Phylogenomics uses genome-scale evidence to investigate evolutionary relationships and gene histories. Many sampled loci can improve resolution, but their histories need not be identical: incomplete lineage sorting, duplication and introgression can make a gene tree differ from a species tree.
Adding sequences therefore creates a modeling question as well as a larger dataset. Concatenating all loci assumes a shared history in a way that methods explicitly representing variation among gene trees need not. Strong support conditional on a model does not by itself validate that model's account of the evolutionary process.
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