signal between a given tree and a trait. In general, Blomberg’sKandδstatistics showed that the functional traits have significant phylogenetic signals (Table S6). We selected a set of functional traits (Table1) related to diet, foraging stratum, foraging time, and body mass to compute the fu...
These indices were calculated running the R packages "ape"57 and "picante"58 based on the phylogenetic tree for the 28 species involved in the experiment built using "V.Phylomaker" package, using phylo.maker function and the "scenario1" option to bind new tips59 (Fig. 2). To ...
many of them introduced for the first time in this work, to elucidate all possible LTR retroelement phylogenetic patterns. These were superimposed over the tree of eukaryotes to investigate the dynamics of the system
and the heterozygosity was 1.19–1.29% (Supplementary Fig.2), thus suggesting a complex genome ofE. davidi. We obtained a draft genome assembly of 2.16 Gb in length with a scaffold N50 value of 146.18 Mb (Supplementary Table2), and the complete BUSCO analysis was 95.4% (of which...
the algorithm does not try to reconstruct particular evolutionary events, and it is still restricted to pairwise comparisons of the sequences based on single nucleotides. It thus does not cope well with the example alignments used here (Table1), a conclusion also reached by Golubchik et al. ...
RAxML analyses with fast-evolving sites removed from the concatenated 295-marker matrix recovered the same topology of [Olpidium,(Zoopagomycota, (Mucoromycota, Dikarya))], with a minor to moderate decrease of branch support compared with analyses included all sites (TableS3). We performed two se...
we used standardized effect size instead of resampling on sequences or the OTU table to reduce the sampling and sequencing effects on the observed phylogenetic diversity14. For beta diversity, we first adopted the beta mean nearest taxon distance (βMNTD) along N gradient29. According to the def...
The reference piggyBac sequence accession number is shown in Supple- mentary Table 4. The reference for chemosensory sequence accession was down- loaded from the dataset by Vizueta115. We used the BITACORA pipeline to identify Ir/iGluR genes116. The "incomplete" (or "partial") genes were ...
oligodontus in Araliaceae, a phylogenetic tree was reconstructed for 22 species of the family Araliaceae (see Table S4) using the 54 common protein-coding genes among the 22 complete chloroplast genome sequences. The best amino acid substitution model was selected using prottest v3.4: HIVb + I...
Therefore, in this paper, we focus on an equidistant tree, which is a rooted phylogenetic tree such that the total weight on an unique path from its root to each leaf is the same, and we focus on the space of all possible equidistant trees. It is well-known that the space of all ...