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The topology of the position-based tree is compatible with that of a sequence-based tree, if low support nodes are ignored, where the root has been manually placed between monocot and eudicot expansins Fig. In conclusion, the analysis of the poplar expansin superfamily reinforces our confidence in the existence of 17 expansin clades in angiosperms that have been independent since the last ancestor of eudicots and monocots.
The bootstrap for this node is low 62 and clade EXPA-X appears at the end of a very long branch that might cause rooting problems. All of these clades are represented in the genome of P.
Segments with expansins are underlined, and the name of the expansin gene is shown below the underlining. Furthermore, when we added the P. Dashed lines indicate polyploidy events detected in the Arabidopsis genome. On the basis of expansin phylogenetic trees, the two poplar segments are shown as the product of a poplar-specific segmental duplication.
In contrast, three Arabidopsis expansin duplications have been attributed to this event: In our previous work we had contemplated the possibility that this clade could actually be the monocot branch of clade EXPA-XII, which is only known from eudicots.
Previous datings of the Arabidopsis genome duplications in relation with the divergence of different lineages did not include P.
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There are no cases of two branches in poplar whose divergence can be clearly attributed to this event. When poplar expansins are added to the neighbor-joining tree, the topology of this clade still shows the same pattern, OsEXPA7 appears nested deep inside the clade, although support for many branches is now very low Fig.
The position of P. This idea is supported by the high ratio of nonsynonymous Ka to synonymous Ks substitution rates observed in pairwise comparisons that include AtEXPA9 Fig.
White boxes indicate the loss of an expansin gene. Other questions are still left open. An important issue is the dating of the divergence of the Arabidopsis and poplar lineages with respect to the polyploidy events previously detected in the Arabidopsis genome.
Thus, it seems that the grouping of these two clades in our previous work was an artifact of long-branch attraction Felsenstein We still believe that the more parsimonious hypothesis is to assume that the root of the clade in family-wide trees is misplaced on account of accelerated rates of evolution in several branches, particularly AtEXPA9.
This suggests that the separation between the two monocot-eudicot clades might have been the product of an ancient tandem duplication or a small-scale segmental duplication. On the basis of position-based phylogeny, we also proposed in our previous study that clade EXPA-IV has a similar rooting problem in sequence-based trees due to divergent branches in the Arabidopsis lineage Sampedro et al.
In the case of genome duplicationthe expansin phylogenetic trees are not very informative. On the basis of an analysis of EST collections Sterck et al.
When the poplar sequences from these two clades are added, the eudicot members of both clades no longer appear as a monophyletic group in either Bayesian or parsimony trees data not shown. Finally, we found no evidence in P.
Synteny diagrams are provided in the ESM S2. Combining these results with our previous analysis of synteny between Arabidopsis and rice, we obtained a position-based tree for the expansins in clade EXPA-IV present in the three sequenced genomes Fig. Poisson correction with complete deletion of gaps was used to calculate protein distances.
Segments with expansins are underlined and the name of the expansin gene shown below the underlining. Based on their short branch length, many of the duplications appear to be recent.
This makes the discovery of many new monocot-eudicot clades very unlikely.
Event is specific to the Arabidopsis lineage, event is common to both lineages and the dating of event is uncertain. The branches represented in Fig. A black circle indicates a segmental duplication in tandem. Bootstrap values are based on iterations. Segments are identified by the species abbreviation, chromosome number and a letter when necessary.
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