Sister Class Research Articles

A REASSESSMENT OF PHYLOGENETIC RELATIONSHIPS WITHIN THE PHAEOPHYCEAE BASED ON RUBISCO LARGE SUBUNIT AND RIBOSOMAL DNA SEQUENCES

To better assess the current state of phaeophycean phylogeny, we compiled all currently availablerbcL, 18S, and 26S rDNA sequences from the EMBL/GenBank database and added 21 newrbcL sequences of our own. We then developed three new alignments designed to maximize taxon sampling while minimizing information loss due to partial sequences. Phylogenetic analyses were performed on separate and combined data sets (with and without taxa from the sister classes Tribophyceae and Phaeothamniophyceae as outgroups) using a variety of assumption sets, tree‐drawing algorithms (parsimony, neighbor joining, and likelihood), and resampling methods (bootstrap, decay, jackknife). Partition homogeneity testing (PHT) by codon position withinrbcL showed that all positions could be used despite mild third position saturation. PHT by gene and domain within rDNA showed that the 26S D1 and D2 regions do not enhance phylogenetic signal even when combined with the 18S. TherbcL and rDNA (excluding the 26S D1 and D2) could be combined under PHT. The topology of the combined tree was the same as that of therbcL tree alone, but bootstrap support was consistently higher in the combined analysis, applied to more branches, and enabled the establishment of sister group relationships among six orders. Although the taxon sampling for the combination tree was lower (n= 22) than for individual gene analyses (n= 58 forrbcL andn= 59 for rDNA), results show that the Laminariales (previously reported) and Sphacelariales (new) are both paraphyletic.Choristocarpus tenellus(Kützing) Zanardini is the most basal phaeophyte and the Dictyotales the most basal order. In contrast, the Laminarialessensu stricto(s.s.) and Ectocarpalessensu lato(s.l.) are the most derived. For phylogenetic studies in the Phaeophyceae,rbcL has more resolving power than rDNA, though the reason for this is unclear based on the fact that both genes are highly conserved.

Allelic diversity at the Mhc-DP locus in rhesus macaques (Macaca mulatta)

Allelic diversity at the major histocompatibility complex class II DP locus of rhesus macaques was studied by sequencing exon 2 of Mamu-DPA1 and -DPB1 genes. The Mamu-DPA1 gene is apparently invariant, whereas the Mamu-DPB1 locus displays polymorphism. Here we report the characterization of 1 Mamu-DPA1 and 13 Mamu-DPB1 alleles which were compared with other available primate Mhc-DPA1 and -DPB1 sequences. As compared with Mhc-DRB and -DQB1, most codons for the contact residues in the antigen binding site of the primate Mhc-DPB1 gene have a relatively low degree of variation in encoding various types of amino acids. In contrast to Mhc-DRB and -DQB, the HLA- and Mamu-DPB1 sequences cluster in a species-specific manner in phylogenetic trees. Mhc-DPB1 polymorphisms, however, are inherited in a transspecies mode of evolution, as is demonstrated by the sharing of lineage members between closely related macaque species. The data demonstrate that the transspecies character of Mhc-DPB1 polymorphism was retained over much shorter periods of time as compared with its sister class II loci, Mhc-DQ and -DR.