evolution; climate change; mating system; genome-wide association study; adaptation
Takeuchi Yayoi, Chaffron Samuel, Salcher Michaela M., Shimizu-Inatsugi Rie, Kobayashi Masaki J., Diway Bibian, von Mering Christian, Pernthaler Jakob, Shimizu Kentaro K. (2015), Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes, in Systematic and Applied Microbiology
, 38(5), 330-339.
Tedder Andrew, Carleial Samuel, Gołębiewska Martyna, Kappel Christian, Shimizu Kentaro K, Stift Marc (2015), Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae)., in PloS one
, 10(6), 0126618-0126618.
Tedder Andrew, Helling Matthias, Pannell John R, Shimizu-Inatsugi Rie, Kawagoe Tetsuhiro, van Campen Julia, Sese Jun, Shimizu Kentaro K (2015), Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae)., in Annals of botany
, 115(5), 763-76.
Kubo Ken-ichi, Paape Timothy, Hatakeyama Masaomi, Entani Tetsuyuki, Takara Akie, Kajihara Kie, Tsukahara Mai, Shimizu-Inatsugi Rie, Shimizu Kentaro K (corresponding author), Takayama Seiji (corresponding author) (2015), Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia, in Nature Plants
, 1(1), 14005.
Akama Satoru, Shimizu-Inatsugi Rie, Shimizu Kentaro K, Sese Jun (2014), Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis., in Nucleic acids research
, 42(6), 46-46.
Zozomová-Lihová Judita, Krak Karol, Mandáková Terezie, Shimizu Kentaro K, Spaniel Stanislav, Vít Petr, Lysak Martin A (2014), Multiple hybridization events in Cardamine (Brassicaceae) during the last 150 years: revisiting a textbook example of neoallopolyploidy., in Annals of botany
, 113(5), 817-30.
Tsuchimatsu Takashi, Shimizu Kentaro K. (2013), Effects of pollen availability and the mutation bias on the fixation of mutations disabling the male specificity of self-incompatibility, in Journal of Evolutionary Biology
Mandakova Terezie, Kovarik Ales, Zozomova-Lihova Judita, Shimizu-Inatsugi Rie, Shimizu Kentaro K., Mummenhoff Klaus, Marhold Karol, Lysak Martin A. (2013), The More the Merrier: Recent Hybridization and Polyploidy in Cardamine, in PLANT CELL
, 25(9), 3280-3295.
Shimizu Kentaro K (2012), Chapter 12 Overview: the evolution of genes responsible for adaptation, in Morinaga Shinichi, Kudoh Hiroshi (ed.), Kyoritsu, Tokyo, Japan, Tokyo, 189-196.
Shimizu-Inatsugi Rie, Shimizu Kentaro K (2012), Chapter 16: Genome duplication - speciation and ecogenomics of polyploid species, in Morinaga Shinichi, Kudoh Hiroshi (ed.), Kyoritsu, Tokyo, Japan, Tokyo, 246-262.
Tsuchimatsu Takashi, Kaiser Pascal, Yew Chow-Lih, Bachelier Julien B, Shimizu Kentaro K (2012), Recent Loss of Self-Incompatibility by Degradation of the Male Component in Allotetraploid Arabidopsis kamchatica., in PLoS genetics
, 8(7), 1002838-1002838.
A central question in biology is the molecular basis of biodiversity. Rapid advances in next-generation sequencing are providing novel tools for addressing key ecological and evolutionary questions in integrated biological sciences. However, the study of adaptive molecular variation has been largely limited to model species. Therefore, general patterns in molecular adaptation and speciation remain unclear, but their discovery is essential to enable understanding and prediction of biological responses to naturally and artificially changing environments. Studying adaptive evolution that occurred many times in parallel is an appropriate approach to investigating recurring patterns.Since our precursor projects (2008-2011, 2011-2012), we have studied the evolution of selfing in Arabidopsis thaliana, and polyploid speciation of A. kamchatica and Cardamine spp. This proposal represents an extension of these earlier projects, and focuses on the evolution of selfing through loss of self-incompatibility (which is considered one of the most frequent evolutionary shifts in flowering plants) and its relationship to speciation by genome duplication. We address the following questions regarding general patterns in the evolution of selfing.Q1. Were mutations in the same genes responsible for the evolution of selfing in different species? In particular, were mutations in the male component of self-incompatibility spread frequently, as predicted by evolutionary theory?Q2. Which type of mutations (regulatory, amino-acid-changing or loss-of-function) contributed to the evolution of selfing?Q3. Are major- or minor-effect mutations more prevalent?Q4. Are dominant, recessive or co-dominant mutations the most prevalent?Q5. Did the evolution of self-compatibility occur recurrently during a particular geological period (the recent glacial-interglacial cycle)?Q6. Does genome duplication or polyploid speciation affect the processes noted above? More specifically, is the epistatic interaction between duplicated loci relevant in the evolution of self-incompatibility genes and other genes?Based on preliminary results, the research plan is divided into four parts. First, we will conduct functional studies of the evolution of self-compatibility in the allopolyploid A. kamchatica. Second, genome-wide polymorphisms in A. kamchatica will be assayed to assess the evolutionary forces and epistatic interactions underlying self-compatibility and other traits. Third, using these data, we will conduct genome-wide association studies (GWASs) in A. thaliana and A. kamchatica to investigate the coordinated sets of floral traits of selfing species, referred to as “selfing syndrome”. Fourth, we will investigate the evolution of self-compatibility in the autopolyploid species Cardamine amara subsp. austriaca.It is noteworthy that plant sexual reproduction may be particularly vulnerable to the effects of natural and artificial environmental changes, through evolutionary and plastic responses. A broad impact of this proposal to the society would be to reinforce our previous key research finding that climate change, including glacial cycles, may induce rapid-and possibly irreversible-evolution.