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

Abstract

Inversion polymorphisms are responsible for many ecologically important phenotypes, and are often found under balancing selection. However, the same features that ensure their large role in local adaptation-especially reduced recombination between alternate arrangements-mean that uncovering the precise loci within inversions that control these phenotypes is unachievable using standard mapping approaches. Here we take advantage of long-term balancing selection on a pair of inversions in the mosquito Anopheles gambiae to map desiccation tolerance via pool-GWAS.Two polymorphic inversions on chromosome 2 of this species (denoted 2La and 2Rb) are associated with arid and hot conditions in Africa, and are maintained in spatially and temporally heterogeneous environments. After measuring thousands of wild-caught individuals for survival under desiccation stress, we used phenotypically extreme individuals homozygous for alternative arrangements at the 2La inversion to construct pools for whole-genome sequencing. Genome-wide association mapping using these pools revealed dozens of significant SNPs within both 2La and 2Rb, many of which neighbored genes controlling ion channels or related functions. Our results ¶ Author Contributions: DA, MWH and NJB designed the research; DA led the phenotypic analysis, including field collections, desiccation testing, survivorship and body mass determination, molecular karyotyping, species delimitation, and modeling to select phenotypically extreme mosquitoes for Pool-Seq, with assistance from MC and CF and logistical support from IM, CC, and NJB; SZ led the computational analysis including read mapping, SNP calling, and association mapping, supported by MWH. SZ, DA, MWH and NJB wrote the paper. point to the promise of similar approaches in systems with inversions maintained by balancing selection, and provide a list of candidate genes underlying the specific phenotypes controlled by the two inversions studied here.

The genomics of trait combinations and their influence on adaptive divergence

“…Past studies have suggested that ancestral inversions from disjunct populations in Mexico have spread north via the same geographically variable selection that favors more intense diapause and later diapause termination in the South (Feder, Berlocher, et al, 2003; Feder et al, 2005). Combined, this evidence strongly hints at a prominent role for reduced recombination between co-adapted variants in mediating adaptation, a genomic signature also observed in other systems (Ayala et al, 2019; Coughlan & Willis, 2019; Lowry & Willis, 2010; Noor, Grams, Bertucci, & Reiland, 2001; Wallberg, Schöning, Webster, & Hasselmann, 2017).…”

“…Moreover, adaptation may be facilitated (or constrained) if adaptive traits are genetically correlated through mechanisms such as pleiotropy, high physical linkage, or structural variation (Via and West 2008; Feder et al 2012). Several theoretical models predict that reduced recombination among combinations of alleles within co-adapted gene complexes should promote adaptation and speciation (Feder & Nosil, 2009; Kirkpatrick & Barton, 2006; Navarro & Barton, 2003), though few studies provide rigorous empirical tests (but, see Ayala et al, 2019; Coughlan & Willis, 2019; Ruegg, Anderson, Boone, Pouls, & Smith, 2014). Such tests are necessary to fully resolve the degree to which the genetic basis of trait correlations influences the predictability of evolution, and at least one study presents clear evidence for antagonistic pleiotropy among fitness related traits mediating the predictability of evolutionary response (Troth et al, 2018).…”

Evolution of the insecticide targetRdlin AfricanAnophelesis driven by interspecific and interkaryotypic introgression

“…gambiae populations with high frequencies of 2La/2La karyotypes such as Burkina Faso ( Figure 5C). While it is generally acknowledged that chromosomal inversions strongly suppress recombination (Sturtevant 1917), genetic exchange can occur via double cross-over recombination or gene conversion (Chovnick 1973;Rozas and Aguadé 1994;Andolfatto et al linked to 2La inversions but are exchanged in 2La/2L+ a heterozygotes (Cheng et al 2012;Ayala et al 2019). Another example, possibly linked to gene conversion, could be the APL1 cluster of hyper-variable immune genes: their pattern of sequence variation is more strongly influenced by geography and species (A. gambiae/A.…”

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

“…Only subsequent to the relatively recent molecular characterization of the 2La breakpoint regions [18] did it become possible to develop a reliable PCR-based diagnostic assay [19] that made karyotyping accessible to non-cytogeneticist and allowed the scoring of large numbers of specimens irrespective of gender, life stage, physiological status, or method of specimen storage. Since then, application of this assay has facilitated the study of ecologically relevant phenotypes associated with the 2La inversion in both laboratory and field settings, such as enhanced desiccation resistance and response to thermal stress [20][21][22][23][24][25][26]. Initial cytogenetic observations made decades ago also associated inversion 2La with phenotypes of epidemiological importance, such as susceptibility to Plasmodium infection [27], indoor resting behaviour and response to vector control interventions [2].…”