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1. There is solid recognition that phylogenetic effects must be acknowledged to appreciate climatic niche variability among species clades properly. Yet, most currently available methods either work at the intra- specific level (hence they ignore phylogeny) or rely on the Brownian motion model of evolution to estimate phylogenetic effects on climatic niche variation. The Brownian mo-tion model may be inappropriate to describe niche evolution in several cases, and even a significant phylogenetic signal in climatic variables does not in-dicate that the effect of shared ancestry was relevant to niche evolution.2. We introduce a new phylogenetic comparative method which describes sig-nificant changes in the width and position of the climatic niche at the inter-specific (clade) level, while making no a priori assumption about how niche evolution took place.3. We devised the R function phylo.niche.shift to estimate whether the climatic niches of individual clades in the tree are either wider or narrower than expected, and whether the niche occupies unexpected climates. We tested phylo.niche.shift on realistic virtual species’ distribution patterns applied to a phylogeny of 365 extant primate species.4. We demonstrate via simulations that the new method is fast and accurate under widely different climatic niche evolution scenarios. phylo.niche.shift showed that the capuchin monkeys and langurs occupy much wider, and prosimian much narrower, climatic niche space than expected by their phylogenetic positions.5. phylo.niche.shift may help to improve research on niche evolution by allow-ing researchers to test specific hypotheses on the factors affecting clades’ realised niche width and position, and the potential effects of climate change on species’ distributions

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.

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.

The ability to develop complex social bonds and an increased capacity for behavioural flexibility in novel environments have both been forwarded as selective forces favouring the evolution of a large brain in mammals. However, large brains are energetically expensive, and in circumstances in which selective pressures are relaxed, e.g. on islands, smaller brains are selected for. Similar reasoning has been offered to explain the reduction of brain size in domestic species relative to their wild relatives. Herein, we assess the effect of domestication, insularity and sociality on brain size evolution at the macroevolutionary scale. Our results are based on analyses of a 426-taxon tree, including both wild species and domestic breeds. We further develop the phylogenetic ridge regression comparative method (RRphylo) to work with discrete variables and compare the rates (tempo) and direction (mode) of brain size evolution among categories within each of three factors (sociality, insularity and domestication). The common assertion that domestication increases the rate of brain size evolution holds true. The same does not apply to insularity. We also find support for the suggested but previously untested hypothesis that species living in medium-sized groups exhibit faster rates of brain size evolution than either solitary or herding taxa.

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. 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. 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. 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. 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. © 2020 British Ecological Society

Assembling informal supertrees inclusive of extinct species is a useful but particularly long and complex procedure. We introduce a new, interactive, piece of software that allows the fast production of large, time-calibrated informal supertrees, single-handedly mixing multiple phylogenetic information from different sources. The software, embodied in the tree.merger function available as part of the RRphylo R package, allows the merging of different trees into one or adding individual species to a target phylogeny. Time calibration is implemented automatically within the function according to user-specified, optional age values that can be provided for nodes and/or tips. We applied tree.merger to two different case-studies. The first, hypothetical, case study pertains to the tree of odontocete cetaceans. The second case study regards the expansion of the new, higher-level phylogeny of dinosaurs proposing the sister clade relationship between Ornithoscelida and Sauropodomorpha from c. 50 to a 357 species tree. The two case studies took less than five seconds each to complete, on a regular personal computer.

Modern phylogenetic comparative methods allow us to estimate evolutionary rates of phenotypic change, how these rates differ across clades, and to assess whether the rates remained constant over time. Unfortunately, currently available phylogenetic comparative tools express the rate in terms of a scalar dimension, and do not allow us to determine rate variations among different parts of a single, complex phenotype, or chart realized rate variation directly onto the phenotype. We present a new method which allows the mapping of evolutionary rate variation directly onto three-dimensional phenotypes, informing on the direction and magnitude of trait change automatically. Implemented using the function rate.map embedded in the R package RRphylo, this method is based on phylogenetic ridge regression rate estimates. Since the latter represent ridge regression slopes, they possess sign and magnitude. In RRphylo, different rates are calculated for different districts of the phenotype, which can then be visualized directly onto the phenotype itself. We present the application of rate.map to the evolution of facial skeleton in Hominoidea, the primate clade inclusive of Homo and the greater apes (including living and fossil taxa). We found that the highly derived, unique shape of the face in modern humans evolved through rapid phenotypic changes affecting the nasal bones, the brow ridge and the maxillary region. The canine fossa, a facial feature unique to Homo sapiens, did not belong to a region of rapid phenotypic change, and could be seen as the by-product of midface evolution as suggested by previous studies. © 2021 The Palaeontological Association

The observation and the quantification of asymmetry in biological structures are deeply investigated in geometric morphometrics. Patterns of asymmetry were explored in both living and fossil species. In living organisms, levels of directional and fluctuating asymmetry are informative about developmental processes and health status of the individuals. Paleontologists are primarily interested in asymmetric features introduced by the taphonomic process, as they may significantly alter the original shape of the biological remains, hampering the interpretation of morphological features which may have profound evolutionary significance. Here, we provide a new R tool that produces the numerical quantification of fluctuating and directional asymmetry and charts asymmetry directly on the specimens under study, allowing the visual inspection of the asymmetry pattern. We tested this show.asymmetry algorithm, written in the R language, on fossil and living cranial remains of the genus Homo. show.asymmetry proved successful in discriminating levels of asymmetry among sexes in Homo sapiens, to tell apart fossil from living Homo skulls, to map effectively taphonomic distortion directly on the fossil skulls, and to provide evidence that digital restoration obliterates natural asymmetry to unnaturally low levels. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

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.

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

The idea that several small, rather than a single large, habitat areas should hold the highest total species richness (the so-called SLOSS debate) brings into question the importance of habitat fragmentation to extinction risk. SLOSS studies are generally addressed over a short time scale, potentially ignoring the long-term dimension of extinction risk. Here, we provide the first long-term evaluation of the role of habitat fragmentation in species extinction, focusing on 22 large mammal species that lived in Eurasia during the last 200 000 years. By combining species distribution models and landscape pattern analysis, we compared temporal dynamics of habitat spatial structure between extinct and extant species, estimating the size, number and degree of the geographical isolation of their suitable habitat patches. Our results evidenced that extinct mammals went through considerable habitat fragmentation during the last glacial period and started to fare worse than extant species from about 50 ka. In particular, our modelling effort constrains the fragmentation of habitats into a narrow time window, from 46 to 36 ka ago, surprisingly coinciding with known extinction dates of several megafauna species. Landscape spatial structure was the second most important driver affecting megafauna extinction risk (ca 38% importance), after body mass (ca 39%) and followed by dietary preferences (ca 20%). Our results indicate a major role played by landscape fragmentation on extinction. Such evidence provides insights on what might likely happen in the future, with climate change, habitat loss and fragmentation acting as the main forces exerting their negative effects on biodiversity. © 2021 The Authors. Ecography published by John Wiley & Sons Ltd on behalf of Nordic Society Oikos

In biological anthropology, parameters relating to cross-sectional geometry are calculated in paired long bones to evaluate the degree of lateralization of anatomy and, by inference, function. Here, we describe a novel approach, newly added to the morphomap R package, to assess the lateralization of the distribution of cortical bone along the entire diaphysis. The sample comprises paired long bones belonging to 51 individuals (10 females and 41 males) from The New Mexico Decedent Image Database with known biological profile, occupational and loading histories. Both males and females show a pattern of right lateralization. In addition, males are more lateralized than females, whereas there is not a significant association between lateralization with occupation and loading history. Body weight, height and long-bone length are the major factors driving the emergence of asymmetry in the humerus, while interestingly, the degree of lateralization decreases in the oldest individuals.

Homo sapiens is possibly the most ecologically plastic animal species ever, capable to overcome climatic variability beyond its physiological limits by means of culture. This adaptability has a strong cultural component which required the development both new technologies and major social changes sometimes in our distant past1,2. Highly contentious archaeological evidence suggests these innovations may have predated the emergence of our own species3. Here we studied climate niche width evolution in Homo, using fine-detailed palaeoclimatic data while controlling for phylogenetic effects. Our results point to sudden widening of the climatic niches exploited by Homo starting with the emergence of H. heidelbergensis. From the Middle Pleistocene, Homo ceased to be confined to physiologically suitable regions, despite progressive harshening of global climatic conditions. These results suggest cultural modernity, and its associated technological advancements, including habitual use of fire and clothing, appeared before the emergence of our own species.

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 by studying the evolution of human brain size, shape, and asymmetry on a phylogenetic tree including 19 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 hominoid 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 archeological record nicely coincide with the same three species sharing the largest and most rapidly evolving brains among all hominoids. © Copyright © 2020 Melchionna, Profico, Castiglione, Sansalone, Serio, Mondanaro, Di Febbraro, Rook, Pandolfi, Di Vincenzo, Manzi and Raia.

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 remain unanswered. Here we address two: (i), does the relationship between the brain size and its shape follow allometric trends and (ii), is this relationship consistent over evolutionary time? We employ three-dimensional geometric morphometrics and phylogenetic comparative methods to answer these questions, based on a large sample representing 151 species and most primate families. We found two distinct trends regarding the relationship between brain shape and brain size. Hominoidea and Cercopithecinae showed significant evolutionary allometry, whereas no allometric trends were discernible for Strepsirrhini, Colobinae or Platyrrhini. Furthermore, we found that in the taxa characterized by significant allometry, brain shape evolution accelerated, whereas for taxa in which such allometry was absent, the evolution of brain shape decelerated. We conclude that although primates in general are typically described as large-brained, strong allometric effects on brain shape are largely confined to the order's representatives that display more complex behavioural repertoires.

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. © 2020, Springer Science+Business Media, LLC, part of Springer Nature.

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.

Saber-toothed cats were armed with formidable weapons. They evolved a number of highly derived morphological features, most notably a pair of extremely long upper canines, which makes them unique within the felid family. Although the sabertooth character evolved several times among carnivorous mammals, sabertooth clades mostly had disjunctive occurrences both in space and time, and no sabertooth is alive today. We studied the rates of phenotypic and taxonomic diversification in the mandible of sabertooths, as compared to the rates calculated for both extinct and extant conical toothed cats. We found that the mandible's shape and physical properties in sabertooth clades evolved at distinctly higher rates than the rest of the felid tree. In addition, sabertooths had similar speciation rate to conical toothed cats, but statistically higher extinction rate. The wealth of morphological specializations required to be a sabertooth, and their tendency to focus on large-sized species as prey, was likely responsible for such high extinction rate, and for the peculiar, disjunctive patterns of sabertooth clade occurrence in the fossil record. © 2018 Elsevier B.V.

* Quantifying phenotypic evolutionary rates and their variation across phylogenetic trees is a major issue in evolutionary biology. A number of phylogenetic comparative methods (PCMs) currently perform such task. However, available PCMs can locate rate shifts pertaining to entire portions of the phylogeny, but not those expected to occur at the level of individual species and lineages, such as with the idea that body size changes more rapidly in insular vertebrates. Still, most PCMs cannot deal with fossil phylogenies, albeit fossils provide highly desirable information when it comes to understand trait variation and evolution. * We developed a PCM based on phylogenetic ridge regression, which we named RRphylo, which assigns an evolutionary rate to each branch of the phylogeny, and is designed to locate rate shifts relating to entire clades, as well as to unrelated tree tips. We tested RRphylo on simulated trees and data to assess its performance under different conditions. Then, we repeated its application with two real case scenarios, the evolution of flight in ornithodirans and mammals and body size evolution in insular mammals, which are usually subsumed to evolve under different range regimes than terrestrial and continental species respectively. * RRphylo performs well across all different conditions. The simulation experiments demonstrated it has low Type I and Type II error rate. We found significant evidence that flight accelerates the rate of body size evolution in vertebrates, and that the acquisition of very large body size slows down the rate. Still, insular mammals body size evolution is not faster than in continental species. * RRphylo is a new PCM ideal to estimate variation and shift in the rate of phenotypic evolution with fossil data. In addition to testing evolutionary rate variation, it is open to a variety of further questions, such as the evolution of rates in time, the estimation of ancestral states and the estimation of phenotypic trends over time.

Mammalian megaherbivores are an essential component of modern day ecosystems. They control a large share of primary productivity, modify habitats by clearing dense vegetation, and keep other herbivores populations small. When rare, small herbivores additionally suffer increased extinction risk by predation. Since megaherbivores are almost immune to predation, it was suggested that the detrimental effect of megaherbivores on smaller competitors has the additional consequence to reduce the prey biomass available to predatory species, thereby increasing their extinction risk. This form of indirect competition between guilds of species is known as apparent competition. These mechanisms are all forms of top-down control on ecosystem functioning, whereby species up on the food chain control diversity at lower levels. We tested these competing hypotheses on a large compilation of Neogene to Recent Old World mammals.We found evidence in favor of apparent competition. However, direct competition effects by both megaherbivores and carnivores on small prey are even more pervasive. Our results suggest that megaherbivores have been a dominant component of the mammal diversity over time and space during the last 22. million. years in Eurasia. © 2017 Elsevier B.V.

A distinctive trait in primate evolution is the expansion in brain mass. The potential drivers of this trend and how and whether encephalization influenced diversification dynamics in this group are hotly debated. We assembled a phylogeny accounting for 317 primate species, including both extant and extinct taxa, to identify macroevolutionary trends in brain mass evolution. Our findings show that Primates as a whole follow a macroevolutionary trend for an increase in body mass, relative brain mass and speciation rate over time. Although the trend for increased encephalization (brain mass) applies to all Primates, hominins stand out for their distinctly higher rates. Within hominins, this unique trend applies linearly over time and starts with Australopithecus africanus. The increases in both speciation rate and encephalization begin in the Oligocene, suggesting the two variables are causally associated. The substitution of early, stem Primates belonging to plesiadapiforms with crown Primates seems to be responsible for these macroevolutionary trends. However, our findings also suggest that cognitive capacities favoured speciation in hominins. © 2019 The Linnean Society of London, Biological Journal of the Linnean Society.

Cave bears (Ursus spelaeus) are an iconic component of the European late Quaternary Ice Age megafauna. Recent demographic analyses based on cave bear mtDNA sequences and refined radiocarbon dating indicate that cave bear population size and genetic diversity started to decline some 50 kilo years ago (kya). Hence, neither the coldest phase of the last glaciation (started some 24 kya), nor the colonization of Europe by Palaeolithic hunters (started some 45 kya) coincides with the beginning of population decline. Here, we reconstructed cave bear climatic niche evolution through time. Then, we performed spatially explicit population viability analyses to assess cave bear demographics through time in response to climatic changes, human effects on bear survival and their combination. We found that climate change was responsible for a 10-fold decrease in cave bear population size after 40 kya. However, climate change on its own could not explain U. spelaeus extinction at 24 kya. Additional negative effects consistent with human population expansion are required to explain both U. spelaeus' retreat from eastern Europe since 40 kya and its final extinction. © 2019 Collegium Boreas. Published by John Wiley & Sons Ltd

Understanding the evolution of bipedal locomotion in humans is of paramount importance to paleoanthropologists. Such endeavor requires well-preserved dynamic evidence of fossil human locomotion we are short of. Physical models of modern human locomotion predict individuals would perform voluntary step length adjustment as a function of slope gradient in order to minimize the energetic cost of locomotion while maintaining balance and reasonably comfortable gait. The famous Roccamonfina volcano "Devil's trails", which are Middle Pleistocene Homo fossilized trackways, provide unique opportunity to validate such predictions for fossil human individuals. We studied the best-preserved Roccamonfina Devil's trail to ascertain the dynamic behavior of the individual who left the trackway. We found Roccamonfina's individual moved in a way which is dynamically equivalent to modern humans, adjusting gait as to minimize energy expenditure. We derived body mass and stature estimates for such individual, which fit perfectly with previously published figures for Middle Pleistocene hominins outside Africa. © Società Geologica Italiana, Roma 2019.

Toothed whales (Odontoceti, Cetacea) are well-known for their ability to produce complex vocalizations, to use tools, to possess self-recognition, and for their extreme behavioural plasticity. The toothed whale intelligence is said to compete with that of primates, so does their extremely large brain to body size ratio. Common explanations for the acquisition of such large brains over the evolutionary time (encephalization) in toothed whales range from their demanding, complex social lives, to their feeding habits, to echolocation. Yet, several studies found no macroevolutionary trend in Odontoceti encephalization, which casts doubts on its selective advantage. We applied a recently developed phylogenetic comparative method to study macroevolutionary trends in relative brain size (RBS) and brain size evolutionary rates in cetaceans, comparing toothed whales to the other cetaceans and contrasting groups of species as ascribed to different feeding categories. We found that cetaceans as a whole followed a trend for increased encephalization over time, starting from small-brained archaeocete ancestors. Toothed whales do not show this same trend in RBS but have possessed larger RBS than any other cetacean ever since the beginning of their existence. The rate of RBS evolution in Odontoceti is significantly slower than in other Cetacea and slower than the rate of Odontoceti body size evolution. These results suggest that toothed whales’ history is characterized by high and conservative relative encephalization. Feeding lifestyle does not explain these patterns, while the appearance of echolocation within stem group Odontoceti remains a viable candidate for them.

One outstanding phenotypic character in Homo is its brain evolution. Pagel (Morphology, shape and phylogeny, CRC Press, Boca Raton, 2002) performed a phylogenetic analysis of the evolution of cranial capacity (as a surrogate of brain size) in fossil hominins, finding evidence for gradual evolutionary change with accelerating rate. Since Pagel’s pioneering investigation, the hominin fossil record expanded backward in time, new species were added to our family tree, different phylogenetic hypotheses were advanced, and new phylogenetic comparative methods became available. Therefore, we feel it is timely to repeat and expand upon Pagel’s seminal paper by including such material and applying novel methodologies. We fitted several evolutionary models to the endocranial volume (ECV) for 21 fossil hominins (including Pagel’s original analyses) and estimated phylogenetic signal using different approaches, while accounting for phylogenetic uncertainty. We then applied the phylogenetic signal-representation curve to the data to look for non-stationarity (discontinuities, rate shifts, or presence of different evolutionary patterns in different parts of the phylogeny) in brain size evolution. Our analyses show that, in principle, Pagel’s findings are robust to the addition of new data and phylogenetic uncertainty and confirm both the strong phylogenetic signal in brain size and acceleration of ECV evolutionary rates towards the present. However, non-stationarity was also detected in about 11% of the simulations, with two significant evolutionary discontinuities occurring close to the origin of the H. sapiens lineage (H. sapiens, H. neanderthalensis, H. heidelbergensis and H. antecessor) and along the phyletic line leading to H. floresiensis. This study calls upon further investigation of these important moments in Homo evolution, in order to understand the processes underling each of these shifts in brain size evolutionary regimes.

Summary 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., Graphical Abstract, Highlights • Homo sapiens oversteps our ecological niche limits by means of culture • The origin of Homo niche-construction ability is unknown • We found Homo species other than H. sapiens were able to construct their own niche, Ecology; Evolutionary History; Paleobiology

The end of the Pleistocene was characterized by an intense, highly selective extinction event, affecting large-bodied terrestrial mammals worldwide. This period coincides with two major events, the last glacial period, and the dispersal of technologically advanced Homo sapiens outside the Old World. Upper Paleolithic hunters were armed with advanced, projectile weapons, and were able to dispatch prey as large as mammoths. As human population size was rapidly expanding, and hence means meat consumption rate was also growing, Paleolithic hunters are often held responsible for the extinction of mammalian megafauna. Yet, whether human focused on megafauna as prey, and drove them to extinction, remains uncertain. Here we model spatial and temporal patterns in habitat suitability for 24 megafauna species and Homo sapiens in Eurasia. We find that within land patches most suitable for humans, the identity of the most abundant herbivorous mammals switched from warm adapted species (such as the wild boar) to cold adapted species (reindeer) as climate switched from mild to cold conditions. Importantly, extinct herbivorous megafauna species were consistently rare within habitat patches optimal for humans. This suggests that humans may have settled under relatively constant climatic conditions, and possibly behaved as efficient predators, exploiting their prey in a cost-effective manner. These results are in accordance with evidence coming from the archaeological record, where medium sized living herbivore species are overrepresented in comparison of their natural abundance. For Late Pleistocene megafauna in Eurasia, human hunting may have been just an additional, non-decisive extinction factor. © 2018 Elsevier B.V.

The geographic range sizes frequency distribution (RFD) within clades is typically right-skewed with untransformed data, and bell-shaped or slightly left-skewed under the log-transformation. This means that most species within clades occupy diminutive ranges, whereas just a few species are truly widespread. A number of ecological and evolutionary explanations have been proposed to account for this pattern. Among the latter, much attention has been given to the issue of how extinction and speciation probabilities influence RFD. Numerous accounts now convincingly demonstrate that extinction rate decreases with range size, both in living and extinct taxa. The relationship between range size and speciation rate, though, is much less obvious, with either small or large ranged species being proposed to originate more daughter taxa. Herein, we used a large fossil database including 21 animal clades and more than 80,000 fossil occurrences distributed over more than 400 million years of marine metazoans (exclusive of vertebrates) evolution, to test the relationship between extinction rate, speciation rate, and range size. As expected, we found that extinction rate almost linearly decreases with range size. In contrast, speciation rate peaks at the large (but not the largest) end of the range size spectrum. This is consistent with the peripheral isolation mode of allopatric speciation being the main mechanism of species origination. The huge variation in phylogeny, fossilization potential, time of fossilization, and the overarching effect of mass extinctions suggest caution must be posed at generalizing our results, as individual clades may deviate significantly from the general pattern. © 2017 Castiglione, Mondanaro, Melchionna, Serio, Di Febbraro, Carotenuto and Raia.

Animal clades tend to follow a predictable path of waxing and waning during their existence, regardless of their total species richness or geographic coverage. Clades begin small and undifferentiated, then expand to a peak in diversity and range, only to shift into a rarely broken decline towards extinction. While this trajectory is now well documented and broadly recognised, the reasons underlying it remain obscure. In particular, it is unknown why clade extinction is universal and occurs with such surprising regularity. Current explanations for paleontological extinctions call on the growing costs of biological interactions, geological accidents, evolutionary traps, and mass extinctions. While these are effective causes of extinction, they mainly apply to species, not clades. Although mass extinctions is the undeniable cause for the demise of a sizeable number of major taxa, we show here that clades escaping them go extinct because of the widespread tendency of evolution to produce increasingly specialised, sympatric, and geographically restricted species over time.

Understanding the effect of climate on the composition of communities and its change over time and space is one of the major aims in ecology and paleoecology. Herein, we tackled on this issue by studying late Quaternary large mammal paleocommunities of Eurasia. The late Quaternary was a period of strong environmental instability, especially characterized by the occurrence of the last glacial maximum (LGM). We used community phylogenetics and joint species distribution models in order to understand the factors determining paleocommunity composition in the late Quaternary. Our results support the existence of strong climatic selection operating on the LGM fauna, both through the disappearance of warm-adapted species such as Elephas antiquus, Hippopothamus amphibious, and Stephanorhinus hemitoechus, and by setting the stage for the existence of a community characterized by cold-adapted large mammals. Patterns of abundance in the fossil record, co-occurrence between species pairs, and the extent of climatic forcing on faunal composition, differ between paleocommunities, but not between extinct and extant species, which is consistent with the idea that climate change, rather than the presence of humans, exerted a major effect on the survival of the late Quaternary megafauna. © 2016 Elsevier Ltd

Members of the hominins – namely the so-called ‘australopiths’ and the species of the genus Homo – are known to possess short and deep mandibles and relatively small incisors and canines. It is commonly assumed that this suite of traits evolved in early members of the clade in response to changing environmental conditions and increased consumption of though food items. With the emergence of Homo, the functional meaning of mandible shape variation is thought to have been weakened by technological advancements and (later) by the control over fire. In contrast to this expectation, we found that mandible shape evolution in hominins is exceptionally rapid as compared to any other primate clade, and that the direction and rate of shape change (from the ape ancestor) are no different between the australopiths and Homo. We deem several factors including the loss of honing complex, canine reduction, and the acquisition of different diets may have concurred in producing such surprisingly high evolutionary rates. This study reveals the evolution of mandibular shape in hominins has strong morpho-functional and ecological significance attached.

Neanderthals lived in Eurasia alongside anatomically modern humans (AMHs) until some 40,000 years ago. The extinction of Neanderthals is attributed to either climatic change, or to the effect of competition with AMHs. We used fossil occurrence records and paleoclimatic data to model the potential distributions of H. sapiens and H. neanderthalensis using Species Distribution Models, and calculated the degree of habitat quality and connectivity at successive time steps. We found that both species potential geographic ranges progressively retreated from their northeastern borders beginning with 44 ka. Although the degree of habitat loss is similar for the two species, the potential range for H. sapiens was constantly some 50% larger on average. The degree of habitat fragmentation, and the size, number, and average distance between optimal habitat patches was initially very similar for the two species. However, all these landscape metrics showed a progressive deterioration for H. neanderthalensis only over time. At the end of their existence, the most suitable habitat patches for Neanderthals were small and isolated, and their inferred climatic niche width was statistically narrower than in H. sapiens. This does not mean that climate worsening drove Neanderthals extinct, yet it suggests extinction risk for the latter markedly increased over time, towards its actual extinction date. © 2018 Elsevier B.V.

Recognizing evolutionary trends in phenotypic means and rates requires the application of phylogenetic comparative methods (PCMs). Most PCMs are unsuited to make full use of fossil information, which is a drawback, given the inclusion of such data improves, and in some cases even corrects, the proper understanding of trait evolution. Here we present a new computer application, written in R, that allows the simultaneous computation of temporal trends in phenotypic mean and evolutionary rate along a phylogeny, and to contrast such patterns among different clades within the tree. By using simulation experiments, we show the new implementation, names search.trend is as powerful as existing PCM tools in discerning macroevolutionary patterns in phenotypic means and rates, but differently from any other PCM allows comparing individual clades to each other, and provides rich information about trait evolution for all lineages in the tree.