Reply to Gatesy and Springer: Claims of homology errors and zombie lineages do not compromise the dating of placental diversification

Gatesy and Springer (1) consider 3 out of 89 nodes in our “preferred STAR tree” (2) unusual, raising suspicions that underlying alignment errors have generated these and other perceived misestimations in our analysis. As in their other critiques of our work, their claims are based on subjective and unrepeatable logic. We acknowledge that our alignments can be improved; in particular, we neglected to align and trim our loci based on more conserved amino acid alignments. However, our alignments still contain substantial phylogenetic information, and our protocols correctly extracted individual codon positions for analysis. Application of a suite of repeatable best practices for quality control in phylogenomics (3, 4) suggests that, after trimming, about 2.5% of individual sequences—a …