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Signatures of adaptation at key insecticide resistance loci in Anopheles gambiae in Southern Ghana revealed by low-coverage WGS

https://doi.org/10.1101/2024.01.17.575856

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

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Chromosomal differentiation and adaptation to human environments in the Anopheles gambiae complex

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Climate, soil and land-use based land suitability evaluation for oil palm production in Ghana

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Accurate whole human genome sequencing using reversible terminator chemistry

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Genetic diversity of the African malaria vector Anopheles gambiae

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Nextflow enables reproducible computational workflows

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Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation

inferredcites →https://doi.org/10.1038/nrg2986openalex-snapshot

Genotype and SNP calling from next-generation sequencing data

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Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae and Anopheles coluzzii

inferredcites →https://doi.org/10.1038/s41598-018-21265-5openalex-snapshot

Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae

inferredcites →https://doi.org/10.1038/s41598-020-76248-2openalex-snapshot

Ecological drivers of genetic connectivity for African malaria vectors Anopheles gambiae and An. arabiensis

inferredcites →https://doi.org/10.1046/j.1365-2583.2000.00206.xopenalex-snapshot

The kdr mutation occurs in the Mopti form of Anopheles gambiae s .s. through introgression

inferredcites →https://doi.org/10.1073/pnas.1719663115openalex-snapshot

Rapid selection of a pyrethroid metabolic enzyme CYP9K1 by operational malaria control activities

inferredcites →https://doi.org/10.1073/pnas.1806760115openalex-snapshot

Systems genetic analysis of inversion polymorphisms in the malaria mosquito Anopheles gambiae

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Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering

inferredcites →https://doi.org/10.1086/688018openalex-snapshot

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

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Robust relationship inference in genome-wide association studies

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fastp: an ultra-fast all-in-one FASTQ preprocessor

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Twelve years of SAMtools and BCFtools

inferredcites →https://doi.org/10.1093/gigascience/giz034openalex-snapshot

Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding

inferredcites →https://doi.org/10.1093/molbev/msaa128openalex-snapshot

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

inferredcites →https://doi.org/10.1093/molbev/msab143openalex-snapshot

Locally Adaptive Inversions Modulate Genetic Variation at Different Geographic Scales in a Seaweed Fly

inferredcites →https://doi.org/10.1093/molbev/msx087openalex-snapshot

Pollutants and Insecticides Drive Local Adaptation in African Malaria Mosquitoes

inferredcites →https://doi.org/10.1093/nar/gku1117openalex-snapshot

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

inferredcites →https://doi.org/10.1101/2023.07.31.23293323openalex-snapshot

LLIN Evaluation in Uganda Project (LLINEUP) – Plasmodium infection prevalence and genotypic markers of insecticide resistance in Anopheles vectors from 48 districts of Uganda

inferredcites →https://doi.org/10.1101/gr.157388.113openalex-snapshot

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

inferredcites →https://doi.org/10.1101/gr.245795.118openalex-snapshot

Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes

inferredcites →https://doi.org/10.1101/gr.262790.120openalex-snapshot

Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii

inferredcites →https://doi.org/10.1111/1755-0998.13520openalex-snapshot

Estimating dispersal using close kin dyads: The kindisperse R package

inferredcites →https://doi.org/10.1111/eva.12075openalex-snapshot

Geographic population structure of the A frican malaria vector A nopheles gambiae suggests a role for the forest‐savannah biome transition as a barrier to gene flow

inferredcites →https://doi.org/10.1111/evo.13176openalex-snapshot

Chromosome inversions and ecological plasticity in the main African malaria mosquitoes

inferredcites →https://doi.org/10.1111/mec.13100openalex-snapshot

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

inferredcites →https://doi.org/10.1111/mec.13572openalex-snapshot

Evolution of GOUNDRY , a cryptic subgroup of Anopheles gambiae s.l., and its impact on susceptibility to Plasmodium infection

inferredcites →https://doi.org/10.1111/mec.13888openalex-snapshot

Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole‐genome sequencing

inferredcites →https://doi.org/10.1111/mec.15756openalex-snapshot

A population genomic unveiling of a new cryptic mosquito taxon within the malaria‐transmitting Anopheles gambiae complex

inferredcites →https://doi.org/10.1111/mec.15845openalex-snapshot

The genetic architecture of target‐site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii

inferredcites →https://doi.org/10.1111/mec.16077openalex-snapshot

A beginner's guide to low‐coverage whole genome sequencing for population genomics

inferredcites →https://doi.org/10.1111/mec.16497openalex-snapshot

Multi‐omics analysis identifies a CYP9K1 haplotype conferring pyrethroid resistance in the malaria vector Anopheles funestus in East Africa

inferredcites →https://doi.org/10.1111/mec.16810openalex-snapshot

Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout

inferredcites →https://doi.org/10.1126/science.1076181openalex-snapshot

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

inferredcites →https://doi.org/10.1126/science.aaw7271openalex-snapshot

Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing

inferredcites →https://doi.org/10.11646/zootaxa.3619.3.2openalex-snapshot

Anopheles coluzzii and Anopheles amharicus, new members of the Anopheles gambiae complex

inferredcites →https://doi.org/10.1186/1475-2875-13-65openalex-snapshot

Behavioural divergence of sympatric Anopheles funestus populations in Burkina Faso

inferredcites →https://doi.org/10.1186/1475-925x-13-94openalex-snapshot

Machine learning, medical diagnosis, and biomedical engineering research - commentary

inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot

ANGSD: Analysis of Next Generation Sequencing Data

inferredcites →https://doi.org/10.1186/s12915-020-00841-0openalex-snapshot

Using spatial genetics to quantify mosquito dispersal for control programs

inferredcites →https://doi.org/10.1186/s12936-015-0989-4openalex-snapshot

Larval ecology of Anopheles coluzzii in Cape Coast, Ghana: water quality, nature of habitat and implication for larval control

inferredcites →https://doi.org/10.1186/s13071-018-2732-9openalex-snapshot

Temporal and spatial trends in insecticide resistance in Anopheles arabiensis in Sudan: outcomes from an evaluation of implications of insecticide resistance for malaria vector control

inferredcites →https://doi.org/10.1186/s13071-018-2826-4openalex-snapshot

Spatio-temporal genetic structure of Anopheles gambiae in the Northwestern Lake Victoria Basin, Uganda: implications for genetic control trials in malaria endemic regions

inferredcites →https://doi.org/10.1186/s13071-023-05876-0openalex-snapshot

Relationship between insecticide resistance profiles in Anopheles gambiae sensu lato and agricultural practices in Côte d’Ivoire

inferredcites →https://doi.org/10.1371/journal.pgen.1003097openalex-snapshot

The Effective Population Size of Malaria Mosquitoes: Large Impact of Vector Control

inferredcites →https://doi.org/10.1371/journal.pgen.1005004openalex-snapshot

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

inferredcites →https://doi.org/10.1371/journal.pgen.1006303openalex-snapshot

The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis

inferredcites →https://doi.org/10.1371/journal.pmed.1000303openalex-snapshot

Ecology: A Prerequisite for Malaria Elimination and Eradication

inferredcites →https://doi.org/10.1371/journal.pone.0002172openalex-snapshot

Evidence of Introgression of the ace-1R Mutation and of the ace-1 Duplication in West African Anopheles gambiae s. s

inferredcites →https://doi.org/10.1371/journal.pone.0039453openalex-snapshot

Anthropogenic Habitat Disturbance and Ecological Divergence between Incipient Species of the Malaria Mosquito Anopheles gambiae

inferredcites →https://doi.org/10.1534/genetics.106.065888openalex-snapshot

Ecological Zones Rather Than Molecular Forms Predict Genetic Differentiation in the Malaria VectorAnopheles gambiaes.s. in Ghana

inferredcites →https://doi.org/10.1534/genetics.111.137794openalex-snapshot

Ecological Genomics of Anopheles gambiae Along a Latitudinal Cline: A Population-Resequencing Approach

inferredcites →https://doi.org/10.1534/genetics.118.301336openalex-snapshot

Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data

inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

inferredcites →https://doi.org/10.5281/zenodo.597309openalex-snapshot

cggh/scikit-allel: v0.21.2

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/2024.06.17.599266openalex-snapshot

Genome-wide association studies unveil major genetic loci driving insecticide resistance in Anopheles funestus in four eco-geographical settings across Cameroon

inferred← citeshttps://doi.org/10.1186/s12864-024-11148-7openalex-snapshot

Genome-wide association studies unveil major genetic loci driving insecticide resistance in Anopheles funestus in four eco-geographical settings across Cameroon

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