Fig 1.
Maximum likelihood tree showing phylogenetic relationships between eukaryotic bHLH+PAS containing proteins.
The 10 major clades representing a majority of the bHLH+PAS gene families are highlighted. The names given to each clade are derived from the human gene names found within those clades. For example, bilaterian NPAS1/3 represents a highly supported clade, Bayesian posterior probability (BPP) ≥ 0.90, that contains bilaterian sequences that group with human NPAS1 and human NPAS3. The one exception is the invertebrate-specific clade that contains the Drosophila melanogaster methoprene-tolerant gene. The unicellular bHLH+PAS genes typically grouped together. Purple circles indicate congruent nodes between both Bayesian and Maximum likelihood trees with a Bayesian posterior probability support value ≥ 0.90.All support values for this Maximum Likelihood tree, along with Bayesian inference tree and its corresponding support values, are found in S1 and S2 Files.
Fig 2.
Phylogenetic distribution of the ARNT and ARNTL gene families in Metazoa.
Schematics for each ARNT, ARNT2, ARNTL, and ARNTL2 identified in each metazoan species are shown. Black boxes represent the bHLH domains, while the blue boxes represent the PAS domains. Invertebrate genes duplicated to give rise to the different vertebrate paralogs, as a result of the vertebrate genome duplication events (green circle). Danio rerio has two ARNTL paralogs, and Takifugu rubripes has two ARNTL2 paralogs, both due to the teleost-specific genome duplication event (blue circle). Proteins are drawn to scale. Species phylogenetic relationships are based [35–38].
Fig 3.
Phylogenetic distribution of the HIF-α genes and associated transactivation domains in Metazoa.
Schematics for each HIF-α identified in each metazoan species are shown. Black boxes represent the bHLH domains, blue boxes represent the PAS domains, yellow boxes represent the NTAD, and red boxes represent the CTAD. Invertebrate genes duplicated to give rise to the different vertebrate paralogs, because of the vertebrate genome duplication events (green circle). Additional paralogs of HIF-1α and HIF-2α in D. rerio are due to the teleost-specific genome duplication event (blue circle). Proteins are drawn to scale. Species phylogenetic relationships are based [35–38].
Table 1.
Summary of results from codon-selection analyses using HYPY.