Data from: Integrating incomplete fossils by isolating conflictive signal in saturated and non-independent morphological characters

Morphological characters are indispensable in phylogenetic analyses for
understanding the pattern, process, and tempo of evolution. If characters
are independent and free of systematic errors, then combining as many
different kinds of characters as are available will result in the
best-supported phylogenetic hypotheses. But since morphological characters
are subject to natural selection for function and arise from the
expression of developmental pathways, they may not be independent, a
situation that may amplify any underlying homoplasy. Here, we use new
dental and multi-locus genetic data from bats (Mammalia: Chiroptera) to
quantify saturation and similarity in morphological characters and
introduce two likelihood-based approaches to identify strongly conflicting
characters and integrate morphological and molecular data. We implement
these methods to analyze the phylogeny of incomplete Miocene fossils in
the radiation of Phyllostomidae (New World Leaf-nosed Bats), perhaps the
most ecologically diverse family of living mammals. Morphological
characters produced trees incongruent with molecular phylogenies, were
saturated, and showed rates of change higher than most molecular
substitution rates. Dental characters encoded variation similar to that in
other morphological characters, while molecular characters encoded highly
dissimilar variation in comparison. Saturation and high rates of change
indicate randomization of phylogenetic signal in the morphological data,
and extensive similarity suggests characters are non-independent and
errors are amplified. To integrate the morphological data into tree
building while accounting for homoplasy, we used statistical molecular
scaffolds and combined phylogenetic analyses excluding a small subset of
strongly conflicting dental characters. The phylogenies revealed the
Miocene nectar-feeding †Palynephyllum nests within the crown
nectar-feeding South American subfamily Lonchophyllinae, while the Miocene
genus †Notonycteris is sister to the extant carnivorous Vampyrum. These
relationships imply new calibration points for timing of radiation of the
ecologically diverse Phyllostomidae.