Among them, there are 16 cases (classified as group 1) that showed both asymmetric sequence rate evolution and expression gain, inferred by the MRCA expression analysis (table 1), further supporting our inference of neofunctionalization.
For efficiency, we then averaged the matrices across SNPs between which GAIN inferred no recombination in the population, and this reduced the mapping dataset to 27,059 intervals.
Forty-two of the 124 genes gained inferred to have been gained in a common ancestor of L. grayi and Listeria sensu strictu were associated with GO terms relating to flagellar biosynthesis.
The non-clock like character of gene gain inferred on a longer timescale [ 19] implies that such periods could be short but would involve massive amounts of genetic material, making detection of such episodes through comparative analysis of tight groups of microbes unlikely.
But Mr Krugman simply repeats that the top 1% and.1% have seen outsized gains, infers from this that "we've become an oligarchy" and then stops.
Indeed, many likely paralog-specific gains are inferred.
Intron losses or gains were inferred by parsimony, taking into account the phylogenetic relationships between the species harboring an intron at a given position.
Massive intron gains were inferred only for several deep branches, most conspicuously the stem of the Metazoa, and to a lesser extent, the stems of Mamiellales (a branch of green algae), Viridiplantae, Opisthokonta, and Metazoa together with Choanoflagellata.
Similar proportions of gene gains are inferred to result from duplication and acquisition by gene transfer across the genus, although duplication is more frequent among recent gains (singleton genes), consistent with the hypothesis that although transient duplication events may be relatively frequent, fixation of exogenous genetic is more probable than fixation of duplicated material.
