title: Widespread selection across coding and noncoding DNA in the pea aphid genome.
abstract: Genome-wide patterns of diversity and selection are critical measures for understanding how evolution has shaped the genome. Yet, these population genomic estimates are available for only a limited number of model organisms. Here we focus on the population genomics of the pea aphid (Acyrthosiphon pisum). The pea aphid is an emerging model system that exhibits a range of intriguing biological traits not present in classic model systems. We performed low-coverage genome resequencing of 21 clonal pea aphid lines collected from alfalfa host plants in North America to characterize genome-wide patterns of diversity and selection. We observed an excess of low-frequency polymorphisms throughout coding and noncoding DNA, which we suggest is the result of a founding event and subsequent population expansion in North America. Most gene regions showed lower levels of Tajima's D than synonymous sites, suggesting that the majority of the genome is not evolving neutrally but rather exhibits significant constraint. Furthermore, we used the pea aphid's unique manner of X-chromosome inheritance to assign genomic scaffolds to either autosomes or the X chromosome. Comparing autosomal vs. X-linked sequence variation, we discovered that autosomal genes show an excess of low frequency variants indicating that purifying selection acts more efficiently on the X chromosome. Overall, our results provide a critical first step in characterizing the genetic diversity and evolutionary pressures on an aphid genome.
authors.affiliation: University of Nebraska, School of Biological Sciences, Lincoln, Nebraska 68588, USA. rbickel2@unl.edu
authors.forename: Ryan D
authors.initials: RD
authors.lastname: Bickel
authors.forename: Joseph P
authors.initials: JP
authors.lastname: Dunham
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Brisson
mesh_terms: D000818:Animals; D001042:Aphids / Q000235:genetics* / Q000254:growth & development; D002140:California; D059006:Chromosomes, Insect / Q000235:genetics; D004247:DNA / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics*; D005260:Female; D017344:Genes, Insect / Q000235:genetics; D050172:Genes, X-Linked / Q000235:genetics; D049750:Genome, Insect / Q000235:genetics*; D008018:Life Cycle Stages / Q000235:genetics; D008297:Male; D009511:New England; D016366:Open Reading Frames / Q000235:genetics*; D018532:Pisum sativum / Q000469:parasitology*; D011110:Polymorphism, Genetic; D012150:Polymorphism, Restriction Fragment Length; D012641:Selection, Genetic; D014960:X Chromosome / Q000235:genetics
chemical_list: D021901:DNA, Intergenic; D004247:DNA
keywords: Acyrthosiphon; pea aphid; population genomics; selection; sex chromosome