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Open Access Open Badges Research article

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

Jennifer A Brisson14*, Sergey V Nuzhdin2 and David L Stern3

Author Affiliations

1 Section of Ecology and Evolution, University of California at Davis, Davis, CA, USA

2 Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA

3 Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA

4 Current address: Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA

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BMC Genetics 2009, 10:22  doi:10.1186/1471-2156-10-22

Published: 26 May 2009



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.


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 ~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.


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.