Phylogenetically Independent

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]. 

There exists a rather broad agreement that the anaerobic ciliates evolved secondarily from aerobic ancestors since several ciliate taxa comprise both aerobic and anaerobic species. Phylogenetic studies indicate that hydrogenosomes have arisen independently at least three to four times in ciliates (Fig. 1 Clarke et al. 1993 Embley and Finlay 1994 Embley et al. 1995, 2003 Fenchel and Finlay 1995 Hirt et al. 1998 Hackstein et al. 2001,2002). The existence in... 

Independent recruitment ot catalytic groups in different phylogenetic lineages to produce the same type of high-activity enzyme... 

Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology 180 4765-4774. 

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