Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae.

Abstract

November 29, 1995) ABSTRACT Chlorarachniophytes are amoeboid algae with chlorophyll a and b containing plastids that are surrounded by four membranes instead of two as in plants and green algae. These extra membranes form important support for the hypothesis that chlorarachniophytes have acquired their plastids by the ingestion of another eukaryotic plastidcontaining alga. Chlorarachniophytes also contain a small nucleus-like structure called the nucleomorph situated between the two inner and the two outer membranes surrounding the plastid. This nucleomorph is a remnant of the endosymbiont's nucleus and encodes, among other molecules, small subunit ribosomal RNA. Previous phylogenetic analyses on the basis of this molecule provided unexpected and contradictory evidence for the origin of the chlorarachniophyte endosymbiont. We developed a new method for measuring the substitution rates of the individual nucleotides of small subunit ribosomal RNA. From the resulting substitution rate distribution, we derived an equation that gives a more realistic relationship between sequence dissimilarity and evolutionary distance than equations previously available. Phylogenetic trees constructed on the basis of evolutionary distances computed by this new method clearly situate the chlorarachniophyte nucleomorphs among the green algae. Moreover, this relationship is confirmed by transversion analysis of the Chlorarachnion plastid small subunit ribosomal RNA.

Virus‐like, double‐stranded RNAs in the parasitic protozoan Cryptosporidium parvum

“…Cryptosporidium spp. and other Apicomplexa are thought by some researchers to have diverged from a dinoflagellate-like, rather than zooflagellate, ancestor (Van de Peer et al, 1996).…”

The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium , Entamoeba , and Mastigamoeba

“…Variable evolutionary rates generate artificial groupings in the eukaryotic molecular tree (36), because of LBA. Taking into account among-site rate variation through a ⌫ law is known to alleviate the LBA problem (37), which has been successfully shown in the case of the eukaryotic rRNA tree (38). Unfortunately, the covarion-like structure of molecular markers could limit the success of this approach (13).…”

Phylogenetic analyses suggest lateral gene transfer from the mitochondrion to the apicoplast

“…It has been shown previously that the transversion analysis is less sensitive to the substitutional bias (Van de Peer et al, 1996). Again, a tree constructed on the basis of evolutionary distances computed according to Van de Peer et al (1996) shows a tree topology similar to that shown in Fig.…”

“…Since the existence of two different mitochondrial genomes within a single cell was quite implausible, the origin of the 35 kb DNA circle had began to be intensively studied. Based on the close phylogenetic relationship between apicomplexans and dinoflagellates (Cavalier-Smith, 1993; Van de Peer et al, 1996) and the fact that the 35 kb circular molecule has a gene content similar to that of chloroplasts, hypothesis that it represents a highly reduced plastid genome started to emerge. The DNA circle was localized in situ to a multimembranous structure, previously described as a 'spherical body' (e.g.…”