Inferring species tree using rice genomes ========================================= History ------- Fri Jun 10 14:27:43 EDT 2011 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The genome sequence was downloaded. Abstract -------- Recently, rice genomes were sequenced in multiple individuals spanning three species. The phylogenetic relationship of these could have been resolved using the data set. The method developed in BEAST was not able handle the data set presumably because the sequence data were not informative enough. Instead, the authors (Molina 2011) used site-frequency spectrum to sidestep the problem. They took advantage of other data sets not the data set they obtained. Here, we consider that Methods and Materials --------------------- We downloaded the rice DNA sequences at http://puruggananlab.bio.nyu.edu/Rice_data/RiceScan.zip. Introduction ------------ .Parts that I need to consider. . Three rice species. . Inferring species tree. .. *BEAST References ---------- . Molina, J.; Sikora, M.; Garud, N.; Flowers, J. M.; Rubinstein, S.; Reynolds, A.; Huang, P.; Jackson, S.; Schaal, B. A.; Bustamante, C. D.; Boyko, A. R. & Purugganan, M. D., 2011 Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci U S A 108: 8351-8356.