@misc{lihova_shimizu_marhold_2006, title={Allopolyploid origin of Cardamine asarifolia (Brassicaceae): Incongruence between plastid and nuclear ribosomal DNA sequences solved by a single-copy nuclear gene}, volume={39}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2006.01.027}, abstractNote={Interspecific hybridization and polyploidization have played central roles in plant diversification. However, technical difficulties in the analyses of low-copy genes have limited the study of the origins of hybrid and polyploid plants. Here, we present a phylogenetic analysis of the hexaploid Cardamine asarifolia, distributed in the southern European Alps and northern Apennines. Our study included all relevant taxa of the genus found in Europe. A marked discrepancy was revealed between the trnL–trnF region of cpDNA and internal transcribed spacer (nrDNA ITS) sequences. To solve the incongruence, we sequenced a single-copy nuclear CHS gene (chalcone synthase) using a novel method to design homoeologue-specific PCR primers to bypass artefacts caused by artificial recombination of homoeologues during PCR and/or cloning. Three homoeologues were isolated from C. asarifolia, providing evidence for its allopolyploid origin. One homoeologue, showing the same phylogenetic position as the ITS sequences, most likely originated from an extinct parent. Furthermore, we documented recurrent polytopic hybridizations between C. asarifolia and diploid C. amara. The allohexaploidization and the following hybridization with a diploid species exemplify the ongoing dynamic processes of speciation in the genus Cardamine.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Lihova, Judita and Shimizu, Kentaro K. and Marhold, Karol}, year={2006}, month={Jun}, pages={759–786} }
 @article{shimizu_2006, title={Evolutionary Genomics (Evolutionary and Ecological Functional Genomics) -- the power of Arabidopsis thaliana to study adaptive evolution}, volume={56}, ISBN={0021-5007}, number={1}, journal={Japanese Journal of Ecology}, author={Shimizu, K.}, year={2006}, pages={28} }
 @article{shimizu_purugganan_2005, title={Evolutionary and ecological genomics of arabidopsis}, volume={138}, ISSN={["1532-2548"]}, DOI={10.1104/pp.105.061655}, abstractNote={Why are some plants self-pollinating? What determines the timing of flowering and germination? Why do resistant and susceptible alleles of pathogen-resistant genes coexist in populations? These are just a few questions traditionally asked in the domain of ecology and evolutionary biology, and}, number={2}, journal={PLANT PHYSIOLOGY}, author={Shimizu, KK and Purugganan, MD}, year={2005}, month={Jun}, pages={578–584} }
 @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} }