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A phylogenetic analysis of PRAME/PRAMEY orthologs in Eutheria identified two major clades, which were subject to diverse selection pressures.
Subsequently, the family has been divided into four major clades, which were recognized as four subgenera [5] and eventually elevated to four genera [3], [6], [7].
Heliconius species fall evenly into two major clades which correspond exactly with mating system [ 13].
The subgenus Agrodiaetus comprises 6 major clades which are in agreement with COI analyses.
As discussed below, these GH5 and GH18 sequences represent major clades which are missing in Arabidopsis.
MaSODs were clustered into three major clades, which showed a good accordance with their metal cofactor types.
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There was one major clade which formed two distinct clusters, encompassing the majority of equid DQA alleles, but also a second smaller, more divergent clade comprised of 6 alleles.
PP2Cs were found to be distributed into several sub-clades inside a major clade, which divide this family into various subfamilies.
Genome sizes and number of duplicated genes within the major clade, which comprises species of varying complexity and choice of habitat (including marine and freshwater, unicellular and filamentous and heterocystous species) evolve at a higher evolutionary rate than the clade of marine picocyanobacteria.
Several major CBC clades, which are based on ancient CBC events, contain nested CBC clades that originated by more recent CBCs.
Figure 4B shows the maximum likelihood transformations for major host clades, which mostly correspond to family-level classification of crinoids and also include Asteroidea de Blainville, 1830 and Ophiuroidea Gray, 1840.
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