The ITS tree shown in Figure 1 is not directly comparable to the Bayesian consensus tree based on five protein coding loci shown in Figure 2, since all V. longisporum isolates only carried a single ITS allele.
The present study describes phylogenetic analysis of fescue-derived endophytes based on three nuclear protein-coding genes (tefA, tub2, perA) and the complete protein-coding gene complement of the mt genome.
We evaluated the phylogenetic relatedness of the mule deer Helicobacter with other Helicobacter based on four of the protein-coding transcripts and on the single 16S rRNA sequence.
Based on GO, human protein-coding genes were divided into four groups: enzyme, transporter, regulation and signal transduction, using a method similar to [ 4].
The reconstructed gastropod phylogeny based on 12 mt protein-coding gene sequence data supports four natural groups within Gastropoda: Vetigastropoda, Caenogastropoda, Patellogastropoda, and Heterobranchia.
NJ, ML, and BI trees based on each of the three protein-coding regions showed the same seven major clades as those detected in the CR-based NJ tree.
We hypothesize that phylogenetic analyses of chelicerate interrelationships based on mitochondrial protein-coding genes is biased by three misleading factors: (a) long-branch attraction, (b) derived AT bias in all chelicerate taxa except Limulus polyphemus, and (c) reversed strand bias in Scorpiones, two species of Araneae and the mite Varroa destructor.
These results are compatible with a previous phylogenetic analysis based on nuclear protein-coding sequences [ 69].
The analyses were based on all available mitochondrial protein-coding genes, as well as two nuclear protein-coding genes.
We reconstruct the evolutionary relationships of 161 cichlid species (152 LT endemics, 9 non-endemics), representing 76% of all LT species (assuming a LT cichlid flock of 200 endemic species, Table S1), based on two mtDNA genes: the protein coding, ND2 (∼1047 bp) and the non-coding, control region (CR), (partial sequence data of 347 bp from the 5'-end) using published sequence data (Table S1).
