Association mapping desiccation resistance within chromosomal inversions in the African malaria vector Anopheles gambiae

The Anopheles coluzzii range extends into Kenya: detection, insecticide resistance profiles and population genetic structure in relation to conspecific populations in West and Central Africa

BACKGROUND

Anopheles coluzzii is a primary vector of malaria found in West and Central Africa, but its presence has hitherto never been documented in Kenya. A thorough understanding of vector bionomics is important as it enables the implementation of targeted and effective vector control interventions. Malaria vector surveillance efforts in the country have tended to focus on historically known primary vectors. The current study sought to determine the taxonomic status of samples collected from five different malaria epidemiological zones in Kenya as well as describe the population genetic structure and insecticide resistance profiles in relation to other An. coluzzii populations.

METHODS

Mosquitoes were sampled as larvae from Busia, Kwale, Turkana, Kirinyaga and Kiambu counties, representing the range of malaria endemicities in Kenya, in 2019 and 2021 and emergent adults analysed using Whole Genome Sequencing (WGS) data processed in accordance with the Anopheles gambiae 1000 Genomes Project phase 3. Where available, historical samples from the same sites were included for WGS. Comparisons were made with An. coluzzii cohorts from West and Central Africa.

RESULTS

This study reports the detection of An. coluzzii for the first time in Kenya. The species was detected in Turkana County across all three time points from which samples were analyzed and its presence confirmed through taxonomic analysis. Additionally, there was a lack of strong population genetic differentiation between An. coluzzii from Kenya and those from the more northerly regions of West and Central Africa, suggesting they represent a connected extension to the known species range. Mutations associated with target-site resistance to DDT and pyrethroids and metabolic resistance to DDT were found at high frequencies up to 64%. The profile and frequencies of the variants observed were similar to An. coluzzii from West and Central Africa but the ace-1 mutation linked to organophosphate and carbamate resistance present in An. coluzzii from coastal West Africa was absent in Kenya.

CONCLUSIONS

These findings emphasize the need for the incorporation of genomics in comprehensive and routine vector surveillance to inform on the range of malaria vector species, and their insecticide resistance status to inform the choice of effective vector control approaches.

The Anopheles coluzzii range extends into Kenya: Detection, insecticide resistance profiles and population genetic structure in relation to conspecific populations in West and Central Africa

Background

Anopheles coluzzii is a primary vector of malaria found in West and Central Africa, but its presence has hitherto never been documented in Kenya. A thorough understanding of vector bionomics is important as it enables the implementation of targeted and effective vector control interventions. Malaria vector surveillance efforts in the country have tended to focus on historically known primary vectors. In the current study, we sought to determine the taxonomic status of samples collected from five different malaria epidemiological zones in Kenya as well asdescribe the population genetic structure and insecticide resistance profiles in relation to other An. coluzzi populations.

Methods

Mosquitoes were sampled as larvae from Busia, Kwale, Turkana, Kirinyaga and Kiambu counties, representing the range of malaria endemicities in Kenya, in 2019 and 2021 and emergent adults analysed using Whole Genome Sequencing data processed in accordance with the Anopheles gambiae 1000 Genomes Project phase 3. Where available, historical samples from the same sites were included for WGS.

Results

This study reports the detection of Anopheles coluzzii for the first time in Kenya. The species was detected in Turkana County across all three time points sampled and its presence confirmed through taxonomic analysis. Additionally, we found a lack of strong population genetic differentiation between An. coluzzii from Kenya and those from the more northerly regions of West and Central Africa, suggesting they represent a connected extension to the known species range. Mutations associated with target-site resistance to DDT and pyrethroids and metabolic resistance to DDT were found at high frequencies of ~60%. The profile and frequencies of the variants observed were similar to An. coluzzii from West and Central Africa but the ace-1 mutation linked to organophosphate and carbamate resistance present in An. coluzzii from coastal West Africa was absent in Kenya.

Conclusions

These findings emphasise the need for the incorporation of genomics in comprehensive and routine vector surveillance to inform on the range of malaria vector species, and their insecticide resistance status to inform the choice of effective vector control approaches.

How chromosomal inversions reorient the evolutionary process

Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.

Dehydration induced AePer50 regulates midgut infection in Ae. aegypti

In the face of climate change, mosquitoes will experience evolving climates including longer periods of drought. An important physiological response to dry environments is the protection against water loss or dehydration, here defined as desiccation tolerance. Various environmental factors including temperature are known to alter interactions between the mosquito, Aedes aegypti , and the arboviruses it transmits, but little is known about how low humidity impacts arboviral infection. Here, we report that a gene upregulated in response to desiccation is important for controlling midgut infection. We have identified two genetically diverse lines of Ae. aegypti with marked differences in desiccation tolerance. To understand if the genetic basis underlying desiccation tolerance is the same between the contrasting lines, we compared gene expression profiles between desiccant treated and non-desiccant treated individuals in both the desiccation tolerant and susceptible lines by RNAseq. Gene expression analysis demonstrates that different genes are differentially expressed in response to desiccation stress between desiccation tolerant and susceptible lines. The most highly expressed transcript under desiccation stress in the desiccation susceptible line encodes a peritrophin protein, Ae Per50. Peritrophins play a crucial role in peritrophic matrix formation after a bloodmeal. Gene silencing of Ae Per50 by RNAi demonstrates that expression of Ae Per50 is required for survival of the desiccation susceptible line under desiccation stress, but not for the desiccation tolerant line. Moreover, the knockdown of Ae Per50 results in higher infection rates and viral replication rates of ZIKV and higher infection rates of CHIKV. Finally, following a bloodmeal, the desiccation susceptible line develops a thicker peritrophic matrix than the desiccation tolerant line. Together these results provide a functional link between the protection against desiccation and midgut infection which has important implications in predicting how climate change will impact mosquito-borne viruses.

Patterns of genetic differentiation imply distinct phylogeographic history of the mosquito species Anopheles messeae and Anopheles daciae in Eurasia

Detailed knowledge of phylogeography is important for control of mosquito species involved in the transmission of human infectious diseases. Anopheles messeae is a geographically widespread and genetically diverse dominant vector of malaria in Eurasia. A closely related species, An. daciae, was originally distinguished from An. messeae based on five nucleotide substitutions in its ribosomal DNA (rDNA). However, the patterns of phylogeographic history of these species in Eurasia remain poorly understood. Here, using internal transcribed spacer 2 (ITS2) of rDNA and karyotyping for the species identification we determined the composition of five Anopheles species in 28 locations in Eurasia. Based on the frequencies of 11 polymorphic chromosomal inversions used as genetic markers, a large-scale population genetics analysis was performed of 1932 mosquitoes identified as An. messeae, An. daciae and their hybrids. The largest genetic differences between the species were detected in the X sex chromosome suggesting a potential involvement of this chromosome in speciation. The frequencies of autosomal inversions in the same locations differed by 13%-45% between the species demonstrating a restricted gene flow between the species. Overall, An. messeae was identified as a diverse species with a more complex population structure than An. daciae. The clinal gradients in frequencies of chromosomal inversions were determined in both species implicating their possible involvement in climate adaptations. The frequencies of hybrids were low ~1% in northern Europe but high up to 50% in south-eastern populations. Thus, our study revealed critical differences in patterns of phylogeographic history between An. messeae and An. daciae in Eurasia. This knowledge will help to predict the potential of the malaria transmission in the northern territories of the continent.

Measuring the Impact of Genetic Heterogeneity and Chromosomal Inversions on the Efficacy of CRISPR-Cas9 Gene Drives in Different Strains of Anopheles gambiae

The human malaria vector Anopheles gambiae is becoming increasingly resistant to insecticides, spurring the development of genetic control strategies. CRISPR-Cas9 gene drives can modify a population by creating double-stranded breaks at highly specific targets, triggering copying of the gene drive into the cut site ("homing"), ensuring its inheritance. The DNA repair mechanism responsible requires homology between the donor and recipient chromosomes, presenting challenges for the invasion of laboratory-developed gene drives into wild populations of target species An. gambiae species complex, which show high levels of genome variation. Two gene drives (vas2-5958 and zpg-7280) were introduced into three An. gambiae strains collected across Africa with 5.3-6.6% variation around the target sites, and the effect of this variation on homing was measured. Gene drive homing across different karyotypes of the 2La chromosomal inversion was also assessed. No decrease in gene drive homing was seen despite target site heterology, demonstrating the applicability of gene drives to wild populations.

Introgression of a synthetic sex ratio distortion transgene into different genetic backgrounds of Anopheles coluzzii

The development of genetically modified mosquitoes (GMM) and their subsequent field release offers innovative approaches for vector control of malaria. A non-gene drive self-limiting male-bias Ag(PMB)1 strain has been developed in a 47-year-old laboratory G3 strain of Anopheles gambiae s.l. When Ag(PMB)1 males are crossed to wild-type females, expression of the endonuclease I-PpoI during spermatogenesis causes the meiotic cleavage of the X chromosome in sperm cells, leading to fertile offspring with a 95% male bias. However, World Health Organization states that the functionality of the transgene could differ when inserted in different genetic backgrounds of Anopheles coluzzii which is currently a predominant species in several West-African countries and thus a likely recipient for a potential release of self-limiting GMMs. In this study, we introgressed the transgene from the donor Ag(PMB)1 by six serial backcrosses into two recipient colonies of An. coluzzii that had been isolated in Mali and Burkina Faso. Scans of informative Single Nucleotide Polymorphism (SNP) markers and whole-genome sequencing analysis revealed a nearly complete introgression of chromosomes 3 and X, but a remarkable genomic divergence in a large region of chromosome 2 between the later backcrossed (BC6) transgenic offspring and the recipient paternal strains. These findings suggested to extend the backcrossing breeding strategy beyond BC6 generation and increasing the introgression efficiency of critical regions that have ecological and epidemiological implications through the targeted selection of specific markers. Disregarding differential introgression efficiency, we concluded that the phenotype of the sex ratio distorter is stable in the BC6 introgressed An. coluzzii strains.

Temporal and biting dynamics of the chromosomal inversion 2La in the malaria vectors Anopheles gambiae and Anopheles coluzzii in Bangui, Central African Republic

The chromosomal rearrangement 2La has been directly involved in the ecological and deadly epidemiological success of the malaria mosquitoes Anopheles gambiae and Anopheles coluzzii in sub-Saharan Africa. However, little is known about the biological and ecological factors that drive the local and temporal dynamics of this inversion in both species. Here, we performed a year-round longitudinal survey in Bangui, Central African Republic. We monthly sampled A. gambiae and A. coluzzii mosquitoes indoor and outdoor using human landing catches (HLC) for 48 h non-stop. We molecularly karyotyped all specimens to study the 2La inversion frequency variations, and monitored the mosquito spatial and temporal biting behavior throughout the year. In total, we successfully karyotyped 5121 A. gambiae and 986 A. coluzzii specimens. The 2La inversion frequency was higher in A. coluzzii than in A. gambiae across the year. In A. gambiae and A. coluzzii, the inversion frequency or karyotypes did not influence the biting behavior, either location or time. Moreover, the inversion frequency variation in both species was also independent of local climatic changes. Overall, our results revealed that in Bangui, the 2La inversion segregates at different frequency in each species, but this is not influenced by their trophic behavior. Studying the impact of urban settings and the population genetic structure of these two A. gambiae complex members could bring insights into the intrinsic relationship between 2La inversion and local conditions. More studies are needed to understand the polymorphic equilibrium of this inversion in Bangui.

The Relative Power of Structural Genomic Variation versus SNPs in Explaining the Quantitative Trait Growth in the Marine Teleost Chrysophrys auratus

Background: Genetic diversity provides the basic substrate for evolution. Genetic variation consists of changes ranging from single base pairs (single-nucleotide polymorphisms, or SNPs) to larger-scale structural variants, such as inversions, deletions, and duplications. SNPs have long been used as the general currency for investigations into how genetic diversity fuels evolution. However, structural variants can affect more base pairs in the genome than SNPs and can be responsible for adaptive phenotypes due to their impact on linkage and recombination. In this study, we investigate the first steps needed to explore the genetic basis of an economically important growth trait in the marine teleost finfish Chrysophrys auratus using both SNP and structural variant data. Specifically, we use feature selection methods in machine learning to explore the relative predictive power of both types of genetic variants in explaining growth and discuss the feature selection results of the evaluated methods. Methods: SNP and structural variant callers were used to generate catalogues of variant data from 32 individual fish at ages 1 and 3 years. Three feature selection algorithms (ReliefF, Chi-square, and a mutual-information-based method) were used to reduce the dataset by selecting the most informative features. Following this selection process, the subset of variants was used as features to classify fish into small, medium, or large size categories using KNN, naïve Bayes, random forest, and logistic regression. The top-scoring features in each feature selection method were subsequently mapped to annotated genomic regions in the zebrafish genome, and a permutation test was conducted to see if the number of mapped regions was greater than when random sampling was applied. Results: Without feature selection, the prediction accuracies ranged from 0 to 0.5 for both structural variants and SNPs. Following feature selection, the prediction accuracy increased only slightly to between 0 and 0.65 for structural variants and between 0 and 0.75 for SNPs. The highest prediction accuracy for the logistic regression was achieved for age 3 fish using SNPs, although generally predictions for age 1 and 3 fish were very similar (ranging from 0–0.65 for both SNPs and structural variants). The Chi-square feature selection of SNP data was the only method that had a significantly higher number of matches to annotated genomic regions of zebrafish than would be explained by chance alone. Conclusions: Predicting a complex polygenic trait such as growth using data collected from a low number of individuals remains challenging. While we demonstrate that both SNPs and structural variants provide important information to help understand the genetic basis of phenotypic traits such as fish growth, the full complexities that exist within a genome cannot be easily captured by classical machine learning techniques. When using high-dimensional data, feature selection shows some increase in the prediction accuracy of classification models and provides the potential to identify unknown genomic correlates with growth. Our results show that both SNPs and structural variants significantly impact growth, and we therefore recommend that researchers interested in the genotype–phenotype map should strive to go beyond SNPs and incorporate structural variants in their studies as well. We discuss how our machine learning models can be further expanded to serve as a test bed to inform evolutionary studies and the applied management of species.

Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii

Almost all regulation of gene expression in eukaryotic genomes is mediated by the action of distant non-coding transcriptional enhancers upon proximal gene promoters. Enhancer locations cannot be accurately predicted bioinformatically because of the absence of a defined sequence code, and thus functional assays are required for their direct detection. Here we used a massively parallel reporter assay, Self-Transcribing Active Regulatory Region sequencing (STARR-seq), to generate the first comprehensive genome-wide map of enhancers in Anopheles coluzzii, a major African malaria vector in the Gambiae species complex. The screen was carried out by transfecting reporter libraries created from the genomic DNA of 60 wild A. coluzzii from Burkina Faso into A. coluzzii 4a3A cells, in order to functionally query enhancer activity of the natural population within the homologous cellular context. We report a catalog of 3,288 active genomic enhancers that were significant across three biological replicates, 74% of them located in intergenic and intronic regions. The STARR-seq enhancer screen is chromatin-free and thus detects inherent activity of a comprehensive catalog of enhancers that may be restricted in vivo to specific cell types or developmental stages. Testing of a validation panel of enhancer candidates using manual luciferase assays confirmed enhancer function in 26 of 28 (93%) of the candidates over a wide dynamic range of activity from two to at least 16-fold activity above baseline. The enhancers occupy only 0.7% of the genome, and display distinct composition features. The enhancer compartment is significantly enriched for 15 transcription factor binding site signatures, and displays divergence for specific dinucleotide repeats, as compared to matched non-enhancer genomic controls. The genome-wide catalog of A. coluzzii enhancers is publicly available in a simple searchable graphic format. This enhancer catalogue will be valuable in linking genetic and phenotypic variation, in identifying regulatory elements that could be employed in vector manipulation, and in better targeting of chromosome editing to minimize extraneous regulation influences on the introduced sequences.

Importance: Understanding the role of the non-coding regulatory genome in complex disease phenotypes is essential, but even in well-characterized model organisms, identification of regulatory regions within the vast non-coding genome remains a challenge. We used a large-scale assay to generate a genome wide map of transcriptional enhancers. Such a catalogue for the important malaria vector, Anopheles coluzzii, will be an important research tool as the role of non-coding regulatory variation in differential susceptibility to malaria infection is explored and as a public resource for research on this important insect vector of disease.

Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii

Anopheles coluzzii is one of the primary vectors of human malaria in sub-Saharan Africa. Recently, it has spread into the main cities of Central Africa threatening vector control programs. The adaptation of An. coluzzii to urban environments partly results from an increased tolerance to organic pollution and insecticides. Some of the molecular mechanisms for ecological adaptation are known, but the role of transposable elements (TEs) in the adaptive processes of this species has not been studied yet. As a first step toward assessing the role of TEs in rapid urban adaptation, we sequenced using long reads six An. coluzzii genomes from natural breeding sites in two major Central Africa cities. We de novo annotated TEs in these genomes and in an additional high-quality An. coluzzii genome, and we identified 64 new TE families. TEs were nonrandomly distributed throughout the genome with significant differences in the number of insertions of several superfamilies across the studied genomes. We identified seven putatively active families with insertions near genes with functions related to vectorial capacity, and several TEs that may provide promoter and transcription factor binding sites to insecticide resistance and immune-related genes. Overall, the analysis of multiple high-quality genomes allowed us to generate the most comprehensive TE annotation in this species to date and identify several TE insertions that could potentially impact both genome architecture and the regulation of functionally relevant genes. These results provide a basis for future studies of the impact of TEs on the biology of An. coluzzii.

Integration of whole genome sequencing and transcriptomics reveals a complex picture of the reestablishment of insecticide resistance in the major malaria vector Anopheles coluzzii

Insecticide resistance is a major threat to gains in malaria control, which have been stalling and potentially reversing since 2015. Studies into the causal mechanisms of insecticide resistance are painting an increasingly complicated picture, underlining the need to design and implement targeted studies on this phenotype. In this study, we compare three populations of the major malaria vector An. coluzzii: a susceptible and two resistant colonies with the same genetic background. The original colonised resistant population rapidly lost resistance over a 6-month period, a subset of this population was reselected with pyrethroids, and a third population of this colony that did not lose resistance was also available. The original resistant, susceptible and re-selected colonies were subject to RNAseq and whole genome sequencing, which identified a number of changes across the transcriptome and genome linked with resistance. Firstly, an increase in the expression of genes within the oxidative phosphorylation pathway were seen in both resistant populations compared to the susceptible control; this translated phenotypically through an increased respiratory rate, indicating that elevated metabolism is linked directly with resistance. Genome sequencing highlighted several blocks clearly associated with resistance, including the 2Rb inversion. Finally, changes in the microbiome profile were seen, indicating that the microbial composition may play a role in the resistance phenotype. Taken together, this study reveals a highly complicated phenotype in which multiple transcriptomic, genomic and microbiome changes combine to result in insecticide resistance.

Insecticide resistance in major malaria vectors represents the single biggest threat to malaria control programs, which are heavily reliant upon insecticide-based interventions. Studying resistance using multi-omics approaches has proven difficult due to the use of susceptible comparator populations that have been colonised in a laboratory setting for decades, leading to substantial noise in the data due to differing genetic backgrounds. Here, we utilise a resistant Anopheles coluzzii population from Burkina Faso, a derived population that rapidly lost resistance over a 6-month period, and a population re-selected after loss of resistance to explore causative mechanisms of insecticide resistance. To determine the underlying cause of this phenotype, we use RNAseq, whole genome sequencing and lab-based validation to show changes in respiratory rate, wide-ranging genomic changes and alterations in the microbiome are linked to resistance in this population. These findings demonstrate the complexity of resistance and the challenges in utilising diagnostic markers for resistance in a field setting.

Stable inversion clines in a grasshopper species group despite complex geographical history

Chromosomal inversions are known to play roles in adaptation and differentiation in many species. They involve clusters of correlated genes (i.e., loci in linkage disequilibrium, LD) possibly associated with environmental variables. The grasshopper "species complex" Trimerotropis pallidipennis comprises several genetic lineages distributed from North to South America in arid and semi-arid high-altitude environments. The southernmost lineage, Trimerotropis sp., segregates for four to seven putative inversions that display clinal variation, possibly through adaptation to temperate environments. We analysed chromosomal, mitochondrial and genome-wide single nucleotide polymorphism data in 19 Trimerotropis sp. populations mainly distributed along two altitudinal gradients (MS and Ju). Populations across Argentina comprise two main chromosomally and genetically differentiated lineages: one distributed across the southernmost border of the "Andes Centrales," adding evidence for a differentiation hotspot in this area; and the other widely distributed in Argentina. Within the latter, network analytical approaches to LD found three clusters of correlated loci (LD-clusters), with inversion karyotypes explaining >79% of the genetic variation. Outlier loci associated with environmental variables mapped to two of these LD-clusters. Furthermore, despite the complex geographical history indicated by population genetic analyses, the clines in inversion karyotypes have remained stable for more than 20 generations, implicating their role in adaptation and differentiation within this lineage. We hypothesize that these clines could be the consequence of a coupling between extrinsic postzygotic barriers and spatially varying selection along environmental gradients resulting in a hybrid zone. These results provide a framework for future investigations about candidate genes implicated in rapid adaptation to new environments.

Genomic analysis of distinct bleaching tolerances among cryptic coral species

Reef-building coral species are experiencing an unprecedented decline owing to increasing frequency and intensity of marine heatwaves and associated bleaching-induced mortality. Closely related species from the Acropora hyacinthus species complex differ in heat tolerance and in their association with heat-tolerant symbionts. We used low-coverage full genome sequencing of 114 colonies monitored across the 2015 bleaching event in American Samoa to determine the genetic differences among four cryptic species (termed HA, HC, HD and HE) that have diverged in these species traits. Cryptic species differed strongly at thousands of single nucleotide polymorphisms across the genome which are enriched for amino acid changes in the bleaching-resistant species HE. In addition, HE also showed two particularly divergent regions with strong signals of differentiation. One approximately 220 kb locus, HES1, contained the majority of fixed differences in HE. A second locus, HES2, was fixed in HE but polymorphic in the other cryptic species. Surprisingly, non-HE individuals with HE-like haplotypes at HES2 were more likely to bleach. At both loci, HE showed particular sequence similarity to a congener, Acropora millepora. Overall, resilience to bleaching during the third global bleaching event was strongly structured by host cryptic species, buoyed by differences in symbiont associations between these species.

Intraspecific Transcriptome Variation and Sex-Biased Expression in Anopheles arabiensis

The magnitude and functional patterns of intraspecific transcriptional variation in the anophelines, including those of sex-biased genes underlying sex-specific traits relevant for malaria transmission, remain understudied. As a result, how changes in expression levels drive adaptation in these species is poorly understood. We sequenced the female, male, and larval transcriptomes of three populations of Anopheles arabiensis from Burkina Faso. One-third of the genes were differentially expressed between populations, often involving insecticide resistance-related genes in a sample type-specific manner, and with the females showing the largest number of differentially expressed genes. At the genomic level, the X chromosome appears depleted of differentially expressed genes compared with the autosomes, chromosomes harboring inversions do not exhibit evidence for enrichment of such genes, and genes that are top contributors to functional enrichment patterns of population differentiation tend to be clustered in the genome. Further, the magnitude of variation for the sex expression ratio across populations did not substantially differ between male- and female-biased genes, except for some populations in which male-limited expressed genes showed more variation than their female counterparts. In fact, female-biased genes exhibited a larger level of interpopulation variation than male-biased genes, both when assayed in males and females. Beyond uncovering the extensive adaptive potential of transcriptional variation in An. Arabiensis, our findings suggest that the evolutionary rate of changes in expression levels on the X chromosome exceeds that on the autosomes, while pointing to female-biased genes as the most variable component of the An. Arabiensis transcriptome.

Transposable elements and introgression introduce genetic variation in the invasive ant Cardiocondyla obscurior

Introduced populations of invasive organisms have to cope with novel environmental challenges, while having reduced genetic variation caused by founder effects. The mechanisms associated with this "genetic paradox of invasive species" has received considerable attention, yet few studies have examined the genomic architecture of invasive species. Populations of the heart node ant Cardiocondyla obscurior belong to two distinct lineages, a New World lineage so far only found in Latin America and a more globally distributed Old World lineage. In the present study, we use population genomic approaches to compare populations of the two lineages with apparent divergent invasive potential. We find that the strong genetic differentiation of the two lineages began at least 40,000 generations ago and that activity of transposable elements (TEs) has contributed significantly to the divergence of both lineages, possibly linked to the very unusual genomic distribution of TEs in this species. Furthermore, we show that introgression from the Old World lineage is a dominant source of genetic diversity in the New World lineage, despite the lineages' strong genetic differentiation. Our study uncovers mechanisms underlying novel genetic variation in introduced populations of C. obscurior that could contribute to the species' adaptive potential.

Genome-environment association methods comparison supports omnigenic adaptation to ecological niche in malaria vector mosquitoes

The concept of a fundamental ecological niche is central to questions of geographic distribution, population demography, species conservation, and evolutionary potential. However, robust inference of genomic regions associated with evolutionary adaptation to particular environmental conditions remains difficult due to the myriad of potential confounding processes that can generate heterogeneous patterns of variation across the genome. Here, we interrogate the potential role of genome environment association (GEA) testing as an initial step in building an understanding of the genetic basis of ecological niche. We leverage publicly available genomic data from the Anopheles gambiae 1000 Genomes (Ag1000g) Consortium to test the ability of multiple analytically unique GEA methods to handle confounding patterns of genetic variation, control false positive rates, and discern associations with broadly relevant climate variables from random allele frequency patterns throughout the genome. We found evidence supporting the ability of commonly implemented GEA methods to account for confounding patterns of spatial and genetic variation, and control false positive rates. However, we fail to find evidence supporting the ability of GEA tests to reject signals of adaptation to randomly simulated environmental variables, indicating that discerning between true signals of genome environment adaptation and genome environment correlations resulting from alternative evolutionary processes, remains challenging. Because signals of environmental adaptation are so diffuse and confounded throughout the genome, we argue that genomic adaptation to ecological niche is likely best understood under an omnigenic model wherein highly interconnected, genome-wide gene regulatory networks shape genomic adaptation to key environmental conditions.

2La Paracentric Chromosomal Inversion and Overexpressed Metabolic Genes Enhance Thermotolerance and Pyrethroid Resistance in the Major Malaria Vector Anopheles gambiae

Changes in global temperature are impacting the spread/intensity of vector-borne diseases, including malaria, and accelerating evolutionary/adaptive changes in vector species. These changes, including chromosomal inversions and overexpression and/or changes in allele frequencies of thermotolerance-associated genes, may facilitate insecticide resistance through pleiotropy. This study investigated the impact of thermotolerance on pyrethroid resistance in four populations of the malaria vector An. gambiae s.l., from the savanna/sub-Sahel of northern Nigeria. Anopheles coluzzii and An. gambiae s.s. were the only malaria vectors found, sympatric in all the sites, with the former species predominant. High thermotolerance was observed, with no mortality at 38 °C, and LT50 of ~44 °C. Significantly high permethrin resistance was observed (mortality < 50%) in 44 °C heat-hardened (exposure to an intermediately high temperature provides protection to a more severe temperature or insecticide) larvae from two sites, BUK and Pantami, compared with the control, and heat-hardened adult females from Auyo (mortality = 3.00% ± 1.20, χ2 = 5.83, p < 0.01) compared with the control (12.00% ± 4.65). The 2La chromosomal inversion was detected at ~50% in subset of larvae and 58% in subset of adult females genotyped. A significant association was observed (OR = 7.2, p < 0.03) between permethrin resistance and the 2La/+a rearrangement compared with 2L+a/+a, in BUK larvae. For all sites, permethrin resistance correlated with 2La/a homozygosity in adult females (R = 5.02, p = 0.01). qRT-PCR identified six genes commonly induced/overexpressed, including the heat shock protein 70 (AGAP004581) which was 2468× and 5× overexpressed in heat-hardened and permethrin-resistant females, respectively; trehalose-6-phosphate synthase (AGAP008227); and the ionotropic glutamate receptor genes, IR25a (AGAP010272) and IR21a (AGAP008511). This study highlights challenges associated with insecticide-based malaria vector control, and the epidemiological significance of taking climate variables into account for the design/choice of control measures.

Inversion breakpoints and the evolution of supergenes

The coexistence of discrete morphs that differ in multiple traits is common within natural populations of many taxa. Such morphs are often associated with chromosomal inversions, presumably because the recombination suppressing effects of inversions help maintain alternate adaptive combinations of alleles across the multiple loci affecting these traits. However, inversions can also harbour selected mutations at their breakpoints, leading to their rise in frequency in addition to (or independent from) their role in recombination suppression. In this review, we first describe the different ways that breakpoints can create mutations. We then critically examine the evidence for the breakpoint-mutation and recombination suppression hypotheses for explaining the existence of discrete morphs associated with chromosomal inversions. We find that the evidence that inversions are favoured due to recombination suppression is often indirect. The evidence that breakpoints harbour mutations that are adaptive is also largely indirect, with the characterization of inversion breakpoints at the sequence level being incomplete in most systems. Direct tests of the role of suppressed recombination and breakpoint mutations in inversion evolution are thus needed. Finally, we emphasize how the two hypotheses of recombination suppression and breakpoint mutation can act in conjunction, with implications for understanding the emergence of supergenes and their evolutionary dynamics. We conclude by discussing how breakpoint characterization could improve our understanding of complex, discrete phenotypic forms in nature.

Improving mosquito control strategies with population genomics

Mosquito control strategies increasingly apply knowledge from population genomics research. This review highlights recent applications to three research domains: mosquito invasions, insecticide resistance evolution, and rear and release programs. Current research trends follow developments in reference assemblies, either as improvements to existing assemblies (particularly Aedes) or assemblies for new taxa (particularly Anopheles). With improved assemblies, studies of invasive and rear and release target populations are better able to incorporate adaptive as well as demographic hypotheses. New reference assemblies are aiding comparisons of insecticide resistance across sister taxa while helping resolve taxon boundaries amidst frequent introgression. Anopheles gene drive deployments and improved Aedes genome assemblies should lead to a convergence in research aims for Anopheles and Aedes in the coming years.

The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi

Mutations in DNA can be limited to one or a few nucleotides, or encompass larger deletions, insertions, duplications, inversions and translocations that span long stretches of DNA or even full chromosomes. These so-called structural variations (SVs) can alter the gene copy number, modify open reading frames, change regulatory sequences or chromatin structure and thus result in major phenotypic changes. As some of the best-known examples of SV are linked to severe genetic disorders, this type of mutation has traditionally been regarded as negative and of little importance for adaptive evolution. However, the advent of genomic technologies uncovered the ubiquity of SVs even in healthy organisms. Moreover, experimental evolution studies suggest that SV is an important driver of evolution and adaptation to new environments. Here, we provide an overview of the causes and consequences of SV and their role in adaptation, with specific emphasis on fungi since these have proven to be excellent models to study SV.

Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis

Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.

Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome

The portion of the mosquito genome that does not code for proteins contains regulatory elements that likely underlie variation for important phenotypes including resistance and susceptibility to infection with arboviruses and Apicomplexan parasites. Filtering the non-coding genome to uncover these functional elements is an expanding area of research, though identification of non-coding regulatory elements is challenging due to the lack of an amino acid-like code for the non-coding genome and a lack of sequence conservation across species. This review focuses on three types of non-coding regulatory elements: (1) microRNAs (miRNAs), (2) long non-coding RNAs (lncRNAs), and (3) enhancers, and summarizes current advances in technical and analytical approaches for measurement of each of these elements on a genome-wide scale. The review also summarizes and highlights novel findings following application of these techniques in mosquito-borne disease research. Looking beyond the protein-coding genome is essential for understanding the complexities that underlie differential gene expression in response to arboviral or parasite infection in mosquito disease vectors. A comprehensive understanding of the regulation of gene and protein expression will inform transgenic and other vector control methods rooted in naturally segregating genetic variation.

Gene regulatory effects of a large chromosomal inversion in highland maize

Chromosomal inversions play an important role in local adaptation. Inversions can capture multiple locally adaptive functional variants in a linked block by repressing recombination. However, this recombination suppression makes it difficult to identify the genetic mechanisms underlying an inversion's role in adaptation. In this study, we used large-scale transcriptomic data to dissect the functional importance of a 13 Mb inversion locus (Inv4m) found almost exclusively in highland populations of maize (Zea mays ssp. mays). Inv4m was introgressed into highland maize from the wild relative Zea mays ssp. mexicana, also present in the highlands of Mexico, and is thought to be important for the adaptation of these populations to cultivation in highland environments. However, the specific genetic variants and traits that underlie this adaptation are not known. We created two families segregating for the standard and inverted haplotypes of Inv4m in a common genetic background and measured gene expression effects associated with the inversion across 9 tissues in two experimental conditions. With these data, we quantified both the global transcriptomic effects of the highland Inv4m haplotype, and the local cis-regulatory variation present within the locus. We found diverse physiological effects of Inv4m across the 9 tissues, including a strong effect on the expression of genes involved in photosynthesis and chloroplast physiology. Although we could not confidently identify the causal alleles within Inv4m, this research accelerates progress towards understanding this inversion and will guide future research on these important genomic features.

Detecting inversions with PCA in the presence of population structure

Chromosomal inversions can lead to reproductive isolation and adaptation in insects such as Drosophila melanogaster and the non-model malaria vector Anopheles gambiae. Inversions can be detected and characterized using principal component analysis (PCA) of single nucleotide polymorphisms (SNPs). To aid in developing such methods, we formed a new benchmark derived from three publicly-available insect data. We then used this benchmark to perform an extended validation of our software for inversion analysis (Asaph). Through that process, we identified and characterized several problematic test cases liable to misinterpretation that can help guide PCA-based inversion detection. Lastly, we re-analyzed the 2R chromosome arm of 150 An. gambiae and coluzzii samples and observed two inversions (2Rc and 2Rd) that were previously known but not annotated in these particular individuals. The resulting benchmark data set and methods will be useful for future inversion detection based solely on SNP data.

The importance of genomic variation for biodiversity, ecosystems and people

The 2019 United Nations Global assessment report on biodiversity and ecosystem services estimated that approximately 1 million species are at risk of extinction. This primarily human-driven loss of biodiversity has unprecedented negative consequences for ecosystems and people. Classic and emerging approaches in genetics and genomics have the potential to dramatically improve these outcomes. In particular, the study of interactions among genetic loci within and between species will play a critical role in understanding the adaptive potential of species and communities, and hence their direct and indirect effects on biodiversity, ecosystems and people. We explore these population and community genomic contexts in the hope of finding solutions for maintaining and improving ecosystem services and nature's contributions to people.

High-Throughput Genotyping of Common Chromosomal Inversions in the Afrotropical Malaria Mosquito Anopheles Funestus

Polymorphic chromosomal inversions have been implicated in local adaptation. In anopheline mosquitoes, inversions also contribute to epidemiologically relevant phenotypes such as resting behavior. Progress in understanding these phenotypes and their mechanistic basis has been hindered because the only available method for inversion genotyping relies on traditional cytogenetic karyotyping, a rate-limiting and technically difficult approach that is possible only for the fraction of the adult female population at the correct gonotrophic stage. Here, we focus on an understudied malaria vector of major importance in sub-Saharan Africa, Anopheles funestus. We ascertain and validate tag single nucleotide polymorphisms (SNPs) using high throughput molecular assays that allow rapid inversion genotyping of the three most common An. funestus inversions at scale, overcoming the cytogenetic karyotyping barrier. These same inversions are the only available markers for distinguishing two An. funestus ecotypes that differ in indoor resting behavior, Folonzo and Kiribina. Our new inversion genotyping tools will facilitate studies of ecotypic differentiation in An. funestus and provide a means to improve our understanding of the roles of Folonzo and Kiribina in malaria transmission.

Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression

The evolution of insecticide resistance mechanisms in natural populations of Anopheles malaria vectors is a major public health concern across Africa. Using genome sequence data, we study the evolution of resistance mutations in the resistance to dieldrin locus (Rdl), a GABA receptor targeted by several insecticides, but most notably by the long-discontinued cyclodiene, dieldrin. The two Rdl resistance mutations (296G and 296S) spread across West and Central African Anopheles via two independent hard selective sweeps that included likely compensatory nearby mutations, and were followed by a rare combination of introgression across species (from A. gambiae and A. arabiensis to A. coluzzii) and across nonconcordant karyotypes of the 2La chromosomal inversion. Rdl resistance evolved in the 1950s as the first known adaptation to a large-scale insecticide-based intervention, but the evolutionary lessons from this system highlight contemporary and future dangers for management strategies designed to combat development of resistance in malaria vectors.

Distribution modelling of an introduced species: do adaptive genetic markers affect potential range?

Biological invasions have increased in the last few decades mostly due to anthropogenic causes such as globalization of trade. Because invaders sometimes cause large economic losses and ecological disturbances, estimating their origin and potential geographical ranges is useful. Drosophila subobscura is native to the Old World but was introduced in the New World in the late 1970s and spread widely. We incorporate information on adaptive genetic markers into ecological niche modelling and then estimate the most probable geographical source of colonizers; evaluate whether the genetic bottleneck experienced by founders affects their potential distribution; and finally test whether this species has spread to all its potential suitable habitats worldwide. We find the environmental space occupied by this species in its native and introduced distributions are notably the same, although the introduced niche has shifted slightly towards higher temperature and lower precipitation. The genetic bottleneck of founding individuals was a key factor limiting the spread of this introduced species. We also find that regions in the Mediterranean and north-central Portugal show the highest probability of being the origin of the colonizers. Using genetically informed environmental niche modelling can enhance our understanding of the initial colonization and spread of invasive species, and also elucidate potential areas of future expansions worldwide.

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 vs. 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.

Chromosomal Differentiation in Genetically Isolated Populations of the Marsh-Specialist Crocidura suaveolens (Mammalia: Soricidae)

The genus Crocidura represents a remarkable model for the study of chromosome evolution. This is the case of the lesser white-toothed shrew (Crocidura suaveolens), a representative of the Palearctic group. Although continuously distributed from Siberia to Central Europe, C. suaveolens is a rare, habitat-specialist species in the southwesternmost limit of its distributional range, in the Gulf of Cádiz (Iberian Peninsula). In this area, C. suaveolens is restricted to genetically isolated populations associated to the tidal marches of five rivers (Guadiana, Piedras, Odiel, Tinto and Guadalquivir). This particular distributional range provides a unique opportunity to investigate whether genetic differentiation and habitat specialization was accompanied by chromosomal variation. In this context, the main objective of this study was to determinate the chromosomal characteristics of the habitat-specialist C. suaveolens in Southwestern Iberia, as a way to understand the evolutionary history of this species in the Iberian Peninsula. A total of 41 individuals from six different populations across the Gulf of Cádiz were collected and cytogenetically characterized. We detected four different karyotypes, with diploid numbers (2n) ranging from 2n = 40 to 2n = 43. Two of them (2n = 41 and 2n = 43) were characterized by the presence of B-chromosomes. The analysis of karyotype distribution across lineages and populations revealed an association between mtDNA population divergence and chromosomal differentiation. C. suaveolens populations in the Gulf of Cádiz provide a rare example of true karyotypic polymorphism potentially associated to genetic isolation and habitat specialization in which to investigate the evolutionary significance of chromosomal variation in mammals and their contribution to phenotypic and ecological divergence.

Highly specific PCR-RFLP assays for karyotyping the widespread 2Rb inversion in malaria vectors of the Anopheles gambiae complex

Background

Chromosomal inversion polymorphisms play a role in adaptation to heterogeneous environments. Inversion polymorphisms are implicated in the very high ecological flexibility of the three main malaria vector species of the Afrotropical Anopheles gambiae complex, facilitating the exploitation of anthropogenic environmental modifications and promoting a strong association with humans. In addition to extending the species’ spatial and temporal distribution, inversions are associated with epidemiologically relevant mosquito behavior and physiology, underscoring their medical importance. We here present novel PCR-RFLP based assays strongly predictive of genotype for the cosmopolitan 2Rb inversion in An. coluzzii and An. gambiae, a development which overcomes the numerous constraints inherent to traditional cytological karyotyping.

Methods

We designed PCR-RFLP genotyping assays based on tag SNPs previously computationally identified as strongly predictive (> 95%) of 2Rb genotype. We targeted those tags whose alternative allelic states destroyed or created the recognition site of a commercially available restriction enzyme, and designed assays with distinctive cleavage profiles for each inversion genotype. The assays were validated on 251 An. coluzzii and 451 An. gambiae cytologically karyotyped specimens from nine countries across Africa and one An. coluzzii laboratory colony.

Results

For three tag SNPs, PCR-RFLP assays (denoted DraIII, MspAI, and TatI) reliably produced robust amplicons and clearly distinguishable electrophoretic profiles for all three inversion genotypes. Results obtained with the DraIII assay are ≥ 95% concordant with cytogenetic assignments in both species, while MspAI and TatI assays produce patterns highly concordant with cytogenetic assignments only in An. coluzzii or An. gambiae, respectively. Joint application of species-appropriate pairs of assays increased the concordance levels to > 99% in An. coluzzii and 98% in An. gambiae. Potential sources of discordance (e.g. imperfect association between tag and inversion, allelic dropout, additional polymorphisms in the restriction target site, incomplete or failed restriction digestion) are discussed.

Conclusions

The availability of highly specific, cost effective and accessible molecular assays for genotyping 2Rb in An. gambiae and An. coluzzii allows karyotyping of both sexes and all developmental stages. These novel tools will accelerate deeper investigations into the role of this ecologically and epidemiologically important chromosomal inversion in vector biology.

Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast

The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.

Minimal genetic differentiation of the malaria vector Nyssorhynchus darlingi associated with forest cover level in Amazonian Brazil

The relationship between deforestation and malaria in Amazonian Brazil is complex, and a deeper understanding of this relationship is required to inform effective control measures in this region. Here, we are particularly interested in characterizing the impact of land use and land cover change on the genetics of the major regional vector of malaria, Nyssorhynchus darlingi (Root). We used nextera-tagmented, Reductively Amplified DNA (nextRAD) genotyping-by-sequencing to genotype 164 Ny. darlingi collected from 16 collection sites with divergent forest cover levels in seven municipalities in four municipality groups that span the state of Amazonas in northwestern Amazonian Brazil: São Gabriel da Cachoeira, Presidente Figueiredo, four municipalities in the area around Cruzeiro do Sul, and Lábrea. Using a dataset of 5,561 Single Nucleotide Polymorphisms (SNPs), we investigated the genetic structure of these Ny. darlingi populations with a combination of model- and non-model-based analyses. We identified weak to moderate genetic differentiation among the four municipality groups. There was no evidence for microgeographic genetic structure of Ny. darlingi among forest cover levels within the municipality groups, indicating that there may be gene flow across areas of these municipalities with different degrees of deforestation. Additionally, we conducted an environmental association analysis using two outlier detection methods to determine whether individual SNPs were associated with forest cover level without affecting overall population genetic structure. We identified 14 outlier SNPs, and investigated functions associated with their proximal genes, which could be further characterized in future studies.

Biological Adaptations Associated with Dehydration in Mosquitoes

Diseases that are transmitted by mosquitoes are a tremendous health and socioeconomic burden with hundreds of millions of people being impacted by mosquito-borne illnesses annually. Many factors have been implicated and extensively studied in disease transmission dynamics, but knowledge regarding how dehydration impacts mosquito physiology, behavior, and resulting mosquito-borne disease transmission remain underdeveloped. The lapse in understanding on how mosquitoes respond to dehydration stress likely obscures our ability to effectively study mosquito physiology, behavior, and vectorial capabilities. The goal of this review is to develop a profile of factors underlying mosquito biology that are altered by dehydration and the implications that are related to disease transmission.

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 single nucleotide polymorphisms (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.

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

BACKGROUND

Anopheles funestus is one of the 3 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.

FINDINGS

Here we present a new high-quality A. funestus reference genome (AfunF3) assembled using 240× coverage of long-read single-molecule sequencing for contigging, combined with 100× 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.

CONCLUSION

This highly contiguous and complete A. funestus reference genome assembly will serve as an improved basis for future studies of genomic variation and organization in this important disease vector.

Genetic Variation in Insect Vectors: Death of Typology?

The issue of typological versus population thinking in biology is briefly introduced and defined. It is then emphasized how population thinking is most relevant and useful in vector biology. Three points are made: (1) Vectors, as they exist in nature, are genetically very heterogeneous. (2) Four examples of how this is relevant in vector biology research are presented: Understanding variation in vector competence, GWAS, identifying the origin of new introductions of invasive species, and resistance to inbreeding. (3) The existence of high levels of vector genetic heterogeneity can lead to failure of some approaches to vector control, e.g., use of insecticides and release of sterile males (SIT). On the other hand, vector genetic heterogeneity can be harnessed in a vector control program based on selection for refractoriness.