Systems genetic analysis of inversion polymorphisms in the malaria mosquitoAnopheles gambiae

Changde Cheng, John C. Tan, Matthew W. Hahn, Nora J. Besansky
2018 Proceedings of the National Academy of Sciences of the United States of America  
Inversion polymorphisms in the African malaria vector Anopheles gambiae segregate along climatic gradients of aridity. Despite indirect evidence of their adaptive significance, little is known of the phenotypic targets of selection or the underlying genetic mechanisms. Here we adopt a systems genetics approach to explore the interaction of two inversions on opposite arms of chromosome 2 with gender, climatic conditions, and one another. We measure organismal traits and transcriptional profiles
more » ... riptional profiles in 8-d-old adults of both sexes and four alternative homokaryotypic classes reared under two alternative climatic regimes. We show that karyotype strongly influences both organismal traits and transcriptional profiles but that the strength and direction of the effects depend upon complex interactions with gender and environmental conditions and between inversions on independent arms. Our data support the suppressed recombination model for the role of inversions in local adaptation, and-supported by transcriptional and physiological measurements following perturbation with the drug rapamycin-suggest that one mechanism underlying their adaptive role may be the maintenance of energy homeostasis. Anopheles gambiae | aridity | chromosomal inversion | climate adaptation | systems genetics C hromosomal inversions are structural mutations causing reversals of gene order arising when a chromosome breaks in two places and rejoins after a 180°rotation. Pioneering population studies of inversions relied on polytene chromosomes found in Drosophila and other dipterans, but the postgenomic era is revealing that inversions have much wider evolutionary impacts across the tree of life (1-4). While direct phenotypic consequences of these mutations can arise from lesions in coding sequences, the creation of fusion genes, or altered regulatory context at inversion breakpoints (5-8), it is their indirect effect on crossing-over that is thought to drive sex chromosome evolution, local adaptation, and speciation (9-12). In inversion heterozygotes, crossing-over between alternative orientations is effectively suppressed (13), due both to physical constraints and to aneuploid recombinant gametes. As a result, beneficial allelic combinations captured by and/or arising on the inverted orientation are protected against homogenization with genetic backgrounds on the opposite (standard) orientation. Under spatially varying selection, suppressed recombination in polymorphic inversions may facilitate local adaptation to environmental heterogeneities even in the face of migration and gene flow (3, 9, 14) . Owing to a rich historical tradition and powerful genetic tools, the most extensive evidence that inversions are adaptive and may be the targets of natural selection comes from studies of the genus Drosophila (1, 4) , although evidence from outside this genus is mounting (e.g., refs. 15-20). In Drosophila melanogaster, latitudinal and altitudinal clines in inversion frequencies associated with climatic variation have persisted over decades despite unimpeded population connectivity (21). Clines have both shifted in response to climate change and formed in parallel on multiple continents. Within localities, inversion frequencies cycle predictably with the season. Moreover, inversion polymorphism has been associated with a variety of fitness-related and ecologically relevant traits, including heat and cold tolerance, desiccation resistance, growth rate, body size, fecundity, and longevity (1, 4) . Population genomic studies of clinal inversion polymorphisms have revealed patterns of nucleotide variation consistent with an adaptive role for inversions (22, 23) . Although the genic targets of selection and the molecular mechanisms underlying inversionassociated phenotypes remain unresolved in most systems (24), there has been some recent progress in the Drosophila model. Using distinctly different species and experimental designs, two studies investigating the effect of chromosomal inversions on patterns of gene expression reached remarkably similar conclusions: (i) inversions significantly affected the transcript abundance of numerous genes, (ii) inversion-affected transcripts were overrepresented inside inverted regions but were not exclusive to these regions, and (iii) there was scant evidence of direct (position) effects near breakpoints (6, 8) . These observations support a model of local adaptation premised on the indirect effect of recombination suppression maintaining combinations of differentially expressed genes (DEGs). Functions enriched among inversion-affected genes included chemoreception (8) and Significance Chromosomal inversions play an important role in local adaptation. Strong evidence exists of selection acting on inversions, but the genic targets inside them are largely unknown. Here we take a systems genetics approach, analyzing two inversion systems implicated in climatic adaption by Anopheles gambiae. We profiled physiology, behavior, and transcription in four different karyotypic backgrounds derived from a common parental colony. Acclimation to different climatic regimes resulted in pervasive inversion-driven phenotypic differences whose magnitude and direction depended upon gender, environment, and epistatic interactions between inversions. Inversion-affected loci were significantly enriched inside inversions, as predicted by local adaptation theory. Drug perturbation supported lipid homeostasis and energy balance as inversion-regulated functions, a finding supported by research on climatic adaptation in multiple systems.
doi:10.1073/pnas.1806760115 pmid:29987007 fatcat:dr5hvlqw45fpzpna3ikqviqbvy