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The 184 species go back to at least 70 ancestors, the 56 to at least 35, numbers obtained by counting the genera in Tables S5 and 6 and adding the number of independent transitions to hummingbird pollination within Penstemon (Plantaginaceae; [ 18]) and Lithospermum (Boraginaceae, cf. chronogram with pollinator coding and inferred transitions in Additional file 3: Figure S2e).
The number of inferred transitions are reduced to five, if clades b and c in Figure 2, which are reconstructed with low support, are collapsed, and Cnemophilus is placed as sister to the 'core Corvoidea' clade (Additional file 2).
"Markov jumps" analyses (27, 28) were used to count inferred transitions from one state to another (e.g., from livestock to human host or from absence to presence of a particular resistance gene).
There was a smaller number of inferred transitions from Scotland to other countries (median = 6; 95% HPD interval = [0, 20]), although there was some overlap between the 95% HPD intervals for the number of jumps in and out of Scotland.
Across the evolutionary history of CC398, there were more inferred transitions from livestock hosts to humans than from humans to livestock (median = 14, 95% HPD = [12, 21] for livestock to humans; median = 2, 95% HPD = [1, 9] for humans to livestock) (Fig. 2).
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For each population of ancestry p, we define an HMM M p) that has a state for each haplotype in each block, inferring transitions between haplotypes and haplotype content using standard software.
A larger number of modules would be able to distinguish finer patterns, but is also more prone to overfitting, to separating co-regulated genes into separate modules, and to inferring "transitions" between modules that are erroneous, thus over estimating divergence.
The FUV studied with FUSE to infer transition-region magnetic activity (Guinan et al., 2003).
Several studies suggest that when a character change has en effect on speciation, inferring transition rates for this character can lead to erroneous conclusions [ 30].
Holocentric insect orders are indicated in blue, and inferred multiple transitions to holocentricity in insects are labeled with 'H'.
For instance, analyses of habitat preference inferred 4 transitions between open and forested habitats for the tribe Oryzomyini ([ 22, 23]).
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