetic recombination. Significance StatementLocal adaptation to heterogeneous environments is pervasive, but its underlying genetic basis is incompletely understood. Within a major African malaria vector, An. funestus, are two chromosomally differentiated groups that are co-localized, morphologically indistinguishable, and reported to differ both in ecology and behavior relevant to malaria transmission and control. Progress in understanding the genetic basis and environmental determinants of vector diversification was impeded by the lack of modern genomic resources. Here we perform deep whole-genome sequencing on individuals from these groups, establishing that they are differentiated genome-wide in a manner consistent with recent ecotype formation associated with the exploitation of a new anthropogenic larval habitat. Such rapid malaria vector diversification was facilitated by standing genetic variation, including evolutionarily old chromosomal rearrangements.

evolutionary biology↗

bioRxiv2020

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↗

bioRxiv2019

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↗

bioRxiv2019

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↗

bioRxiv2019

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↗

bioRxiv2018

A chromosome-scale assembly of the major African malaria vector Anopheles funestus

BackgroundAnopheles funestus is one of the three most consequential and widespread vectors of human malaria in tropical Africa. However, the lack of a high-quality reference genome has hindered the association of phenotypic traits with their genetic basis in this important mosquito.\n\nFindingsHere we present a new high-quality An. funestus reference genome (AfunF3) assembled using 240x coverage of long-read single-molecule sequencing for contigging, combined with 100x coverage of short-read Hi-C data for chromosome scaffolding. The assembled contigs total 446 Mbp of sequence and contain substantial duplication due to alternative alleles present in the sequenced pool of mosquitos from the FUMOZ colony. Using alignment and depth-of-coverage information, these contigs were deduplicated to a 211 Mbp primary assembly, which is closer to the expected haploid genome size of 250 Mbp. This primary assembly consists of 1,053 contigs organized into 3 chromosome-scale scaffolds with an N50 contig size of 632 kbp and an N50 scaffold size of 93.811 Mbp, representing a 100-fold improvement in continuity versus the current reference assembly, AfunF1.\n\nConclusionThis highly contiguous and complete An. funestus reference genome assembly will serve as an improved basis for future studies of genomic variation and organization in this important disease vector.

bioinformatics↗

bioRxiv2018

Leveraging evolutionary relationships to improve Anopheles genome assemblies

While new sequencing technologies have lowered financial barriers to whole genome sequencing, resulting assemblies are often fragmented and far from finished. Subsequent improvements towards chromosomal-level status can be achieved by both experimental and computational approaches. Requiring only annotated assemblies and gene orthology data, comparative genomics approaches that aim to capture evolutionary signals to predict scaffold neighbours (adjacencies) offer potentially substantive improvements without the costs associated with experimental scaffolding or re-sequencing. We leverage the combined detection power of three such gene synteny-based methods applied to 21 Anopheles mosquito assemblies with variable contiguity levels to produce consensus sets of scaffold adjacency predictions. Three complementary validations were performed on subsets of assemblies with additional supporting data: six with physical mapping data; 13 with paired-end RNA sequencing (RNAseq) data; and three with new assemblies based on re-scaffolding or incorporating Pacific Biosciences (PacBio) sequencing data. Improved assemblies were built by integrating the consensus adjacency predictions with supporting experimental data, resulting in 20 new reference assemblies with improved contiguities. Combined with physical mapping data for six anophelines, chromosomal positioning of scaffolds improved assembly anchoring by 47% for A. funestus and 38% A. stephensi. Reconciling an A. funestus PacBio assembly with synteny-based and RNAseq-based adjacencies and physical mapping data resulted in a new 81.5% chromosomally mapped reference assembly and cytogenetic photomap. While complementary experimental data are clearly key to achieving high-quality chromosomal-level assemblies, our assessments and validations of gene synteny-based computational methods highlight the utility of applying comparative genomics approaches to improve community genomic resources.

genomics↗

bioRxiv2018

Assessing connectivity despite high diversity in island populations of the malaria mosquito Anopheles gambiae

Documenting isolation is notoriously difficult for species with vast polymorphic populations. High proportions of shared variation impede estimation of connectivity, even despite leveraging information from many genetic markers. We overcome these impediments by combining classical analysis of neutral variation with assays of the structure of selected variation, demonstrated using populations of the principal African malaria vector Anopheles gambiae. Accurate estimation of mosquito migration is crucial for efforts to combat malaria. Modeling and cage experiments suggest that mosquito gene drive systems will enable malaria eradication, but establishing safety and efficacy requires identification of isolated populations in which to conduct field-testing. We assess Lake Victoria islands as candidate sites, finding one island 30 kilometers offshore is as differentiated from mainland samples as populations from across the continent. Collectively, our results suggest sufficient contemporary isolation of these islands to warrant consideration as field-testing locations and illustrate shared adaptive variation as a useful proxy for connectivity in highly polymorphic species.

evolutionary biology↗