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Significance was set at P<0.01 for all analyses, with a Bonferroni correction of 5 and 36 for the maximum landmarks and maximum taxa (including ecological splits) datasets, respectively, to account for repeated use of the same data.
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Alternatively, the maximum deviation across taxa was used as a global statistic.
During our work, we set an approximate maximum of 1,500 taxa and 100,000 sites.
Here we have expanded the analysis of ZP2 to include 18 taxa (maximum previously tested = 8 [ 31]).
Minimum and maximum number of taxa in a trees and average number of genes per taxon can also be chosen to sample differing levels of gene family complexity.
The degree of range expansion or lineage mixing after the last glacial maximum varies among taxa and may reflect species level differences in dispersal ability, reproductive strategy, competitive ability, or habitat requirements.
We strongly suggest that anyone contemplating research in this area should consider studying these exemplar taxa, for maximum comparability with existing data.
Phylogenetic analysis of six Halicephalobus sequences and four outgroup taxa by maximum parsimony yielded one tree with five well-supported clades.
As taxonomic ranks are not equivalent among different groups of organisms, the maximum molecular divergence among taxa sharing a common gene arrangement in this genome segment was compared.
Each of the included taxa has maximum 70% missing characters (for further information about the taxa and included genes, see supporting Table 1).
In the following we thus do not use the 16S data further to discuss the distribution of sequence divergences among birds, but report the cob data as a complement to cox1 in order to base our comparisons on the maximum available number of taxa.
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