Data from: PlaceMyFossils: An integrative approach to analyse and visualize the phylogenetic placement of fossils using backbone trees

In recent years, there has been a growing interest in using morphology to
establish the placement of species on phylogenetic trees derived from
molecular data. This is relevant in the case of recently extinct or fossil
species, which are usually represented only by fragmentary morphology. In
the latter case, constrained analyses using backbone trees have also
proven helpful in evaluating the placement of fragmentary specimens on
phylogenetic trees derived from morphological data. Consequently, several
available phylogenetic programs now include functions to run constrained
searches. However, a comprehensive evaluation of the results obtained is
not readily available within existing analytical tools. Here, we present
an integrated approach—PlaceMyFossils—specifically designed to (1)
thoroughly evaluate the phylogenetic placement of given query species
(especially fossils) on a reference tree, (2) determine which characters
and character partitions are most relevant in defining the phylogenetic
placement, (3) assess the confidence of the results, and (4) define the
optimal analytical conditions to place the query species. PlaceMyFossils
combines several analyses implemented as an interactive script for TNT
(Tree Analysis Using New Technologies software), a popular—and
free—phylogenetic software that is widely used in paleontological studies.
Finally, we demonstrate the utility and investigate the performance of
PlaceMyFossils as compared with other available tools using two disparate
empirical datasets drawn from conifers and dinosaurs. While primarily
designed for working with fossils, this tool also holds great potential
for advancing morphological and molecular systematics. It offers a
powerful resource for empirical systematists aiming to integrate molecular
and morphological data. This is particularly relevant given the growing
interest in morphological evolution as a complementary perspective on
evolutionary processes and the drivers of diversification.