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Lineage specific duplicates are distinguished by numbers (in species without the fish-specific duplication) or by letters (with fish-specific duplication); however, the numbers or letters do not infer orthology relationships (see Figure 1 and Additional files 1, 2, 11, and 13: Tables S1 and S2 and Figures S8 and S10).
As lineage specific duplicates are often found to be the subject to adaptive evolution [11] [13] these genes offer and exciting insight into the specific biology of T. brucei and were investigated further.
It does not contain any extra fish specific duplicates.
Since screening was database specific, duplicates were only removed once this process was complete.
They may then represent specific duplicates of kcna genes in the amphioxus lineage.
We find that 3R specific duplicates can be observed outflanking each pair of Acsl duplicates (Casp3, Ephb1 and Stag2).
Similar(50)
The other three gene orders were derived from the duplicate tRNAThr CR gene order by further degenerations or deletions of one copy of specific duplicated genes.
To test the hypothesis that lineage specific expansion (LSE) of gene families enhances adaptation we compared positive (Darwinian) selection footprints in lineages containing recent and specific duplicated genes to reference lineages containing only single-copy genes.
Based on the phyletic patterns and following the nomenclature for NASP paralogs already established for Caenorhabditis lineages, we designated the two paralogs as NASP1 and NASP2 for each of the lineage specific duplicated genes.
Second, the cellulase genes evolve dynamically by gene duplications as indicated by species-specific duplicates in P. pacificus, P. sp. 11 and P. sp. 15, respectively.
For both superfamilies, the lineage-specific duplicates are often physically linked, suggesting that they have been produced by tandem duplication, an apparently frequent event in the evolutionary lineage leading to Nematostella vectensis.
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