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1. Testing the phylogeny of Periptychidae and "archaic" Paleocene mammals uner different optimality criteria

   Puschel, H. P.; Shelley, S. L.; Williamson, T. E.; Wible, J. R.; Brusatte, S. L. (October 2019, Journal of Vertebrate Paleontology, Abstracts and Program)

   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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2. Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation

   https://doi.org/10.1146/annurev-animal-061220-023149  

   Murphy, William J.; Foley, Nicole M.; Bredemeyer, Kevin R.; Gatesy, John; Springer, Mark S. (February 2021, Annual Review of Animal Biosciences)

   null (Ed.)

   The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species. 

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3. Journal of Vertebrate Paleontology, Program and Abstracts

   Bertrand, O.C.; Brusatte, S. L.; Shelley, S. L.; Wible, J. R.; Williamson, T. E.; Chester, S. G.; Holbrook, L. T.; Lyson, T. R.; Smith, T.; Meng, J. (October 2020, Society of Vertebrate paleontology)

   The end-Cretaceous mass extinction, 66 million years ago, profoundly reshaped the biodiversity of our planet. After likely originating in the Cretaceous, placental mammals (species giving live birth to well-developed young) survived the extinction and quickly diversified in the ensuing Paleocene. Compared to Mesozoic species, extant placentals have advanced neurosensory abilities, enabled by a proportionally large brain with an expanded neocortex. This brain construction was acquired by the Eocene, but its origins, and how its evolution relates to extinction survivorship and recovery, are unclear, because little is known about the neurosensory systems of Paleocene species. We used high-resolution computed tomography (CT) scanning to build digital brain models in 29 extinct placentals (including 23 from the Paleocene). We added these to data from the literature to construct a database of 98 taxa, from the Jurassic to the Eocene, which we assessed in a phylogenetic context. We find that the Phylogenetic Encephalization Quotient (PEQ), a measure of relative brain size, increased in the Cretaceous along branches leading to Placentalia, but then decreased in Paleocene clades (taeniodonts,phenacodontids, pantodonts, periptychids, and arctocyonids). Later, during the Eocene, the PEQ increased independently in all crown groups (e.g., euarchontoglirans and laurasiatherians). The Paleocene decline in PEQ was driven by body mass increasing much more rapidly after the extinction than brain volume. The neocortex remained small, relative to the rest of the brain, in Paleocene taxa and expanded independently in Eocene crown groups. The relative size of the olfactory bulbs, however, remained relatively stable over time, except for a major decrease in Euarchontoglires and some Eocene artiodactyls, while the petrosal lobules (associated with eye movement coordination) decreased in size in Laurasiatheria but increased in Euarchontoglires. Our results indicate that an enlarged, modern-style brain was not instrumental to the survival of placental mammal ancestors at the end-Cretaceous, nor to their radiation in the Paleocene. Instead, opening of new ecological niches post-extinction promoted the diversification of larger body sizes, while brain and neocortex sizes lagged behind. The independent increase in PEQ in Eocene crown groups is related to the expansion of the neocortex, possibly a response to ecological specialization as environments changed, long after the extinction. 

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4. Putting the F into FBD analysis: tree constraints or morphological data?

   https://doi.org/10.1111/pala.12679  

   Barido‐Sottani, Joëlle; Pohle, Alexander; De_Baets, Kenneth; Murdock, Duncan; Warnock, Rachel_C_M (November 2023, Palaeontology)

   Abstract The fossilized birth–death (FBD) process provides an ideal model for inferring phylogenies from both extant and fossil taxa. Using this approach, fossils are directly integrated into the tree, leading to a statistically coherent prior on divergence times. Since fossils are typically not associated with molecular sequences, additional information is required to place fossils in the tree. We use simulations to evaluate two different approaches to handling fossil placement in FBD analyses: using topological constraints, where the user specifies monophyletic clades based on established taxonomy, or using total‐evidence analyses, which use a morphological data matrix in addition to the molecular alignment. We also explore how rate variation in fossil recovery or diversification rates impacts these approaches. We find that the extant topology is well recovered under all methods of fossil placement. Divergence times are similarly well recovered across all methods, with the exception of constraints which contain errors. We see similar patterns in datasets which include rate variation, however, relative errors in extant divergence times increase when more variation is included in the dataset, for all approaches using topological constraints, and particularly for constraints with errors. Finally, we show that trees recovered under the FBD model are more accurate than those estimated using non‐time calibrated inference. Overall, we show that both fossil placement approaches are reliable even when including uncertainty. Our results underscore the importance of core taxonomic research, including morphological data collection and species descriptions, irrespective of the approach to handling phylogenetic uncertainty using the FBD process. 

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5. Virtual endocranial and inner ear endocasts of the Paleocene ‘condylarth’ Chriacus : new insight into the neurosensory system and evolution of early placental mammals

   https://doi.org/10.1111/joa.13084  

   Bertrand, Ornella C.; Shelley, Sarah L.; Wible, John R.; Williamson, Thomas E.; Holbrook, Luke T.; Chester, Stephen G. B.; Butler, Ian B.; Brusatte, Stephen L. (October 2019, Journal of Anatomy)

   Abstract The end‐Cretaceous mass extinction allowed placental mammals to diversify ecologically and taxonomically as they filled ecological niches once occupied by non‐avian dinosaurs and more basal mammals. Little is known, however, about how the neurosensory systems of mammals changed after the extinction, and what role these systems played in mammalian diversification. We here use high‐resolution computed tomography (CT) scanning to describe the endocranial and inner ear endocasts of two species,Chriacus pelvidensandChriacus baldwini, which belong to a cluster of ‘archaic’ placental mammals called ‘arctocyonid condylarths’ that thrived during theca. 10 million years after the extinction (the Paleocene Epoch), but whose relationships to extant placentals are poorly understood. The endocasts provide new insight into the paleobiology of the long‐mysterious ‘arctocyonids’, and suggest thatChriacuswas an animal with anencephalization quotient (EQ)range of 0.12–0.41, which probably relied more on its sense of smell than vision, because the olfactory bulbs are proportionally large but the neocortex and petrosal lobules are less developed. Agility scores, estimated from the dimensions of the semicircular canals of the inner ear, indicate thatChriacuswas slow to moderately agile, and its hearing capabilities, estimated from cochlear dimensions, suggest similarities with the extant aardvark.Chriacusshares many brain features with other Paleocene mammals, such as a small lissencephalic brain, large olfactory bulbs and small petrosal lobules, which are likely plesiomorphic for Placentalia. The inner ear ofChriacusalso shares derived characteristics of the elliptical and spherical recesses with extinct species that belong to Euungulata, the extant placental group that includes artiodactyls and perissodactyls. This lends key evidence to the hypothesized close relationship betweenChriacusand the extant ungulate groups, and demonstrates that neurosensory features can provide important insight into both the paleobiology and relationships of early placental mammals. 

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