Showing papers by "Pasquale Raia published in 2020"

Past Extinctions of Homo Species Coincided with Increased Vulnerability to Climatic Change

Abstract: Summary At least six different Homo species populated the World during the latest Pliocene to the Pleistocene. The extinction of all but one of them is currently shrouded in mystery, and no consistent explanation has yet been advanced, despite the enormous importance of the matter. Here, we use a recently implemented past climate emulator and an extensive fossil database spanning 2,754 archaeological records to model climatic niche evolution in Homo. We find statistically robust evidence that the three Homo species representing terminating, independent lineages, H. erectus, H. heidelbergensis, and H. neanderthalensis, lost a significant portion of their climatic niche space just before extinction, with no corresponding reduction in physical range. This reduction coincides with increased vulnerability to climate change. In the case of Neanderthals, the increased extinction risk was probably exacerbated by competition with H. sapiens. This study suggests that climate change was the primary factor in the extinction of Homo species.

Decoupling Functional and Morphological Convergence, the Study Case of Fossorial Mammalia

Abstract: The original specimens are stored at the Tsukuba Natural History Museum, Tsukuba, Japan; Los Angeles County Natural History Museum, US; Wien Natural History Museum, Austria, Paris Natural History Museum, France; Lyon Natural History Museum, France; Lisbon Natural History Museum, Portugal.

Variation in the strength of allometry drives rates of evolution in primate brain shape.

Abstract: Large brains are a defining feature of primates, as is a clear allometric trend between body mass and brain size. However, important questions on the macroevolution of brain shape in primates remai...

A 450 million years long latitudinal gradient in age‐dependent extinction

Abstract: Leigh Van Valen famously stated that under constant conditions extinction probability is independent of species age. To test this 'law of constant extinction', we developed a new method using deep learning to infer age-dependent extinction and analysed 450 myr of marine life across 21 invertebrate clades. We show that extinction rate significantly decreases with age in > 90% of the cases, indicating that most species died out soon after their appearance while those which survived experienced ever decreasing extinction risk. This age-dependent extinction pattern is stronger towards the Equator and holds true when the potential effects of mass extinctions and taxonomic inflation are accounted for. These results suggest that the effect of biological interactions on age-dependent extinction rate is more intense towards the tropics. We propose that the latitudinal diversity gradient and selection at the species level account for this exceptional, yet little recognised, macroevolutionary and macroecological pattern.

Endomaker, a new algorithm for fully automatic extraction of cranial endocasts and the calculation of their volumes.

Abstract: Objectives Reproducing cranial endocasts is a major goal of researchers interested in vertebrate brain evolution. We present a new R software, named endomaker, which allows the automatic extraction of endocasts from skull meshes along with the calculation of its volume. Materials and methods We applied endomaker on non-primate and primate skulls including the Australopithecus africanus specimen Sts-5. Results We proved endomaker is faster, more feature-rich and possibly more accurate than competing software. Discussion Endomaker is the only available program endowed with the possibility to process an entire mesh directory straight away, promising to expand the scope and phylogenetic breadth of comparative studies of brain evolution.

Target deformation of the Equus stenonis holotype skull: a virtual reconstruction

Abstract: Equus stenonis is one of the most prevalent European Pleistocene fossil horses It is believed to be the possible ancestor of all Old World Early Pleistocene Equus, extant zebras and asses, and as such provides insights into Equus evolution and its biogeography and paleoecology The Equus stenonis holotype skull (IGF560) was first described by Igino Cocchi in 1867, from the Early Pleistocene locality of Terranuova (Upper Valdarno basin, Italy) IGF560 is a nearly complete, although medio-laterally crushed and badly compressed skull Here we provide the first application of a new virtual reconstruction protocol, termed Target Deformation, to the Equus stenonis holotype The protocol extends beyond classic retrodeformation by using target specimens as a guide for the virtual reconstruction The targets used as a reference are two fragmentary, yet well-preserved E stenonis skulls, coming from Olivola (Italy; IGF11023) and Dmanisi (Georgia; Dm 5/1543/4A45), both Early Pleistocene in age These two specimens do not display any major deformation, but preserve different, only slightly overlapping portions of the skull The virtual reconstruction protocol we carried out has shown its feasibility, by producing two 3D models whose final morphology is perfectly congruent with the natural variability of a comparative sample of E stenonis specimens This study shows the potential of using even broken or otherwise fragmentary specimens to guide retrodeformation in badly distorted and damaged specimens The application of Target Deformation will allow us to increase the availability of comparative specimens in studies of fossil species morphology and evolution, as well as to the study of taphonomic processes

Ancestral State Estimation with Phylogenetic Ridge Regression

Abstract: The inclusion of fossil phenotypes as ancestral character values at nodes in phylogenetic trees is known to increase both the power and reliability of phylogenetic comparative methods (PCMs) applications We implemented the R function RRphylo as to integrate fossil phenotypic information as ancestral character values We tested the new implementation, named RRphylo-noder (which is available as part of the RRphylo R package) on tree and data generated according to evolutionary processes of differing complexity and under variable sampling conditions We compared RRphylo-noder performance to other available methods for ancestral state estimation, including Bayesian approaches and methods allowing rate variation between the tree branches We additionally applied RRphylo-noder to two real cases studies, the evolution of body size in baleen whales and in caniform carnivores Variable-rate methods proved to be more accurate than single-rate methods in estimating ancestral states when the pattern of phenotypic evolution changes across the tree RRphylo-noder proved to be slightly more accurate and sensibly faster than Bayesian approaches, and the least sensitive to the kind of phenotypic pattern simulated The use of fossil phenotypes as ancestral character values noticeably increases the probability to find a phenotypic trend through time when it applies to either the entire tree or just to specific clades within it We found Cope’s rule to apply to both mysticete cetaceans and caniform carnivores The RRphylo-noder implementation is particularly appropriate to study phenotypic evolution in the presence of complex phenotypes generated by different processes acting in different parts the tree, and when suitable information about fossil phenotypes is at hand

Current Options for Visualization of Local Deformation in Modern Shape Analysis Applied to Paleobiological Case Studies

Abstract: In modern shape analysis deformation is quantified in different ways depending on algorithms used and on the scale at which it is evaluated. While global affine and non-affine deformation components can be decoupled and computed using a variety of methods, the very local deformation can be considered, infinitesimally, as an affine deformation. The deformation gradient tensor F can be computed locally using a direct calculation by exploiting triangulation or tetrahedralization structures or by evaluating locally the first derivative of an appropriate interpolation function mapping the global deformation from the undeformed to the deformed state. A suitable function is represented by the Thin Plate Spline (TPS) that separates affine from non affine deformation components. F, also known as Jacobian, encodes both the locally affine deformation and local rotation. This implies that it should be used for visualizing Primary Strain Directions (PSD) and deformation ellipses and ellipsoids on the target configuration. Using C=FTF allows, instead, to compute PSD and to visualize them on the source configuration. Moreover, C allows the computation of the strain energy that can be evaluated and mapped locally at any point of a body using an interpolation function. In addition, it is possible, by exploiting the second order Jacobian, to calculate the amount of the non affine deformation in the neighborhood of the evaluation point by computing the body bending energy enclosed in the deformation. In this contribution, we present i) the main computational methods for evaluating local deformation metrics, ii) a number of different strategies to visualize them on both undeformed and deformed configurations and iii) the potential pitfalls in ignoring the actual three-dimensional nature of F when it is evaluated along a surface identified by a triangulation in three dimensions.

Locomotory Adaptations in 3D Humerus Geometry of Xenarthra: Testing for Convergence

Abstract: Three-dimensional (3D) models of fossil bones are increasingly available, thus opening a novel frontier in the study of organismal size and shape evolution. We provide an example of how photogrammetry can be combined with Geometric Morphometrics (GMM) techniques to study patterns of morphological convergence in the mammalian group of Xenarthra. Xenarthrans are currently represented by armadillos, sloths, and anteaters. However, this clade shows an incredibly diverse array of species and ecomorphotypes in the fossil record, including gigantic ground sloths and glyptodonts. Since the humerus is a weight-bearing bone in quadrupedal mammals and its morphology correlates with locomotor behavior, it provides an ideal bone to gain insight into adaptations of fossil species. A 3D sample of humerii belonging to extant and fossil Xenarthra allowed us to identify a significant phylogenetic signal and a strong allometric component in the humerus shape. Although no rate shift in the evolution of the humerus shape was recorded for any clade, fossorial and arboreal species humerii did evolve at significantly slower and faster paces, respectively, than the rest of the Xenarthran species. Significant evidence for morphological convergence found among the fossorial species and between the two tree sloth genera explains these patterns. These results suggest that the highly specialized morphologies of digging taxa and tree sloths represent major deviations from the plesiomorphic Xenarthran body plan, evolved several times during the history of the group.

Editorial: Evolving Virtual and Computational Paleontology

Abstract: During the last few decades, the development of new technologies and methods, and increases in computational power, are widening Paleontology’s research frontiers, moving this discipline—situated halfway between Biology and Geology—toward increasing use of (paleo) biological and (paleo)ecological approaches, and providing the opportunity to fully explore quantitative aspects of phenotypic evolution as well as new clues to the history of life. The everincreasing availability of 3D models obtained by CT, surface scanning (SC) and/or photogrammetry (PT) is increasing the visibility and accessibility of rare, difficult to handle, remains, and therefore the number of virtual fossil representations that feature in scientific papers, contributing to this “revolution” and leading to the dawn of the “Virtual and Computational Paleontology” era. The pioneering steps toward this new era were taken in the early 1980s, when Tate and Cann (1982) and Conroy and Vannier (1984) became the first research teams to apply CT to Vertebrate Paleontology. Almost two decades later, the first applications of SC and PT to Vertebrate Paleontology opened the door to many new ideas and approaches (Lyons et al., 2000; Breithaupt and Matthews, 2001). Since the beginning of this digital paleontological era, the number of scientists merging traditional techniques with virtualization and computational advances has greatly increased, a process that still continues (and the first comprehensive reviews were published a few years later see Zollikofer and Ponce de Leon, 2005; Cardini and Loy, 2013; Sutton et al., 2014). Virtual (digital) representations have a great variety of non-invasive applications, including but not limited to digital curation (based on 3D models libraries), virtual restoration of specimens, and anatomical studies of both external and internal morphological structures, and open up the opportunities for development of new analytical tools. Thanks to virtualization, many Computational analyses and techniques (including geometric morphometrics, finite element analysis, multibody dynamic analysis, computational fluid dynamics, machine-learning, etc.) have been widely applied in Vertebrate Paleontology. Furthermore, their use is currently rapidly increasing thanks to continuing efforts to create more and better 3D virtual models, which are the basis for new computational approaches. Despite these many benefits, Virtual and Computational Paleontology is still not prevalent as it might be. Virtual data are therefore not broadly shared and new methodologies and techniques usually do not easily reach the widest audience, in particular younger researchers who usually show an insatiable hunger for learning and acquiring new skills. This Research Topic was conceived with the principal goal of spreading this technological knowledge and, by taking advantage of the Open Access format of Frontiers, was intended to reach the widest possible number of researchers. The volume includes 15 different papers on the use and analysis of virtual representations and new computational methods, applied to several vertebrate taxa. Edited and reviewed by: Corwin Sullivan, University of Alberta, Canada

From smart apes to human brain boxes. A uniquely derived brain shape in late hominins clade

Abstract: Modern humans have larger and more globular brains when compared to other primates. Such anatomical features are further reflected in the possession of a moderately asymmetrical brain with the two hemispheres apparently rotated counterclockwise and slid anteroposteriorly on one another, in what is traditionally described as the Yakovlevian Torque. Developmental disturbance in human brain asymmetry, or lack thereof, has been linked to several cognitive disorders including schizophrenia and depression. More importantly, the presence of the Yakovlevian Torque is often advocated as the exterior manifestation of our unparalleled cognitive abilities. Consequently, studies of brain size and asymmetry in our own lineage indirectly address the question of what, and when, made us humans, trying to trace the emergence of brain asymmetry and expansion of cortical areas back in our Homo antecedents. Here we tackle this same issue studying the evolution of human brain size, shape and asymmetry on a phylogenetic tree including nineteen apes and Homo species, inclusive of our fellow ancestors. We found that a significant positive shift in the rate of brain shape evolution pertains to the clade including modern humans, Neanderthals and Homo heidelbergensis. Although the Yakovlevian Torque is well evident in these species and levels of brain asymmetry are correlated to changes in brain shape, further early Homo species possess the torque. Even though, a strong allometric component is present in hominoids brain shape variability, this component seems unrelated to asymmetry and to the rate shift we recorded. These results suggest that changes in brain size and asymmetry were not the sole factors behind the fast evolution of brain shape in the most recent Homo species. The emergence of handedness and early manifestations of cultural modernity in the archaeological record nicely coincide with the same three species sharing the largest and most rapidly evolving brains among all hominoids.

Human footprints from Italy: the state of the art

Abstract: The ichnological record of human traces from Italy is rich and quite diversified. In recent years, the development and dissemination of various methodologies and technological facilities has implemented the re-analysis of this record, enabling to reach different, sometimes deeper, interpretations favoured by the integration of external data, both geological and palaeontological. The oldest occurrence of the human ichnological record from Italy is represented by the Middle Pleistocene ‘Devil’s Trails’ ichnosite in the “Foresta” area (Roccamonfina volcano, southern Italy), depicting human trackmakers trampling a pyroclastic flow deposit while descending a slope about 349 ka. Most of the record is Holocene in age and is constituted by the Upper Palaeolithic Grotta della Basura site (Toirano, northern Italy, about 14 ky), the protohistoric sites of Afragola, Nola and Palma, the area of Pompei and the site of Aosta. The record is enriched by the ichnological evidences preserved in military structures of Trentino region (northern Italy) during the First World War. An updated report and discussion of these sites is here provided .

MInOSSE: A new method to reconstruct geographic ranges of fossil species

Abstract: Handling Editor: Huijie Qiao Abstract 1. Estimating fossil species' geographic range is a major goal for paleobiologists. In the deep time, this is most commonly performed by using polygon-based methods such as the minimum convex polygon (MCP) or the Alpha-Hull. Unfortunately, such methods provide a poor representation of the fossil species' actual range, because they are unable to take control of the severe stochastic and taphonomic biases. 2. Here, we introduce MInOSSE (massively interpolated occurrences for species spatial estimation), a model-based method that combines a machine learning algorithm and geostatistical approaches to reconstruct a target fossil species' geographic ranges by relying on the distribution of other coeval species and without using environmental predictors. 3. We tested MInOSSE by using many simulated fossil species' distributions, comparing its performance with MCP and Alpha-Hull outcomes and applying it to real case studies. 4. In all simulations, MInOSSE outperformed the competing methods. Interestingly, the superior performance of MInOSSE becomes more apparent when the fossil record of the target species is scarce, that is, when appropriate range reconstruction is most problematic with polygon-based methods. 5. MInOSSE is a powerful tool for researchers interested in studying geographic range evolution, effects of range size on extinction risk, as well as biodiversity dynamics and macroecological patterns in the deep time.

Oichnus taddeii, a new fossil trace produced by capulids on brachiopod shells

Abstract: We describe the new ichnospecies Oichnus taddeii, a bioerosion trace left by parasitic capulids on fossil brachiopods, prevalently Quaternary Terebratula species. We present the diagnosis of the new ichnospecies and discuss its status. The trace was previously attributed to either Oichnus or Lacrimichnus ichngenera. We provide a statistical assessment of the trace distribution on brachiopod shells, in order to infer the capulid behaviour, and the parasitic activity the trace represents