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BEAST provides the ability to analyze multiple data partitions simultaneously.
Hence, CADM accurately detects completely incongruent matrices even when multiple data partitions are tested simultaneously.
Bayesian dating (BD) was performed as implemented in Multidivtime, which allows multiple data partitions [ 92, 93].
A phylogenetic analysis of the combined multiple data partitions using exhaustive tree searches resulted in a single most parsimonious tree.
The simultaneous analysis approach produced a more robust phylogenetic hypothesis for Lagenorhynchus than previous studies, thus supporting a phylogenetic approach employing multiple data partitions that vary in overall rate of evolution.
Regardless of the exact cause, short branch lengths of these internodes can result in a high number of anomalous gene trees (and gene tree discordance [ 44]), leading to an incorrectly inferred species tree, especially when data from multiple data partitions is concatenated [ 45].
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With the growing amount of taxa and sequences that are used in phylogenomics, CADM offers a simple alternative to compare multiple matrices and identify congruent data partitions.
In addition, none of the data used in the Brower study were corrected for multiple hits with data partitioning or the use of gamma-distributed rates, as most data are today [ 21- 24].
The variation in the evolutionary histories of multiple independent genes are typically addressed with either data partitions with different nucleotide substitution models, or with mixture models allowing for random variation between sites [ 55].
However, distinguishing between alternative phylogenetic hypotheses requires the addition of more data from multiple loci and a detailed evaluation of the utility of various data partitions to resolve relationships within this group.
One strategy, often used in the context of partitioning methods, is to build a new network whose edge weights are determined by multiple data sources (Hanisch et al., 2002).
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