@article{cork_purugganan_2005, title={High-diversity genes in the Arabidopsis genome}, volume={170}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.104.036152}, abstractNote={High-diversity genes represent an important class of loci in organismal genomes. Since elevated levels of nucleotide variation are a key component of the molecular signature for balancing selection or local adaptation, high-diversity genes may represent loci whose alleles are selectively maintained as balanced polymorphisms. Comparison of 4300 random shotgun sequence fragments of the Arabidopsis thaliana Ler ecotype genome with the whole genomic sequence of the Col-0 ecotype identified 60 genes with putatively high levels of intraspecific variability. Eleven of these genes were sequenced in multiple A. thaliana accessions, 3 of which were found to display elevated levels of nucleotide polymorphism. These genes encode the myb-like transcription factor MYB103, a putative soluble starch synthase I, and a homeodomain-leucine zipper transcription factor. Analysis of these genes and 4–7 flanking genes in 14–20 A. thaliana ecotypes revealed that two of these loci show other characteristics of balanced polymorphisms, including broad peaks of nucleotide diversity spanning multiple linked genes and an excess of intermediate-frequency polymorphisms. Scanning genomes for high-diversity genomic regions may be useful in approaches to adaptive trait locus mapping for uncovering candidate balanced polymorphisms.}, number={4}, journal={GENETICS}, author={Cork, JM and Purugganan, MD}, year={2005}, month={Aug}, pages={1897–1911} }
 @article{shimizu_cork_caicedo_mays_moore_olsen_ruzsa_coop_bustamante_awadalla_et al._2004, title={Darwinian selection on a selfing locus (Retracted Article. See vol 320, pg 176, 2008)}, volume={306}, ISSN={["1095-9203"]}, DOI={10.1126/science.1103776}, abstractNote={The shift to self-pollination is one of the most prevalent evolutionary transitions in flowering plants. In the selfing plant Arabidopsis thaliana, pseudogenes at the SCR and SRK self-incompatibility loci are believed to underlie the evolution of self-fertilization. Positive directional selection has driven the evolutionary fixation of pseudogene alleles of SCR, leading to substantially reduced nucleotide variation. Coalescent simulations indicate that this adaptive event may have occurred very recently and is possibly associated with the post-Pleistocene expansion of A. thaliana from glacial refugia. This suggests that ancillary morphological innovations associated with self-pollination can evolve rapidly after the inactivation of the self-incompatibility response.}, number={5704}, journal={SCIENCE}, author={Shimizu, KK and Cork, JM and Caicedo, AL and Mays, CA and Moore, RC and Olsen, KM and Ruzsa, S and Coop, G and Bustamante, CD and Awadalla, P and et al.}, year={2004}, month={Dec}, pages={2081–2084} }
 @misc{cork_purugganan_2004, title={The evolution of molecular genetic pathways and networks}, volume={26}, ISSN={["1521-1878"]}, DOI={10.1002/bies.20026}, abstractNote={There is growing interest in the evolutionary dynamics of molecular genetic pathways and networks, and the extent to which the molecular evolution of a gene depends on its position within a pathway or network, as well as over‐all network topology. Investigations on the relationships between network organization, topological architecture and evolutionary dynamics provide intriguing hints as to how networks evolve. Recent studies also suggest that genetic pathway and network structures may influence the action of evolutionary forces, and may play a role in maintaining phenotypic robustness in organisms. BioEssays 26:479–484, 2004. © 2004 Wiley Periodicals, Inc.}, number={5}, journal={BIOESSAYS}, author={Cork, JM and Purugganan, MD}, year={2004}, month={May}, pages={479–484} }