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It is now well established that the end-Cretaceous mass extinction had enormous repercussions for mammalian evolution. Following the extinction, during the Paleocene, mammals started to radiate, occupying new and diverse ecological niches. However, the phylogenetic relationships between the socalled “archaic” mammals of this time, and their position within Placentalia, remain contentious. The Periptychidae are a clade of distinctive “archaic” ungulates, composed of ~17 genera of small to large bodied, highly bunodont, terrestrial herbivores that were among the first placental mammals to appear after the end-Cretaceous mass extinction. Although the Periptychidae has been historically considered a distinctive “condylarth” subgroup, their higherlevel relationships have been rarely tested. Here, we present an inclusive cladistic analysis to determine and test the phylogenetic affinities of Periptychidae and other key Paleocene groups within Placentalia under different cladistic optimality criteria. We scored 140 taxa for 503 dental, cranial and postcranial characters, incorporating new morphological and taxonomic data. The data were then subject to parsimony and Bayesian tree of morphological evolution, running 5000000 generations with samples every 200 generations and discarding 25% of the samples as burn-in. Stationarity was achieved and a 50 percent majority rule consensus tree from the sampled trees was obtained. The parsimony analysis recovered 48 most parsimonious trees. The two consensus trees derived from the different analyses are largely congruent and recover a monophyletic Periptychidae, although the parsimony consensus tree is better resolved. These results are consistent with simulation studies showing that parsimony tends to be more precise (more nodes reconstructed) than Bayesian analyses, although less accurate. The main topological differences between the results relate to the position of poorly known Puercan (earliest Paleocene) species. Our results affirm the monophyly of Periptychidae and its nesting within a group of “condylarths” positioned at the base of Laurasiatheria and closely related to Artiodactyla. Within Periptychidae we found support for the three major subfamilial divisions in both analyses. These results highlight the importance of using different optimality criteria when resolving a phylogeny and provide a new insight into how placental mammals were evolving after the end-Cretaceous extinction. Grant Information: CONICYT PFCHA/DOCTORADO BECAS CHILE/2018, European Research Council Starting Grant (ERC StG 2017, 756226, PalM), National Science Foundation (NSF EAR 1654952, DEB 1654949)
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Investigating the Genomic Distribution of Phylogenetic Signal with CloudForest
A central focus of evolutionary biology is inferring the historical relationships among species and using this context to learn about how evolution has shaped diverse organisms. These historical relationships are represented by phylogenetic trees, and the methods used to infer these trees have been an active area of research for several decades. Despite this attention, phylogenetic workflows have changed little, even though extraordinary advances have occurred in the scale and pace at which genomic data have been collected in the past 20 years. Modern phylogenomic datasets have also raised fascinating new questions. Why do different parts of a genome often support different relationships among species? How are these different signals distributed across chromosomes? We developed a new computational framework, CloudForest, to tackle such questions. CloudForest is flexible, efficient, and tightly integrates a diverse set of tools. Here, we briefly describe the architecture of CloudForest, including the advantages it provides, and use it to investigate the distribution of phylogenetic signal along the entire X chromosome of 24 cat (Felidae) species.
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- PAR ID:
- 10310280
- Date Published:
- Journal Name:
- Proceedings of the Practice and Experience on Advanced Research Computing
- Issue:
- 34
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1145/3437359.3465605
