A 450 million years long latitudinal gradient in age-dependent extinction.

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.

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.

Reproducing the internal and external anatomy of fossil bones: Two new automatic digital tools.

OBJECTIVES: We present two new automatic tools, developed under the R environment, to reproduce the internal and external structures of bony elements. The first method, Computer-Aided Laser Scanner Emulator (CA-LSE), provides the reconstruction of the external portions of a 3D mesh by simulating the action of a laser scanner. The second method, Automatic Segmentation Tool for 3D objects (AST-3D), performs the digital reconstruction of anatomical cavities. MATERIALS AND METHODS: We present the application of CA-LSE and AST-3D methods to different anatomical remains, highly variable in terms of shape, size and structure: a modern human skull, a malleus bone, and a Neanderthal deciduous tooth. Both methods are developed in the R environment and embedded in the packages "Arothron" and "Morpho," where both the codes and the data are fully available. RESULTS: The application of CA-LSE and AST-3D allows the isolation and manipulation of the internal and external components of the 3D virtual representation of complex bony elements. In particular, we present the output of the four case studies: a complete modern human endocast and the right maxillary sinus, the dental pulp of the Neanderthal tooth and the inner network of blood vessels of the malleus. DISCUSSION: Both methods demonstrated to be much faster, cheaper, and more accurate than other conventional approaches. The tools we presented are available as add-ons in existing software within the R platform. Because of ease of application, and unrestrained availability of the methods proposed, these tools can be widely used by paleoanthropologists, paleontologists and anatomists.

The evolution of cranial base and face in Cercopithecoidea and Hominoidea: Modularity and morphological integration.

The evolutionary relationship between the base and face of the cranium is a major topic of interest in primatology. Such areas of the skull possibly respond to different selective pressures. Yet, they are often said to be tightly integrated. In this paper, we analyzed shape variability in the cranial base and the facial complex in Cercopithecoidea and Hominoidea. We used a landmark-based approach to single out the effects of size (evolutionary allometry), morphological integration, modularity, and phylogeny (under Brownian motion) on skull shape variability. Our results demonstrate that the cranial base and the facial complex exhibit different responses to different factors, which produces a little degree of morphological integration between them. Facial shape variation appears primarily influenced by body size and sexual dimorphism, whereas the cranial base is mostly influenced by functional factors. The different adaptations affecting the two modules suggest they are best studied as separate and independent units, and that-at least when dealing with Catarrhines-caution must be posed with the notion of strong cranial integration that is commonly invoked for the evolution of their skull shape.

Modelling reveals the effect of climate and land use change on Madagascar's chameleons fauna.

The global biodiversity crisis is generated by the combined effects of human-induced climate change and land conversion. Madagascar is one of the World's most renewed hotspots of biodiversity. Yet, its rich variety of plant and animal species is threatened by deforestation and climate change. Predicting the future of Madagascar's chameleons, in particular, is complicated by their ecological rarity, making it hard to tell which factor is the most menacing to their survival. By applying an extension of the ENphylo species distribution model algorithm to work with extremely rare species, we find that Madagascar chameleons will face intense species loss in the north-western sector of the island. Land conversion by humans will drive most of the loss, and will intersect in a complex, nonlinear manner with climate change. We find that some 30% of the Madagascar's chameleons may lose in the future nearly all their habitats, critically jeopardizing their chance for survival.

RRmorph-a new R package to map phenotypic evolutionary rates and patterns on 3D meshes.

The study of evolutionary rates and patterns is the key to understand how natural selection shaped the current and past diversity of phenotypes. Phylogenetic comparative methods offer an array of solutions to undertake this challenging task, and help understanding phenotypic variation in full in most circumstances. However, complex, three-dimensional structures such as the skull and the brain serve disparate goals, and different portions of these phenotypes often fulfil different functions, making it hard to understand which parts truly were recruited by natural selection. In the recent past, we developed tools apt to chart evolutionary rate and patterns directly on three-dimensional shapes, according to their magnitude and direction. Here, we present further developments of these tools, which now allow to restitute the mapping of rates and patterns with full biological realism. The tools are condensed in a new R software package.

Climate shifts orchestrated hominin interbreeding events across Eurasia.

When, where, and how often hominin interbreeding happened is largely unknown. We study the potential for Neanderthal-Denisovan admixture using species distribution models that integrate extensive fossil, archaeological, and genetic data with transient coupled general circulation model simulations of global climate and biomes. Our Pleistocene hindcast of past hominins' habitat suitability reveals pronounced climate-driven zonal shifts in the main overlap region of Denisovans and Neanderthals in central Eurasia. These shifts, which influenced the timing and intensity of potential interbreeding events, can be attributed to the response of climate and vegetation to past variations in atmospheric carbon dioxide and Northern Hemisphere ice-sheet volume. Therefore, glacial-interglacial climate swings likely played an important role in favoring gene flow between archaic humans.

Homo sapiens and Neanderthals share high cerebral cortex integration into adulthood.

There is controversy around the mechanisms that guided the change in brain shape during the evolution of modern humans. It has long been held that different cortical areas evolved independently from each other to develop their unique functional specializations. However, some recent studies suggest that high integration between different cortical areas could facilitate the emergence of equally extreme, highly specialized brain functions. Here, we analyse the evolution of brain shape in primates using three-dimensional geometric morphometrics of endocasts. We aim to determine, firstly, whether modern humans present unique developmental patterns of covariation between brain cortical areas; and secondly, whether hominins experienced unusually high rates of evolution in brain covariation as compared to other primates. On the basis of analyses including modern humans and other extant great apes at different developmental stages, we first demonstrate that, unlike our closest living relatives, Homo sapiens retain high levels of covariation between cortical areas into adulthood. Among the other great apes, high levels of covariation are only found in immature individuals. Secondly, at the macro-evolutionary level, our analysis of 400 endocasts, representing 148 extant primate species and 6 fossil hominins, shows that strong covariation between different areas of the brain in H. sapiens and Homo neanderthalensis evolved under distinctly higher evolutionary rates than in any other primate, suggesting that natural selection favoured a greatly integrated brain in both species. These results hold when extinct species are excluded and allometric effects are accounted for. Our findings demonstrate that high covariation in the brain may have played a critical role in the evolution of unique cognitive capacities and complex behaviours in both modern humans and Neanderthals.

Correction: A new, fast method to search for morphological convergence with shape data.

[This corrects the article DOI: 10.1371/journal.pone.0226949.].

A Major Change in Rate of Climate Niche Envelope Evolution during Hominid History.

Homo sapiens is the only species alive able to take advantage of its cognitive abilities to inhabit almost all environments on Earth. Humans are able to culturally construct, rather than biologically inherit, their occupied climatic niche to a degree unparalleled within the animal kingdom. Precisely, when hominins acquired such an ability remains unknown, and scholars disagree on the extent to which our ancestors shared this same ability. Here, we settle this issue using fine-grained paleoclimatic data, extensive archaeological data, and phylogenetic comparative methods. Our results indicate that whereas early hominins were forced to live under physiologically suitable climatic conditions, with the emergence of H. heidelbergensis, the Homo climatic niche expanded beyond its natural limits, despite progressive harshening in global climates. This indicates that technological innovations providing effective exploitation of cold and seasonal habitats predated the emergence of Homo sapiens.

A New Tool for Digital Alignment in Virtual Anthropology.

The study of the fossil record is fundamental to understand the evolution of traits. Because fossil remains are often fragmented and/or deformed by taphonomic processes, a preliminary realignment of their constituent parts is often necessary to properly interpret their shapes. In virtual anthropology, these procedures are carried out using digital models of the remains. We present a new semi-automatic alignment R software, Digital Tool for Alignment (DTA), which uses the shape information contained in a reference sample to find the best alignment solution for the disarticulated regions. We tested DTA on three different case-studies: (1) a sample of 14 primate species including both male and female individuals, (2) a simulated, disarticulated skull of Homo sapiens, and (3) a real disarticulated human fossil specimen, Amud 1 (Homo neanderthalensis). In the first case study, we simulated disarticulation directly on digital models of the primate skulls and tested alignment quality as a function of phylogenetic proximity, sex, and body size. In the second, we compared DTA to manual alignments conducted for the same digital models. Finally, we performed DTA on a real-world case study. We found that phylogenetic proximity provides is the most important factor for alignment efficiency. However, sex and allometric effects might also be important and should therefore be taken into account at selecting reference models for alignments. DTA performs at least as well as manual alignments. Yet, as compared to manual procedures, it is faster, requires no prior anatomical knowledge and expertise and allows indefinite manipulation of the fossil items. Anat Rec, 302:1104-1115, 2019. © 2019 Wiley Periodicals, Inc.

A new, fast method to search for morphological convergence with shape data.

Morphological convergence is an intensely studied macroevolutionary phenomenon. It refers to the morphological resemblance between phylogenetically distant taxa. Currently available methods to explore evolutionary convergence either: rely on the analysis of the phenotypic resemblance between sister clades as compared to their ancestor, fit different evolutionary regimes to different parts of the tree to see whether the same regime explains phenotypic evolution in phylogenetically distant clades, or assess deviations from the congruence between phylogenetic and phenotypic distances. We introduce a new test for morphological convergence working directly with non-ultrametric (i.e. paleontological) as well as ultrametric phylogenies and multivariate data. The method (developed as the function search.conv within the R package RRphylo) tests whether unrelated clades are morphologically more similar to each other than expected by their phylogenetic distance. It additionally permits using known phenotypes as the most recent common ancestors of clades, taking full advantage of fossil information. We assessed the power of search.conv and the incidence of false positives by means of simulations, and then applied it to three well-known and long-discussed cases of (purported) morphological convergence: the evolution of grazing adaptation in the mandible of ungulates with high-crowned molars, the evolution of mandibular shape in sabertooth cats, and the evolution of discrete ecomorphs among anoles of Caribbean islands. The search.conv method was found to be powerful, correctly identifying simulated cases of convergent morphological evolution in 95% of the cases. Type I error rate is as low as 4-6%. We found search.conv is some three orders of magnitude faster than a competing method for testing convergence.