| Method |
P.2 right column 2nd paragraph: "In order to obtain additional evidence for a large-scale or genome-wide duplication in P. patens, as well as to date this duplication event, [investigators] constructed linearized trees (see Methods). [They] constructed neighbor-joining trees for 487 gene families which contained two to ten P. patens genes, one Chlamydomonas reinhardtii or Ostreococcus tauri gene as an outgroup sequence, and genes from at least two different seed plants (Arabidopsis thaliana, poplar, or rice) as reference points. Sequences that were evolving too fast or too slow were removed, after which linearized trees, in which branch lengths are directly proportional to time, were constructed for each gene family [refs 29, 30]. This left 330 trees, and after removing nodes with bootstrap values < 70%, [they] obtained 179 nodes representing the duplication events of P. patens in 159 trees that could be used for dating the gene duplications in P. patens by comparing the time of duplication with the time of speciation between A. thaliana and poplar, assumed 100 MYA [ref 31] and A. thaliana or poplar and rice, assumed 150 MYA [ref 32] (see Figure 1B)." |
| Comments |
P.2 right column 3rd paragraph: "Next, [investigators] plotted the estimated dates of the 179 P. patens duplication events, which are shown in Figure 1C. As can be clearly observed, a majority of the gene duplicates seem to have been created between 30–60 MYA (average 45 MYA), indicating that a large-scale gene duplication or a whole-genome duplication is indeed likely to have occurred around this time. Although using two different calibration dates (100 MYA for the Arabidopsis-poplar split, and 150 MYA for the monocot-eudicot split) may affect the age distribution if one of the two calibration dates is unrealistic compared to the other, age distributions obtained for each calibration point separately were very similar (data not shown), suggesting that the dates of 100 MYA and 150 MYA [refs 31, 32] are in good agreement with inferred dates from tree topologies." |