Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum

Jennifer A Brisson,Sergey V Nuzhdin,David L Stern

doi:10.1186/1471-2156-10-22

Jennifer A Brisson, Sergey V Nuzhdin + Show 1 more

Open Access

https://doi.org/10.1186/1471-2156-10-22

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Abstract

BackgroundThe 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.ResultsWe 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 ~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 ~1 kb but reached much lower levels over ~10 kb. Contrary to our expectations, neither LD nor nucleotide diversity were significantly different between native and introduced populations.ConclusionBoth 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.

Highlights

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
Sequence Diversity To measure levels of sequence diversity and linkage disequilibrium (LD) decay over short distances as well as over longer distances, we sequenced two amplicons spaced by about 10 kb at four different genomic regions for 12 clones from New York, 12 clones from California, and 24 clones from Europe (22 clones from France and two clones from Germany)
Sequence Diversity and Linkage Disequilibrium We have investigated the levels of nucleotide diversity and LD across four genomic regions in two introduced pea aphid populations, New York and California, and two host races from native populations in Europe

Summary

Introduction

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. We provide estimates of nucleotide diversity and linkage disequilibrium (LD) in native (European) and introduced (United States) populations of the pea aphid. One important goal of evolutionary biology is to identify the genetic causes of phenotypic variation in wild populations. In large, randomly mating populations where all loci are in linkage equilibrium, genotype can be connected to phenotype by assaying every DNA polymorphism and associating those polymorphisms with phenotypic variation [1]. LD can be exploited, to identify genomic regions, rather than individual nucleotides, that are associated with phenotypic variation [e.g., [2]]. The scale at which polymorphisms must be sampled depends on the level and decay of LD across the genome. Higher levels of LD allow shallower sampling of polymorphisms, but provide reduced resolution for locating causal (page number not for citation purposes)

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