title: Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum.
abstract: BACKGROUND
  The pea aphid, Acyrthosiphon pisum, is an emerging genomic model system for studies of polyphenisms, bacterial symbioses, host-plant specialization, and the vectoring of plant viruses. Here we provide estimates of nucleotide diversity and linkage disequilibrium (LD) in native (European) and introduced (United States) populations of the pea aphid. Because introductions can cause population bottlenecks, we hypothesized that U.S. populations harbor lower levels of nucleotide diversity and higher levels of LD than native populations.
  
  
  RESULTS
  We sampled four non-coding loci from 24 unique aphid clones from the U. S. (12 from New York and 12 from California) and 24 clones from Europe (12 alfalfa and 12 clover specialists). For each locus, we sequenced approximately 1 kb from two amplicons spaced approximately 10 kb apart to estimate both short range and longer range LD. We sequenced over 250 kb in total. Nucleotide diversity averaged 0.6% across all loci and all populations. LD decayed slowly within approximately 1 kb but reached much lower levels over approximately 10 kb. Contrary to our expectations, neither LD nor nucleotide diversity were significantly different between native and introduced populations.
  
  
  CONCLUSIONS
  Both introduced and native populations of pea aphids exhibit low levels of nucleotide diversity and moderate levels of LD. The introduction of pea aphids to North America has not led to a detectable reduction of nucleotide diversity or increase in LD relative to native populations.
authors.affiliation: Section of Ecology and Evolution, University of California at Davis, Davis, CA, USA. jennifer.brisson@gmail.com
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Brisson
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Nuzhdin
authors.forename: David L
authors.initials: DL
authors.lastname: Stern
mesh_terms: D000818:Animals; D001042:Aphids / Q000235:genetics*; D005060:Europe; D014644:Genetic Variation; D005828:Genetics, Population; D054643:INDEL Mutation; D015810:Linkage Disequilibrium; D009656:North America; D009711:Nucleotides / Q000235:genetics
chemical_list: D009711:Nucleotides