Using a simplified phylogeny composed of the nine species analysed here, we then mapped the presence/absence of each DEG-containing orthogroup (hereafter called DEOG for differentially expressed orthogroups) on each tip of the tree, allowing us to determine at which evolutionary node the genes have...
Ancestral sequences at each focused node in the phylogenetic tree were inferred using Graphical Representation of Ancestral Sequence Predictions (GRASP;http://grasp.scmb.uq.edu.au/)72, a new method that can infer insertion-deletion (indel) reconstruction. The WAG was selected as the evolutionary ...
In general, an increased taxa sampling is considered to improve the power to detect positive selection43, so future study incorporating more taxa with intensive sampling in a supertree context may be more powerful in detecting positive selection. iv) For the large-scale phylogenetic analyses ...
This tree is rooted by using the fungus sequence of Coprinopsis cinerea galectin-1 (AF130360.1) as the outgroup. The proteins indicated with asterisk were used for the inference of the previous ancestor (Con-anc). (B) Amino acid sequences of ancestral congerins, ConI, and ConII. Amino ...
The Sp-family of transcription factors are evolutionarily conserved zinc finger proteins present in many animal species. The orthology of the Sp genes in different animals is unclear and their evolutionary history is therefore controversially discussed.
The phylogenetic tree of the haplotypes was consistent with the previous analysis, where two main haplotypes exist among the mutation carriers. The mutation haplotype likely diverged in Spain prior to the mutation migrating to the other countries (Fig. 2). Fig. 2 Phylogenetic tree as calculated ...
DNA fragments as well as the fact that most of the tested reactions failed, we can conclude that the PCR products presented in Fig. S4 in Additional file1were not amplified on the mitochondrial genome template. The D-F and D-R primers as well as the applied PCRs are highly specific and...
bailii CLIB 213T and IST302 sequences, as input, MrBayes phylogenetic software suite was used to construct a phylogenetic tree representing this family of transcription factors with copper-fist binding domain. After running two MCMC simulations for 1200000 generations, the standard deviation of split...
using the primers M13(-20) and M13(reverse) on an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA), using the Big Dye Termination Reaction chemistry (Applied Biosystems). Suitable clone inserts were used as DNA template for the preparation of a 233-bpshh-specific...
Using our tree, we inferred the evolutionary timing, patterns of host use, and biogeographic history of butterflies. We addressed three long-standing questions related to butterfly evolution: (1) did butterflies originate in the northern (Laurasia) or southern (Gondwana) hemisphere4; (2) what ...