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These phenomena complicate the tree of life.
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We modelled a very conservative system- allowing only nucleotide substitution, not gene gain or loss as that would complicate the tree-building process to generate optimal data with a high but realistic amount of phylogenetic signal.
Although gene trees can be discordant and complicate the recovery of species trees, they can also be concordant and provide strong support for species delimitation.
Recombination events complicate the inference of species trees, and so it is important to investigate the extent of recombination in the Rickettsia genus.
The combined action of incomplete lineage sorting and introgression of genes between species are known to greatly complicate the resolution of species trees [ 41- 43] weakening single loci phylogenetic inferences [ 44].
The tee shot goes into the rough and nearby trees could complicate the next shot.
If Elymus relationships are in some ways similar on the pepC and β-amylase trees, and relatively straightforward to interpret, the GBSSI results complicate the interpretation.
Complicate the spelling.
Clearly, the possibility that such processes contribute to observed incongruence in gene trees complicates the inference of species phylogenies from multilocus data [ 5].
However, in this paper, we focus specifically on the history of the NCLDV ligases; for this analysis, we used representative sets of ATP-dependent and NAD-dependent ligases from bacteria (and bacterial viruses), archaea, and eukaryotes, so we do not expect that inclusion of more exhaustive sequence sets (which complicates the construction of ML trees) would affect the message.
This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task.
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