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OBJECTIVES: The statistical analysis of fossil remains is essential to understand the evolution of the genus Homo. Unfortunately, the human fossil record is straight away scarce and plagued with severe loss of information caused by taphonomic processes. The recently developed field of Virtual Anthropology helps to ameliorate this situation by using digital techniques to restore damaged and incomplete fossils. MATERIALS AND METHODS: We present the package Arothron, an R software suite meant to process and analyze digital models of skeletal elements. Arothron includes tools to digitally extract virtual cavities such as cranial endocasts, to statistically align disarticulated or broken bony elements, and to visualize local variations between surface meshes and landmark configurations. RESULTS: We describe the main functionalities of Arothron and illustrate their usage through reproducible case studies. We describe a tool for segmentation of skeletal cavities by showing its application on a malleus bone, a Neanderthal tooth, and a modern human cranium, reproducing their shape and calculating their volume. We illustrate how to digitally align a disarticulated model of a modern human cranium, and how to combine piecemeal shape information on individual specimens into one. In addition, we present useful visualization tools by comparing the morphological differences between the right hemisphere of the Neanderthal and the modern human brain. CONCLUSIONS: The Arothron R package is designed to study digital models of fossil specimens. By using Arothron, scientists can handle digital models with ease, investigate the inner morphology of 3D skeletal models, gain a full representation of the original shapes of damaged specimens, and compare shapes across specimens.

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., We developed a new method using deep learning to infer age‐dependent extinction and analyzed 450 myr of marine life across 21 invertebrate clades. We found that extinction rate significantly decreases with age in > 90% of the cases. We propose that the latitudinal diversity gradient and selection at the species level account for this exceptional, yet little recognized, macroevolutionary and macroecological pattern.

Table S1. Procrustes ANOVA test for the significance of the species, life stage effects and their interaction on shape differences; Table S2. Test for a common multivariate allometric trajectory. (PDF 17 kb)

 Supplementary methods and results. (DOCX 316 kb)

The geometric morphometric (GM) analysis of complex anatomical structures is an ever more powerful tool to study biological variability, adaptation and evolution. Here, we propose a new method (combinland), developed in R, meant to combine the morphological information contained in different landmark coordinate sets into a single dataset, under a GM context. combinland builds a common ordination space taking into account the entire shape information encoded in the starting configurations. We applied combinland to a Primate case study including 133 skulls belonging to 14 species. On each specimen, we simulated photo acquisitions converting the 3D landmark sets into six 2D configurations along standard anatomical views. The application of combinland shows statistically negligible differences in the ordination space compared to that of the original 3D objects, in contrast to a previous method meant to address the same issue. Hence, we argue combinland allows to correctly retrieve 3D-quality statistical information from 2D landmark configurations. This makes combinland a viable alternative when the extraction of 3D models is not possible, recommended, or too expensive, and to make full use of disparate sources (and views) of morphological information regarding the same specimens. The code and examples for the application of combinland are available in the Arothron R package. © 2018 Associazione Teriologica Italiana.

We characterized motion attributes arising from LV spatio-temporal analysis of motion distributions in myocardial infarction. Time-varying 3D finite element shape models were obtained in 300 Controls and 300 patients with myocardial infarction. Inter-individual left ventricular shape differences were eliminated using parallel transport to the grand mean of all cases. The first three principal component (PC) scores were used to characterize trajectory attributes. Scores were tested with ANOVA/MANOVA using patient disease status (Infarcts vs. Controls) as a factor. Infarcted patients had significantly different magnitude, orientation and shape of left ventricular trajectories in comparison to Controls. Significant differences were found for the angle between PC scores 1 and 2 in the endocardium, and PC scores 1 and 3 in the epicardium. The largest differences were found in the magnitude of endocardial motion. Endocardial PC scores in shape space showed the highest classification power using support vector machine, with higher total accuracy in comparison to previous methods. Shape space performed better than size-and-shape space for both epicardial and endocardial features. In conclusion, LV spatio-temporal motion attributes accurately characterize the presence of infarction. This approach is easily generalizable to different pathologies, enabling more precise study of the pathophysiological consequences of a wide spectrum of cardiac diseases.

The generic attribution of the Plio-Pleistocene Polish moles Neurotrichus? polonicus and Neurotrichus? skoczeni has been questioned several times in the past. The fossil material belonging to Neurotrichus? polonicus and Neurotrichus? skoczeni is re-evaluated here and a new diagnosis is provided on the basis of qualitative considerations. In addition, a Geometric Morphometric analysis of the humerus has been performed including both extant and extinct Neurotrichini and Urotrichini taxa for comparison. Our results proved the unique morphology of the Polish material suggesting a distinct taxonomic state. The morphological variations evidenced by the humeral shape analysis agree with the observed qualitative differences and support a new generic allocation. The new genus Rzebikia gen. nov. is proposed for all the material previoulsly ascribed to Neurotrichus? polonicus and Neurotrichus? skoczeni.

The study of more than 100 skeletal remains of Hispanochampsa muelleri Kälin, 1936, from the Oligocene of El Talladell (Lleida Province, Catalonia, Spain), has been decisive in revealing misinterpretations about its anatomy and phylogenetic position. Hispanochampsa muelleri is shown to be a member of the clade Diplocynodontinae, and is here considered a junior synonym of Diplocynodon. This analysis provides strong evidence for this monophyletic grouping, which is made up of the species Baryphracta deponiae, Diplocynodon darwini, Diplocynodon muelleri, D. tormis, D. ratelii, and D. hantoniensis. All of these species bear ventral osteoderms with paired ossifications, and a deep posterior tip of the iliac blade, which are synapomorphies of Diplocynodontinae. However, the interrelationships of the Diplocynodontinae remain unresolved. D. muelleri shares with D. hantoniensis, D. tormis, and D. ratelii the presence of an enlarged jugal foramen, and the particular dentary occlusion in line with the maxillary tooth row. It is highly likely that the two Spanish species, Diplocynodon muelleri and Diplocynodon tormis, were close relatives.

Among non-marine Paleogene vertebrates of Italy, freshwater fishes, amphibians and birds are very rare. Also reptiles and mammals are few and they lack from Paleocene strata. Eocene reptiles have been collected in some localities of Veneto. Aquatic snakes have been described from Monte Bolca whilst in sediments of freshwater origin of the same sequence, at Purga di Bolca, relatively well .preserved turtles and crocodiles have been found. A beautiful skull of crocodile has been discovered in late Middle Eocene coastal sediments of Monte Duello (Veneto), together with scanty remains of a bird and abundant remains of marine organisms. Oligocene reptiles (turtles and crocodiles) have been collected at Monteviale (Veneto) and in some others sites of Veneto and Liguria. Eocene mammals have been described only from the Sulcis area (Sardinia). Two perissodactyls (the first of late Early Eocene and the second of early Middle Eocene age) and a marsupial (of early Middle Eocene age) have been collected. All the species indicate close affinities with taxa of western Europe. Affinities with central Europe and Balkan area faunas are testified by the oldest (Early Oligocene) and richest Oligocene mammalian assemblage, collected at Monteviale (Veneto). A small faunula from Agnana (Calabria), of late Early Oligocene age, immigrated into this area from Western Europe through Corsica-Sardinia. Typical western European mammalian faunas have been collected from some localities in Liguria and Piedmont. The most important fossiliferous sites in this area are Cadibona (Liguria) and Bagnasco (Piedmont) where slightly different faunas of early Late Oligocene age have been collected. In the same area isolated mammal remains of latest Oligocene age have been found.

HYLAEOCHAMPSIDAE ANDREWS, 1913 Definition A node-based clade stemming from the most recent common ancestor of Hylaeochampsa vectiana Andrews, 1913, Iharkutosuchus makadii Ösi et al., 2007, Pachycheilosuchus trinquei Rogers, 2003, and Pietraroiasuchus ormezzanoi. Revised diagnosis of hylaeochampsidae: Small eusuchians with brevirostral skull and thickned cranial and postcranial bones. Premaxillary (unknown in Hylaeochampsa and in Pachycheilosuchus) and anterior maxillary alveolar series of subequal size, maxilla posteriorly extends in a process devoid of teeth, minimal sculpturing of maxillary surface, reduced number of maxillary teeth, prefrontal longer than lachrymal (differing in Pietraroiasuchus, whereby the prefrontal and lachrymal are the same size, and unknown in P. trinquei); extremely narrow suborbital fenestra (unambiguous synapomorphy for the clade); choana anteriorly set in pterygoid (unknown in P. trinquei), pterygoid flanges relatively short and not reaching laterally the level of the quadrate medial condyle (unknown in P. trinquei), extremely robust ectopterygoid with expanded jugal and maxilla sutures, protuberance in the ventral surface of the quadrate with prominent muscle scars (unambiguous synapomorphy for the clade); vertical ridge at the occipital surface (unambiguous synapomorphy for the clade, unknown in P. trinquei), reduced anteroposterior extension of the quadrate articular process that does not (but may almost) reach the level of the occipital condyle (unambiguous synapomorphy for the clade, unknown in P. trinquei), anterodorsal margin of surangular elevated and extended (unknown in Hylaeochampsa)., Published as part of Buscalioni, Angela D., Piras, Paolo, Vullo, Romain, Signore, Marco & Barbera, Carmela, 2011, Early eusuchia crocodylomorpha from the vertebrate-rich Plattenkalk of Pietraroia (Lower Albian, southern Apennines, Italy), pp. 644-645 in Zoological Journal of the Linnean Society 163 (5) on pages 644-645, DOI: 10.1111/j.1096-3642.2011.00718.x, http://zenodo.org/record/5441720, {"references":["Andrews CW. 1913. On the skull and part of the skeleton a crocodile from the Middle Purbeck of Swanage, with the description of a new species (Pholidosaurus laevis) and a note on the skull of Hylaeochampsa. Annals and Magazine of Natural History 8: 485 - 494.","Osi A, Clark J, Weishampel DB. 2007. First report on a new basal eusuchian crocodyliform with multicusped teeth from the Upper Cretaceous (Santonian) of Hungary. Neues Jarhbuch fur Geologie und Palaontologie-Abhandlungen 243: 169 - 177.","Rogers JVI. 2003. Pachycheilosuchus trinquei, a new procoelous crocodyliform from the Lower Cretaceous (Albian) Glen Rose Formation of Texas. Journal of Vertebrate Paleontology 23: 128 - 145."]}