Phylogenetically Independent Contrasts

Garland, T. Jr., P.H. Harvey, and A.R. Ives (1992). Procedures for the analysis of comparative data using phylogenetically independent contrasts. System. Biol. 41 18-32. 

H3 replacement variants are also present in plants [108] and Tetrahymena [109]. Phylogenetic analyses indicates that these H3 replacement variants arose independently of animal H3.3 [109]. Like H3.3, the plant H3 replacement variant also appears to be preferentially deposited into transcriptionally active chromatin [110]. The H3 replacement variant in Tetrahymena, hv2, is found only in the transcriptionally active macronucleus [49]. In contrast to H3.3, the amino acid differences between hv2 and the replication dependent H3 of Tetrahymena do not appear to be essential for replication independent incorporation into chromatin [111]. In this case constitutive expression appears to be the dominant factor that can drive replication independent deposition of hv2 or an H3 variant that is normally replication dependent. This difference between hv2 and H3.3 is not necessarily surprising because hv2 appears to have arisen independently of H3.3 and does not have the structural features characteristic of H3.3 [109]. 

Phylogenetic studies have shown that the cis- and trans-AI PKSs have evolved independently from FASs and, although both systems appear very similar, the tvans-AT PKSs harbour far more enzymatic functionality than their cis-AT counterparts [27, 28]. As a result, many more module variations exist for trans-AI systems. Eight modnle variants are known for cis-AT PKSs KS-AT-ACP, KS-AT-KR-ACP, KS-AT-DH-KR-ACP, KS-AT-DH-KR-ER-ACP and their MT-based ana-lognes. In contrast, over 50 module architectures have already been identified in trans-AT PKSs [15]. 

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