Data from: Selecting question-specific genes to reduce incongruence in phylogenomics: a case study of jawed vertebrate backbone phylogeny

Incongruence between different phylogenomic analyses is the main challenge
faced by phylogeneticists in the genomic era. To reduce incongruence,
phylogenomic studies normally adopt some data filtering approaches, such
as reducing missing data or using slowly evolving genes, to improve the
signal quality of data. Here, we assembled a phylogenomic data set of 58
jawed vertebrate taxa and 4682 genes to investigate the backbone phylogeny
of jawed vertebrates under both concatenation and coalescent-based
frameworks. To evaluate the efficiency of extracting phylogenetic signals
among different data filtering methods, we chose six highly intractable
internodes within the backbone phylogeny of jawed vertebrates as our test
questions. We found that our phylogenomic data set exhibits substantial
conflicting signal among genes for these questions. Our analyses showed
that non-specific data sets that are generated without bias toward
specific questions are not sufficient to produce consistent results when
there are several difficult nodes within a phylogeny. Moreover,
phylogenetic accuracy based on non-specific data is considerably
influenced by the size of data and the choice of tree inference methods.
To address such incongruences, we selected genes that resolve a given
internode but not the entire phylogeny. Notably, not only can this
strategy yield correct relationships for the question, but it also reduces
inconsistency associated with data sizes and inference methods. Our study
highlights the importance of gene selection in phylogenomic analyses,
suggesting that simply using a large amount of data cannot guarantee
correct results. Constructing question-specific data sets may be more
powerful for resolving problematic nodes.