Climate effects on archaic human habitats and species successions.

It has long been believed that climate shifts during the last 2 million years had a pivotal role in the evolution of our genus Homo1-3. However, given the limited number of representative palaeo-climate datasets from regions of anthropological interest, it has remained challenging to quantify this linkage. Here, we use an unprecedented transient Pleistocene coupled general circulation model simulation in combination with an extensive compilation of fossil and archaeological records to study the spatiotemporal habitat suitability for five hominin species over the past 2 million years. We show that astronomically forced changes in temperature, rainfall and terrestrial net primary production had a major impact on the observed distributions of these species. During the Early Pleistocene, hominins settled primarily in environments with weak orbital-scale climate variability. This behaviour changed substantially after the mid-Pleistocene transition, when archaic humans became global wanderers who adapted to a wide range of spatial climatic gradients. Analysis of the simulated hominin habitat overlap from approximately 300-400 thousand years ago further suggests that antiphased climate disruptions in southern Africa and Eurasia contributed to the evolutionary transformation of Homo heidelbergensis populations into Homo sapiens and Neanderthals, respectively. Our robust numerical simulations of climate-induced habitat changes provide a framework to test hypotheses on our human origin.

Phase synchronization between culture and climate forcing.

Over the history of humankind, cultural innovations have helped improve survival and adaptation to environmental stress. This has led to an overall increase in human population size, which in turn further contributed to cumulative cultural learning. During the Anthropocene, or arguably even earlier, this positive sociodemographic feedback has caused a strong decline in important resources that, coupled with projected future transgression of planetary boundaries, may potentially reverse the long-term trend in population growth. Here, we present a simple consumer/resource model that captures the coupled dynamics of stochastic cultural learning and transmission, population growth and resource depletion in a changing environment. The idealized stochastic mathematical model simulates boom/bust cycles between low-population subsistence, high-density resource exploitation and subsequent population decline. For slow resource recovery time scales and in the absence of climate forcing, the model predicts a long-term global population collapse. Including a simplified periodic climate forcing, we find that cultural innovation and population growth can couple with climatic forcing via nonlinear phase synchronization. We discuss the relevance of this finding in the context of cultural innovation, the anthropological record and long-term future resilience of our own predatory species.

Too simple models may predict the island rule for the wrong reasons.

Biddick & Burns (2021) proposed a null/neutral model that reproduces the island rule as a product of random drift. We agree that it is unnecessary to assume adaptive processes driving island dwarfing or gigantism, but several flaws make their approach unrealistic and thus unsuitable as a stochastic model for evolutionary size changes.

morphomap: An R package for long bone landmarking, cortical thickness, and cross-sectional geometry mapping.

OBJECTIVES: This study describes and demonstrates the functionalities and application of a new R package, morphomap, designed to extract shape information as semilandmarks in multiple sections, build cortical thickness maps, and calculate biomechanical parameters on long bones. METHODS: morphomap creates, from a single input (an oriented 3D mesh representing the long bone surface), multiple evenly spaced virtual sections. morphomap then directly and rapidly computes morphometric and biomechanical parameters on each of these sections. The R package comprises three modules: (a) to place semilandmarks on the inner and outer outlines of each section, (b) to extract cortical thicknesses for 2D and 3D morphometric mapping, and (c) to compute cross-sectional geometry. RESULTS: In this article, we apply morphomap to femora from Homo sapiens and Pan troglodytes to demonstrate its utility and show its typical outputs. morphomap greatly facilitates rapid analysis and functional interpretation of long bone form and should prove a valuable addition to the osteoarcheological analysis software toolkit. CONCLUSIONS: Long bone loading history is commonly retrodicted by calculating biomechanical parameters such as area moments of inertia, analyzing external shape and measuring cortical thickness. morphomap is a software written in the open source R environment, it integrates the main methodological approaches (geometric morphometrics, cortical morphometric maps, and cross-sectional geometry) used to parametrize long bones.

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.

Impact of transition to a subterranean lifestyle on morphological disparity and integration in talpid moles (Mammalia, Talpidae).

BACKGROUND: Understanding the mechanisms promoting or constraining morphological diversification within clades is a central topic in evolutionary biology. Ecological transitions are of particular interest because of their influence upon the selective forces and factors involved in phenotypic evolution. Here we focused on the humerus and mandibles of talpid moles to test whether the transition to the subterranean lifestyle impacted morphological disparity and phenotypic traits covariation between these two structures. RESULTS: Our results indicate non-subterranean species occupy a significantly larger portion of the talpid moles morphospace. However, there is no difference between subterranean and non-subterranean moles in terms of the strength and direction of phenotypic integration. CONCLUSIONS: Our study shows that the transition to a subterranean lifestyle significantly reduced morphological variability in talpid moles. However, this reduced disparity was not accompanied by changes in the pattern of traits covariation between the humerus and the mandible, suggesting the presence of strong phylogenetic conservatism within this pattern.

Quantitative genetics of body size evolution on islands: an individual-based simulation approach.

According to the island rule, small-bodied vertebrates will tend to evolve larger body size on islands, whereas the opposite happens to large-bodied species. This controversial pattern has been studied at the macroecological and biogeographical scales, but new developments in quantitative evolutionary genetics now allow studying the island rule from a mechanistic perspective. Here, we develop a simulation approach based on an individual-based model to model body size change on islands as a progressive adaptation to a moving optimum, determined by density-dependent population dynamics. We applied the model to evaluate body size differentiation in the pigmy extinct hominin Homo floresiensis, showing that dwarfing may have occurred in only about 360 generations (95% CI ranging from 150 to 675 generations). This result agrees with reports suggesting rapid dwarfing of large mammals on islands, as well as with the recent discovery that small-sized hominins lived in Flores as early as 700 kyr ago. Our simulations illustrate the power of analysing ecological and evolutionary patterns from an explicit quantitative genetics perspective.

Bacteria and parasites in Podarcis sicula and P. sicula klemmerii.

BACKGROUND: New epidemiological data on bacterial and parasitic infections in 24 Italian wall lizards, namely Podarcis sicula (mainland population) and P. sicula klemmerii (insular population) in southern Italy were provided. To achieve this goal, samples were collected from individuals belonging to the two populations and analysed by microbiological and parasitological methods. RESULTS: A wide range of bacteria (e.g. Pantoea spp., Citrobacter spp., Morganella spp., Pseudomonas, Enterobacter spp., Staphylococcus spp. and Escherichia coli) and parasites (e.g. Ophionyssus natricis, coccidia, Dicrocoelidae) were detected in both P. sicula and P. sicula klemmerii individuals. Insular population presented similar bacterial and parasitic diversity to its mainland counterpart. Ampicillin was the antimicrobial with the highest resistance rate. CONCLUSION: This study highlighted various bacteria and parasites, some of them potentially zoonotic. Further studies are needed to better understand the epidemiology and transmission routes of these pathogens along with their impact on the welfare and behaviour of Italian wall lizards.

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.

Island Rule, quantitative genetics and brain-body size evolution in Homo floresiensis.

Colonization of islands often activate a complex chain of adaptive events that, over a relatively short evolutionary time, may drive strong shifts in body size, a pattern known as the Island Rule. It is arguably difficult to perform a direct analysis of the natural selection forces behind such a change in body size. Here, we used quantitative evolutionary genetic models, coupled with simulations and pattern-oriented modelling, to analyse the evolution of brain and body size in Homo floresiensis, a diminutive hominin species that appeared around 700 kya and survived up to relatively recent times (60-90 kya) on Flores Island, Indonesia. The hypothesis of neutral evolution was rejected in 97% of the simulations, and estimated selection gradients are within the range found in living natural populations. We showed that insularity may have triggered slightly different evolutionary trajectories for body and brain size, which means explaining the exceedingly small cranial volume of H. floresiensis requires additional selective forces acting on brain size alone. Our analyses also support previous conclusions that H. floresiensis may be most likely derived from an early Indonesian H. erectus, which is coherent with currently accepted biogeographical scenario for Homo expansion out of Africa.

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.

From Evolutionary Allometry to Sexual Display: (A Reply to Holman and Bro-Jørgensen).

Conventional wisdom holds that the complex shapes of deer antlers are produced under the sole influence of sexual selection. We questioned this view by demonstrating that trends for increased body size evolution passively yield more-complex ornaments, even in organisms where no effect of sexual selection is possible, with similar allometric slopes. Recent investigations suggest that sexual selection on antlers of larger deer species is stronger than that in smaller species; hence, the use of conspicuous antlers for display in large male deer is a secondary function driven by especially intense sexual selection on these large-bodied species. Since ancestral deer were small and had very simple antlers, such an intense selection on antlers shape was probably absent in early deer. Therefore, the evolution of complex ornaments is coupled with body size evolution, even in deer.

Modeling the Population-Level Processes of Biodiversity Gain and Loss at Geological Timescales.

The path of species diversification is commonly observed by inspecting the fossil record. Yet, how species diversity changes at geological timescales relate to lower-level processes remains poorly understood. Here we use mathematical models of spatially structured populations to show that natural selection and gradual environmental change give rise to discontinuous phenotype changes that can be connected to speciation and extinction at the macroevolutionary level. In our model, new phenotypes arise in the middle of the environmental gradient, while newly appearing environments are filled by existing phenotypes shifting their adaptive optima. Slow environmental change leads to loss of phenotypes in the middle of the extant environmental range, whereas fast change causes extinction at one extreme of the environmental range. We compared our model predictions against a well-known yet partially unexplained pattern of intense hoofed mammal diversification associated with grassland expansion during the Late Miocene. We additionally used the model outcomes to cast new insight into Cope's law of the unspecialized. Our general finding is that the rate of environmental change determines where generation and loss of diversity occur in the phenotypic and physical spaces.

Cope's Rule and the Universal Scaling Law of Ornament Complexity.

Luxuriant, bushy antlers, bizarre crests, and huge, twisting horns and tusks are conventionally understood as products of sexual selection. This view stems from both direct observation and from the empirical finding that the size of these structures grows faster than body size (i.e., ornament size shows positive allometry). We contend that the familiar evolutionary increase in the complexity of ornaments over time in many animal clades is decoupled from ornament size evolution. Increased body size comes with extended growth. Since growth scales to the quarter power of body size, we predicted that ornament complexity should scale according to the quarter power law as well, irrespective of the role of sexual selection in the evolution and function of the ornament. To test this hypothesis, we selected three clades (ammonites, deer, and ceratopsian dinosaurs) whose species bore ornaments that differ in terms of the importance of sexual selection to their evolution. We found that the exponent of the regression of ornament complexity to body size is the same for the three groups and is statistically indistinguishable from 0.25. We suggest that the evolution of ornament complexity is a by-product of Cope's rule. We argue that although sexual selection may control size in most ornaments, it does not influence their shape.

Polyostotic Chondroblastic Osteosarcoma in a Kestrel ( Falco tinnunculus ).

We report a case of polyostotic chondroblastic osteosarcoma in a kestrel ( Falco tinnunculus ) admitted to the Wildlife Rehabilitation and Rescue Center (Naples, Italy). A consolidated fracture of the left tibiotarsus bone and a deviation of the limb were evident. After radiographic, cytologic, and histopathologic examinations, a diagnosis of polyostotic chondroblastic osteosarcoma was made. To our knowledge, this is the first report on polyostotic chondroblastic osteosarcoma in a kestrel.

Bite of the cats: relationships between functional integration and mechanical performance as revealed by mandible geometry.

Cat-like carnivorous mammals represent a relatively homogeneous group of species whose morphology appears constrained by exclusive adaptations for meat eating. We present the most comprehensive data set of extant and extinct cat-like species to test for evolutionary transformations in size, shape and mechanical performance, that is, von Mises stress and surface traction, of the mandible. Size and shape were both quantified by means of geometric morphometrics, whereas mechanical performance was assessed applying finite element models to 2D geometry of the mandible. Additionally, we present the first almost complete composite phylogeny of cat-like carnivorans for which well-preserved mandibles are known, including representatives of 35 extant and 59 extinct species of Felidae, Nimravidae, and Barbourofelidae. This phylogeny was used to test morphological differentiation, allometry, and covariation of mandible parts within and among clades. After taking phylogeny into account, we found that both allometry and mechanical variables exhibit a significant impact on mandible shape. We also tested whether mechanical performance was linked to morphological integration. Mechanical stress at the coronoid process is higher in sabertoothed cats than in any other clade. This is strongly related to the high degree of covariation within modules of sabertooths mandibles. We found significant correlation between integration at the clade level and per-clade averaged stress values, on both original data and by partialling out interclade allometry from shapes when calculating integration. This suggests a strong interaction between natural selection and the evolution of developmental and functional modules at the clade level.

The number of competitor species is unlinked to sexual dimorphism.

Sexual size dimorphism (SSD) can allow males and females of the same species to specialize on different sized food items and therefore minimize intraspecific competition. Interspecific competition, however, is thought to limit sexual dimorphism, as larger competitors in the community will prevent the larger sex from evolving larger size, and smaller species may prevent the smaller sex from becoming even smaller. We tested this prediction using data on the sexual size dimorphism of lizards, and mammalian carnivores, on islands world-wide. Because insular communities are depauperate, and guilds are species-poor, it is often assumed that enhanced sexual size dimorphism is common on islands. The intensity of interspecific competition, hindering enhanced dimorphism, is thought to increase with competitor richness. We tested whether intraspecific sexual size dimorphism of mammalian carnivores and lizards decreases with increasing island species richness. We further computed the average sexual dimorphism of species on islands and tested whether species-rich islands are inhabited by relatively monomorphic species. Within families and guilds across carnivores and lizards, and with both intraspecific and interspecific approaches, we consistently failed to find support for the notion that species-poor islands harbour more sexually dimorphic individuals or species. We conclude that either interspecific competition does not affect the sexual size dimorphism of insular lizards and carnivores (i.e. character displacement and species sorting are rare in these taxa), or that the number of species in an assemblage or guild is a poor proxy for the intensity of interspecific competition in insular assemblages.

Campylobacter spp. and birds of prey.

A total of 170 birds of prey admitted to two Wildlife Rescue and Rehabilitation Centers of Italy were examined. Birds were divided by diurnal (n = 15) and nocturnal (n = 7) species, sampled by cloacal swabs, and examined for Campylobacter spp. by cultural and molecular methods. Campylobacter spp. were isolated in 43 out of the 170 (25.3%) birds of prey examined. Among these, 43/43 (100%) were identified as Campylobacter jejuni and 10/43 (23.3%) were identified as Campylobacter coli recovered from mixed infections. Diurnal birds of prey showed a significantly higher prevalence value (P = 0.0006) for Campylobacter spp. than did nocturnal birds of prey.

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.