PlaceMyFossils : an integrative approach to analyze and visualize the phylogenetic placement of fossils using backbone trees
Catalano, Santiago Andres (American Museum of Natural History (Nova York))
Escapa, Ignacio (Museo Paleontológico Egidio Feruglio)
Pugh, Kelsey D. (American Museum of Natural History (Nova York))
Hammond, Ashley S. (American Museum of Natural History (Nova York))
Goloboff, Pablo Augusto (Fundación Miguel Lillo)
Almécija, Sergio (Institut Català de Paleontologia Miquel Crusafont)

Data:	2025
Resum:	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 obtained results 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 compared to 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.
Nota:	Ajuts: Agencia Estatal de Investigación of the Spanish Ministerio de Ciencia e Innovación (AEI/10.13039/501100011033), and the Generalitat de Catalunya (CERCA Programme).
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió acceptada per publicar
Matèria:	Backbone topology ; Error in placement ; Fossils ; Maximum likelihood ; Maximum parsimony ; Molecular scaffolds
Publicat a:	Systematic biology, (2025) , art. syaf025, ISSN 1076-836X

DOI: 10.1093/sysbio/syaf025
PMID: 40244059

Postprint 29 p, 1.7 MB

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