Because of the well-known long-branch attraction (LBA) phenomenon [16], fast-evolving sequences tend to be artifactually attracted to each other in phylogenetic trees [17]. In the case of eukaryotic phylogenies, this is especially problematic when prokaryotic sequences are used to root the tree...
Today, cladograms are still used and interpreted as specific types of molecular phylogenetic trees. While phenograms and cladograms represented dif- ferent forms of knowledge during the time of the Systematist Wars, today they are both used to represent evolutionary relationships. This indicates...
Previous phylogenetic analyses [25] recovered a deep split into twoPontohedyleclades: theP. milaschewitchiiclade and theP. verrucosaclade. This is supported by novel analyses in a larger phylogenetic framework and additionally including a second nuclear marker (18S rRNA) (own unpublished data). S...
Read placement also allows the implementation of quantitative species delimitation methods to automatically assess taxonomic diversity, an approach already integrated into the phylogenetic binning approach (Zhang et al. 2013). Broad reference trees can be assembled and centrally maintained to be used in ...
e, phylogenetic trees to estimate confidence limits of fn internal branches. This method proceeds by resamp- ling the species (or subpopulation) x character matrix Assumptions of the bootstrap rtd across characters, with replacement, such that the resamples consist of a set of characters with ...
Untangling the role of these different characteristics in explaining the rate of sex chromosome divergence will require very large- scale comparative datasets and phylogenetic methods. Work in this direction has started104, but much more work is needed. References 1. Bachtrog, D. et al. Are all...
Because PDIs are not phylogenetically related to their bacterial analogs in the Dsb family [111], plastid PDIs cannot be of cyanobacterial origin; rather, they must have come from the eukaryotic host. Phylogenetic trees recovered using different methods show similar topologies with two large eukaryotic...
Evolutionary relationships can be estimated through construction of phylogenetic trees or networks, and there are many methods through which this can be achieved. The inputs for these analyses can be derived from the results of either reference-based mapping or de novo assembly. In the latter case...
(a) Profile of the margin of a water body with characteristic vegetation; (b) Phylogenetic tree of the symbionts; (c) Phylogenetic tree of the hosts (reed beetles); (d) Congruent branching pattern within the Sparganium-group. The trees in (b) and (c) are schematic representations of the...