Reconstructing the ups and downs of primate brain evolution: implications for adaptive hypotheses and Homo floresiensis

Four errors and a fallacy: pitfalls for the unwary in comparative brain analyses

Comparative analyses are the backbone of evolutionary analysis. However, their record in producing a consensus has not always been good. This is especially true of attempts to understand the factors responsible for the evolution of large brains, which have been embroiled in an increasingly polarised debate over the past three decades. We argue that most of these disputes arise from a number of conceptual errors and associated logical fallacies that are the result of a failure to adopt a biological systems-based approach to hypothesis-testing. We identify four principal classes of error: a failure to heed Tinbergen's Four Questions when testing biological hypotheses, misapplying Dobzhansky's Dictum when testing hypotheses of evolutionary adaptation, poorly chosen behavioural proxies for underlying hypotheses, and the use of inappropriate statistical methods. In the interests of progress, we urge a more careful and considered approach to comparative analyses, and the adoption of a broader, rather than a narrower, taxonomic perspective.

From fossils to mind

Fossil endocasts record features of brains from the past: size, shape, vasculature, and gyrification. These data, alongside experimental and comparative evidence, are needed to resolve questions about brain energetics, cognitive specializations, and developmental plasticity. Through the application of interdisciplinary techniques to the fossil record, paleoneurology has been leading major innovations. Neuroimaging is shedding light on fossil brain organization and behaviors. Inferences about the development and physiology of the brains of extinct species can be experimentally investigated through brain organoids and transgenic models based on ancient DNA. Phylogenetic comparative methods integrate data across species and associate genotypes to phenotypes, and brains to behaviors. Meanwhile, fossil and archeological discoveries continuously contribute new knowledge. Through cooperation, the scientific community can accelerate knowledge acquisition. Sharing digitized museum collections improves the availability of rare fossils and artifacts. Comparative neuroanatomical data are available through online databases, along with tools for their measurement and analysis. In the context of these advances, the paleoneurological record provides ample opportunity for future research. Biomedical and ecological sciences can benefit from paleoneurology's approach to understanding the mind as well as its novel research pipelines that establish connections between neuroanatomy, genes and behavior.

Evolutionary history of hominin brain size and phylogenetic comparative methods

An absolutely and relatively large brain has traditionally been viewed as a distinctive characteristic of the Homo genus, with anatomically modern humans presented at the apex of a long line of progressive increases in encephalization. Many studies continue to focus attention on increasing brain size in the Homo genus, while excluding measures of absolute and relative brain size of more geologically recent, smaller brained, hominins such as Homo floresiensis, and Homo naledi and smaller brained Homo erectus specimens. This review discusses the benefits of using phylogenetic comparative methods to trace the diverse changes in hominin brain evolution and the drawbacks of not doing so.

Signatures of adaptive evolution in platyrrhine primate genomes

The platyrrhine family Cebidae (capuchin and squirrel monkeys) exhibit among the largest primate encephalization quotients. Each cebid lineage is also characterized by notable lineage-specific traits, with capuchins showing striking similarities to Hominidae such as high sensorimotor intelligence with tool use, advanced cognitive abilities, and behavioral flexibility. Here, we take a comparative genomics approach, performing genome-wide tests for positive selection across five cebid branches, to gain insight into major periods of cebid adaptive evolution. We uncover candidate targets of selection across cebid evolutionary history that may underlie the emergence of lineage-specific traits. Our analyses highlight shifting and sustained selective pressures on genes related to brain development, longevity, reproduction, and morphology, including evidence for cumulative and diversifying neurobiological adaptations across cebid evolution. In addition to generating a high-quality reference genome assembly for robust capuchins, our results lend to a better understanding of the adaptive diversification of this distinctive primate clade.

Equivocal evidence for a link between megalencephaly-related genes and primate brain size evolution

A large brain is a defining feature of modern humans, and much work has been dedicated to exploring the molecular underpinnings of this trait. Although numerous studies have focused on genes associated with human microcephaly, no studies have explicitly focused on genes associated with megalencephaly. Here, we investigate 16 candidate genes that have been linked to megalencephaly to determine if: (1) megalencephaly-associated genes evolved under positive selection across primates; and (2) selection pressure on megalencephaly-associated genes is linked to primate brain size. We found evidence for positive selection for only one gene, OFD1, with 1.8% of the sites estimated to have dN/dS values greater than 1; however, we did not detect a relationship between selection pressure on this gene and brain size across species, suggesting that selection for changes to non-brain size traits drove evolutionary changes to this gene. In fact, our primary analyses did not identify significant associations between selection pressure and brain size for any candidate genes. While we did detect positive associations for two genes (GPC3 and TBC1D7) when two phyletic dwarfs (i.e., species that underwent recent evolutionary decreases in brain size) were excluded, these associations did not withstand FDR correction. Overall, these results suggest that sequence alterations to megalencephaly-associated genes may have played little to no role in primate brain size evolution, possibly due to the highly pleiotropic effects of these genes. Future comparative studies of gene expression levels may provide further insights. This study enhances our understanding of the genetic underpinnings of brain size evolution in primates and identifies candidate genes that merit further exploration.

Ancient volcanos as species pumps: A case study of freshwater amphipods in Northeast Asia

Volcano-tectonic processes have been viewed as primary drivers in the formation of present-day diversity. Volcanos associated with mountain uplifts drive allopatric speciation through vicariance and may impact the surrounding areas like species pump or species attractor. However, the application of these hypotheses to aquatic fauna has rarely been tested explicitly. We tested these hypotheses in the Changbai Mountains (Mts), which are one of the most typical, active volcanic ranges in Northeast (NE) Asia with a long and turbulent geological history. The Gammarus nekkensis species complex of amphipod crustaceans, widely distributed throughout NE Asia with poor dispersal abilities and a long evolutionary history, is a suitable model for testing hypotheses of species pump or species attractor. Phylogenetic and ancestral range reconstructions demonstrated that the studied amphipod originated from the Changbai Mts ~27 Ma and diverged into eastern (Clade I) and western (Clade II) clades, which corresponds well with the initial volcanic eruption of the Changbai Mts in the Late Oligocene. The subsequent diversifications of subclades CI-3, CII-1a and CII-2a were probably driven by second and third eruptions of the Changbai Mts during the Miocene. In particular, the Changbai lineages had spread to the Russian Far East multiple times since the Early Miocene, and widely colonized the region during the Pleistocene. Our discoveries suggest that the ancient volcanos of the Changbai Mts act as species pumps in NE Asia, resulted in burst of diversification around the Changbai Mts and subsequent dispersals into adjacent regions.

An agent-based model clarifies the importance of functional and developmental integration in shaping brain evolution

Background

Vertebrate brain structure is characterised not only by relative consistency in scaling between components, but also by many examples of divergence from these general trends.. Alternative hypotheses explain these patterns by emphasising either ‘external’ processes, such as coordinated or divergent selection, or ‘internal’ processes, like developmental coupling among brain regions. Although these hypotheses are not mutually exclusive, there is little agreement over their relative importance across time or how that importance may vary across evolutionary contexts.

Results

We introduce an agent-based model to simulate brain evolution in a ‘bare-bones’ system and examine dependencies between variables shaping brain evolution. We show that ‘concerted’ patterns of brain evolution do not, in themselves, provide evidence for developmental coupling, despite these terms often being treated as synonymous in the literature. Instead, concerted evolution can reflect either functional or developmental integration. Our model further allows us to clarify conditions under which such developmental coupling, or uncoupling, is potentially adaptive, revealing support for the maintenance of both mechanisms in neural evolution. Critically, we illustrate how the probability of deviation from concerted evolution depends on the cost/benefit ratio of neural tissue, which increases when overall brain size is itself under constraint.

Conclusions

We conclude that both developmentally coupled and uncoupled brain architectures can provide adaptive mechanisms, depending on the distribution of selection across brain structures, life history and costs of neural tissue. However, when constraints also act on overall brain size, heterogeneity in selection across brain structures will favour region specific, or mosaic, evolution. Regardless, the respective advantages of developmentally coupled and uncoupled brain architectures mean that both may persist in fluctuating environments. This implies that developmental coupling is unlikely to be a persistent constraint, but could evolve as an adaptive outcome to selection to maintain functional integration.

Brain Allometry Across Macroevolutionary Scales in Squamates Suggests a Conserved Pattern in Snakes

Despite historical interest in brain size evolution in vertebrates, few studies have assessed variation in brain size in squamate reptiles such as snakes and lizards. Here, we analyzed the pattern of brain allometry at macroevolutionary scale in snakes and lizards, using body mass and snout vent length as measures of body size. We also assessed potential energetic trade-offs associated with relative brain size changes in Crotalinae vipers. Body mass showed a conserved pattern of brain allometry across taxa of snakes, but not in lizards. Body length favored changes of brain allometry in both snakes and lizards, but less variability was observed in snakes. Moreover, we did not find evidence for trade-offs between brain size and the size of other organs in Crotalinae. Thus, despite the contribution of body elongation to changes in relative brain size in squamate reptiles, snakes present low variation in brain allometry across taxa. Although the mechanisms driving this conserved pattern are unknown, we hypothesize that the snake body plan plays an important role in balancing the energetic demands of brain and body size increase at macroevolutionary scales. We encourage future research on the evolution of brain and body size in snakes to test this hypothesis.

Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution

Quantifying speciation times during human evolution is fundamental as it provides a timescale to test for the correlation between key evolutionary transitions and extrinsic factors such as climatic or environmental change. Here, we applied a total evidence dating approach to a hominin phylogeny to estimate divergence times under different topological hypotheses. The time-scaled phylogenies were subsequently used to perform ancestral state reconstructions of body mass and phylogenetic encephalization quotient (PEQ). Our divergence-time estimates are consistent with other recent studies that analysed extant species. We show that the origin of the genus Homo probably occurred between 4.30 and 2.56 million years ago. The ancestral state reconstructions show a general trend towards a smaller body mass before the emergence of Homo, followed by a trend towards a greater body mass. PEQ estimations display a general trend of gradual but accelerating encephalization evolution. The obtained results provide a rigorous temporal framework for human evolution.

The evolution of mammalian brain size

Relative brain size has long been considered a reflection of cognitive capacities and has played a fundamental role in developing core theories in the life sciences. Yet, the notion that relative brain size validly represents selection on brain size relies on the untested assumptions that brain-body allometry is restrained to a stable scaling relationship across species and that any deviation from this slope is due to selection on brain size. Using the largest fossil and extant dataset yet assembled, we find that shifts in allometric slope underpin major transitions in mammalian evolution and are often primarily characterized by marked changes in body size. Our results reveal that the largest-brained mammals achieved large relative brain sizes by highly divergent paths. These findings prompt a reevaluation of the traditional paradigm of relative brain size and open new opportunities to improve our understanding of the genetic and developmental mechanisms that influence brain size.

Static allometry of a small-bodied omnivore: body size and limb scaling of an island fox and inferences for Homo floresiensis

Island dwarfing is a paraphyletic adaptation across numerous mammalian genera. From mammoths to foxes, extreme body size reduction is shared by diverse organisms that migrate to an island environment. Because it largely occurs owing to ecological variables, not phylogenetic ones, skeletal characters in a dwarfed taxon compared with its ancestor may appear abnormal. As a result, allometric patterns between body size and morphological traits may differ for an island dwarf compared with its ancestor. The diminutive Late Pleistocene hominin, Homo floresiensis, displays a unique character suite that is outside of the normal range of variation for any extinct or extant hominin species. To better explain these as ecological traits due to island dwarfing, this research looks at how dwarfing on islands influences limb scaling and proportions in an organism in a similar ecological niche as H. floresiensis. Here, I analyze absolute limb lengths and static allometry of limb lengths regressed on predicted body mass of dwarfed island foxes and their nondwarfed relatives. Dwarfed island foxes have significantly smaller intercepts but steeper slopes of all limb elements regressed on predicted body mass than the mainland gray fox. These allometric alterations produce limbs in the island fox that are significantly shorter than predicted for a nondwarfed gray fox of similar body mass. In addition, the humerofemoral, intermembral, and brachial indices are significantly different. These results provide a novel model for understanding skeletal variation of island endemic forms. Unique body size and proportions of H. floresiensis are plausible as ecological adaptations and likely not examples of symplesiomorphies with Australopithecus sp. Caution should be exerted when comparing an island dwarf with a closely related species as deviations from allometric expectations may be common.

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

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.

Macroevolutionary trends of brain mass in Primates

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.

Life history changes accompany increased numbers of cortical neurons: A new framework for understanding human brain evolution

Narratives of human evolution have focused on cortical expansion and increases in brain size relative to body size, but considered that changes in life history, such as in age at sexual maturity and thus the extent of childhood and maternal dependence, or maximal longevity, are evolved features that appeared as consequences of selection for increased brain size, or increased cognitive abilities that decrease mortality rates, or due to selection for grandmotherly contribution to feeding the young. Here I build on my recent finding that slower life histories universally accompany increased numbers of cortical neurons across warm-blooded species to propose a simpler framework for human evolution: that slower development to sexual maturity and increased post-maturity longevity are features that do not require selection, but rather inevitably and immediately accompany evolutionary increases in numbers of cortical neurons, thus fostering human social interactions and cultural and technological evolution as generational overlap increases.

Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models

Phylogenetic comparative methods (PCMs) are used to study the evolution of various biological species, ranging from microorganisms to animals and plants. These methods combine trait measurements, such as body masses measured in a set of species, with the species’ phylogenetic tree, to quantify the trait’s evolution along the tree. Here, we show that current PCMs fail to reproduce the patterns of evolution of brain and body mass in mammals, because they use mathematical models that cannot represent the heterogeneity of the evolutionary processes acting in different lineages of the tree. As a solution, we propose mixed Gaussian phylogenetic models allowing one to infer changes in the type and magnitude of evolutionary forces occurring on specific branches of the tree.

Phylogenetic comparative methods are widely used to understand and quantify the evolution of phenotypic traits, based on phylogenetic trees and trait measurements of extant species. Such analyses depend crucially on the underlying model. Gaussian phylogenetic models like Brownian motion and Ornstein–Uhlenbeck processes are the workhorses of modeling continuous-trait evolution. However, these models fit poorly to big trees, because they neglect the heterogeneity of the evolutionary process in different lineages of the tree. Previous works have addressed this issue by introducing shifts in the evolutionary model occurring at inferred points in the tree. However, for computational reasons, in all current implementations, these shifts are “intramodel,” meaning that they allow jumps in 1 or 2 model parameters, keeping all other parameters “global” for the entire tree. There is no biological reason to restrict a shift to a single model parameter or, even, to a single type of model. Mixed Gaussian phylogenetic models (MGPMs) incorporate the idea of jointly inferring different types of Gaussian models associated with different parts of the tree. Here, we propose an approximate maximum-likelihood method for fitting MGPMs to comparative data comprising possibly incomplete measurements for several traits from extant and extinct phylogenetically linked species. We applied the method to the largest published tree of mammal species with body- and brain-mass measurements, showing strong statistical support for an MGPM with 12 distinct evolutionary regimes. Based on this result, we state a hypothesis for the evolution of the brain–body-mass allometry over the past 160 million y.

Quantitative uniqueness of human brain evolution revealed through phylogenetic comparative analysis

While the human brain is clearly large relative to body size, less is known about the timing of brain and brain component expansion within primates and the relative magnitude of volumetric increases. Using Bayesian phylogenetic comparative methods and data for both extant and fossil species, we identified that a distinct shift in brain-body scaling occurred as hominins diverged from other primates, and again as humans and Neanderthals diverged from other hominins. Within hominins, we detected a pattern of directional and accelerating evolution towards larger brains, consistent with a positive feedback process in the evolution of the human brain. Contrary to widespread assumptions, we found that the human neocortex is not exceptionally large relative to other brain structures. Instead, our analyses revealed a single increase in relative neocortex volume at the origin of haplorrhines, and an increase in relative cerebellar volume in apes.

The Pertinence of Studying Neuroethology in Nonhuman Primates for Human Behavior in Groups and Organizations

Are we the only living beings endowed with a complex communicative system and sharp sociocognitive skills? How did these remarkable abilities develop? Even raised several centuries ago, those questions are still nourishing the current research and debates. A relevant approach for identifying the dynamics in the evolution of humans’ social and communicative abilities appears to study our closest living relatives, the nonhuman primates. In this article I focus on two abilities that drove the building of our unique sociality and are still playing a crucial role in daily human behaviors in groups and organizations: (a) the origins of human language, through the study of nonhuman primates gestures, vocalizations, and facial expressions and (b) the precursors and underpinning neural mechanisms of our ability to assess others’ mental states, that is, theory of mind. In each part, examples illustrate the advantages and limitations of the different methodological approaches used in research on nonhuman primates’ communication and social abilities and discuss the results in light of the current hypotheses and still open debates on what make the singularity of our species.

Brain evolution and development: adaptation, allometry and constraint

Phenotypic traits are products of two processes: evolution and development. But how do these processes combine to produce integrated phenotypes? Comparative studies identify consistent patterns of covariation, or allometries, between brain and body size, and between brain components, indicating the presence of significant constraints limiting independent evolution of separate parts. These constraints are poorly understood, but in principle could be either developmental or functional. The developmental constraints hypothesis suggests that individual components (brain and body size, or individual brain components) tend to evolve together because natural selection operates on relatively simple developmental mechanisms that affect the growth of all parts in a concerted manner. The functional constraints hypothesis suggests that correlated change reflects the action of selection on distributed functional systems connecting the different sub-components, predicting more complex patterns of mosaic change at the level of the functional systems and more complex genetic and developmental mechanisms. These hypotheses are not mutually exclusive but make different predictions. We review recent genetic and neurodevelopmental evidence, concluding that functional rather than developmental constraints are the main cause of the observed patterns.

Evidence of a Conserved Molecular Response to Selection for Increased Brain Size in Primates

The adaptive significance of human brain evolution has been frequently studied through comparisons with other primates. However, the evolution of increased brain size is not restricted to the human lineage but is a general characteristic of primate evolution. Whether or not these independent episodes of increased brain size share a common genetic basis is unclear. We sequenced and de novo assembled the transcriptome from the neocortical tissue of the most highly encephalized nonhuman primate, the tufted capuchin monkey (Cebus apella). Using this novel data set, we conducted a genome-wide analysis of orthologous brain-expressed protein coding genes to identify evidence of conserved gene–phenotype associations and species-specific adaptations during three independent episodes of brain size increase. We identify a greater number of genes associated with either total brain mass or relative brain size across these six species than show species-specific accelerated rates of evolution in individual large-brained lineages. We test the robustness of these associations in an expanded data set of 13 species, through permutation tests and by analyzing how genome-wide patterns of substitution co-vary with brain size. Many of the genes targeted by selection during brain expansion have glutamatergic functions or roles in cell cycle dynamics. We also identify accelerated evolution in a number of individual capuchin genes whose human orthologs are associated with human neuropsychiatric disorders. These findings demonstrate the value of phenotypically informed genome analyses, and suggest at least some aspects of human brain evolution have occurred through conserved gene–phenotype associations. Understanding these commonalities is essential for distinguishing human-specific selection events from general trends in brain evolution.

Evidence of a chimpanzee-sized ancestor of humans but a gibbon-sized ancestor of apes

Body mass directly affects how an animal relates to its environment and has a wide range of biological implications. However, little is known about the mass of the last common ancestor (LCA) of humans and chimpanzees, hominids (great apes and humans), or hominoids (all apes and humans), which is needed to evaluate numerous paleobiological hypotheses at and prior to the root of our lineage. Here we use phylogenetic comparative methods and data from primates including humans, fossil hominins, and a wide sample of fossil primates including Miocene apes from Africa, Europe, and Asia to test alternative hypotheses of body mass evolution. Our results suggest, contrary to previous suggestions, that the LCA of all hominoids lived in an environment that favored a gibbon-like size, but a series of selective regime shifts, possibly due to resource availability, led to a decrease and then increase in body mass in early hominins from a chimpanzee-sized LCA.The pattern of body size evolution in hominids can provide insight into historical human ecology. Here, Grabowski and Jungers use comparative phylogenetic analysis to reconstruct the likely size of the ancestor of humans and chimpanzees and the evolutionary history of selection on body size in primates.

Why are there so many explanations for primate brain evolution?

The question as to why primates have evolved unusually large brains has received much attention, with many alternative proposals all supported by evidence. We review the main hypotheses, the assumptions they make and the evidence for and against them. Taking as our starting point the fact that every hypothesis has sound empirical evidence to support it, we argue that the hypotheses are best interpreted in terms of a framework of evolutionary causes (selection factors), consequences (evolutionary windows of opportunity) and constraints (usually physiological limitations requiring resolution if large brains are to evolve). Explanations for brain evolution in birds and mammals generally, and primates in particular, have to be seen against the backdrop of the challenges involved with the evolution of coordinated, cohesive, bonded social groups that require novel social behaviours for their resolution, together with the specialized cognition and neural substrates that underpin this. A crucial, but frequently overlooked, issue is that fact that the evolution of large brains required energetic, physiological and time budget constraints to be overcome. In some cases, this was reflected in the evolution of 'smart foraging' and technical intelligence, but in many cases required the evolution of behavioural competences (such as coalition formation) that required novel cognitive skills. These may all have been supported by a domain-general form of cognition that can be used in many different contexts.This article is part of the themed issue 'Physiological determinants of social behaviour in animals'.

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.

Do monkeys have a theory of mind? How to answer the question?

Since Premack and Woodruf (1978), the study of mindreading abilities in nonhumans, especially primates, has been thoroughly investigated. But attempts to understand the evolution of this aspect of human intelligence have mainly focused on comparisons between apes and human infants, while relatively little is known about the abilities of monkeys. This lack of data on monkeys seems mainly due to the hypothesis of a cognitive "gap" between apes and monkeys. However, in recent years monkeys have been featuring more prominently in the landscape of social cognition research, and some of these systematic studies appear promising. This paper reviews i) current knowledge about monkeys' socio-cognitive abilities, especially regarding gaze processing, attention and intention reading, and perspective-taking, ii) alternative hypotheses regarding the underlying mechanisms of such complex behaviors, and iii) potential new perspectives and future directions for studying ToM in monkeys.

The domesticated brain: genetics of brain mass and brain structure in an avian species

As brain size usually increases with body size it has been assumed that the two are tightly constrained and evolutionary studies have therefore often been based on relative brain size (i.e. brain size proportional to body size) rather than absolute brain size. The process of domestication offers an excellent opportunity to disentangle the linkage between body and brain mass due to the extreme selection for increased body mass that has occurred. By breeding an intercross between domestic chicken and their wild progenitor, we address this relationship by simultaneously mapping the genes that control inter-population variation in brain mass and body mass. Loci controlling variation in brain mass and body mass have separate genetic architectures and are therefore not directly constrained. Genetic mapping of brain regions indicates that domestication has led to a larger body mass and to a lesser extent a larger absolute brain mass in chickens, mainly due to enlargement of the cerebellum. Domestication has traditionally been linked to brain mass regression, based on measurements of relative brain mass, which confounds the large body mass augmentation due to domestication. Our results refute this concept in the chicken.

Life history of the most complete fossil primate skeleton: exploring growth models for Darwinius

Darwinius is an adapoid primate from the Eocene of Germany, and its only known specimen represents the most complete fossil primate ever found. Its describers hypothesized a close relationship to Anthropoidea, and using a Saimiri model estimated its age at death. This study reconstructs the ancestral permanent dental eruption sequences for basal Euprimates, Haplorhini, Anthropoidea, and stem and crown Strepsirrhini. The results show that the ancestral sequences for the basal euprimate, haplorhine and stem strepsirrhine are identical, and similar to that of Darwinius. However, Darwinius differs from anthropoids by exhibiting early development of the lower third molars relative to the lower third and fourth premolars. The eruption of the lower second premolar marks the point of interruption of the sequence in Darwinius. The anthropoid Saimiri as a model is therefore problematic because it exhibits a delayed eruption of P2. Here, an alternative strepsirrhine model based on Eulemur and Varecia is presented. Our proposed model shows an older age at death than previously suggested (1.05-1.14 years), while the range for adult weight is entirely below the range proposed previously. This alternative model is more consistent with hypotheses supporting a stronger relationship between adapoids and strepsirrhines.

Scaling of cerebral blood perfusion in primates and marsupials

The evolution of primates involved increasing body size, brain size and presumably cognitive ability. Cognition is related to neural activity, metabolic rate and rate of blood flow to the cerebral cortex. These parameters are difficult to quantify in living animals. This study shows that it is possible to determine the rate of cortical brain perfusion from the size of the internal carotid artery foramina in skulls of certain mammals, including haplorrhine primates and diprotodont marsupials. We quantify combined blood flow rate in both internal carotid arteries as a proxy of brain metabolism in 34 species of haplorrhine primates (0.116-145 kg body mass) and compare it to the same analysis for 19 species of diprotodont marsupials (0.014-46 kg). Brain volume is related to body mass by essentially the same exponent of 0.70 in both groups. Flow rate increases with haplorrhine brain volume to the 0.95 power, which is significantly higher than the exponent (0.75) expected for most organs according to 'Kleiber's Law'. By comparison, the exponent is 0.73 in marsupials. Thus, the brain perfusion rate increases with body size and brain size much faster in primates than in marsupials. The trajectory of cerebral perfusion in primates is set by the phylogenetically older groups (New and Old World monkeys, lesser apes) and the phylogenetically younger groups (great apes, including humans) fall near the line, with the highest perfusion. This may be associated with disproportionate increases in cortical surface area and mental capacity in the highly social, larger primates.

Microcephaly genes evolved adaptively throughout the evolution of eutherian mammals

BACKGROUND

Genes associated with the neurodevelopmental disorder microcephaly display a strong signature of adaptive evolution in primates. Comparative data suggest a link between selection on some of these loci and the evolution of primate brain size. Whether or not either positive selection or this phenotypic association are unique to primates is unclear, but recent studies in cetaceans suggest at least two microcephaly genes evolved adaptively in other large brained mammalian clades.

RESULTS

Here we analyse the evolution of seven microcephaly loci, including three recently identified loci, across 33 eutherian mammals. We find extensive evidence for positive selection having acted on the majority of these loci not just in primates but also across non-primate mammals. Furthermore, the patterns of selection in major mammalian clades are not significantly different. Using phylogenetically corrected comparative analyses, we find that the evolution of two microcephaly loci, ASPM and CDK5RAP2, are correlated with neonatal brain size in Glires and Euungulata, the two most densely sampled non-primate clades.

CONCLUSIONS

Together with previous results, this suggests that ASPM and CDK5RAP2 may have had a consistent role in the evolution of brain size in mammals. Nevertheless, several limitations of currently available data and gene-phenotype tests are discussed, including sparse sampling across large evolutionary distances, averaging gene-wide rates of evolution, potential phenotypic variation and evolutionary reversals. We discuss the implications of our results for studies of the genetic basis of brain evolution, and explicit tests of gene-phenotype hypotheses.

The evolution of self-control

Cognition presents evolutionary research with one of its greatest challenges. Cognitive evolution has been explained at the proximate level by shifts in absolute and relative brain volume and at the ultimate level by differences in social and dietary complexity. However, no study has integrated the experimental and phylogenetic approach at the scale required to rigorously test these explanations. Instead, previous research has largely relied on various measures of brain size as proxies for cognitive abilities. We experimentally evaluated these major evolutionary explanations by quantitatively comparing the cognitive performance of 567 individuals representing 36 species on two problem-solving tasks measuring self-control. Phylogenetic analysis revealed that absolute brain volume best predicted performance across species and accounted for considerably more variance than brain volume controlling for body mass. This result corroborates recent advances in evolutionary neurobiology and illustrates the cognitive consequences of cortical reorganization through increases in brain volume. Within primates, dietary breadth but not social group size was a strong predictor of species differences in self-control. Our results implicate robust evolutionary relationships between dietary breadth, absolute brain volume, and self-control. These findings provide a significant first step toward quantifying the primate cognitive phenome and explaining the process of cognitive evolution.

The evolutionary history of cetacean brain and body size

Cetaceans rival primates in brain size relative to body size and include species with the largest brains and biggest bodies to have ever evolved. Cetaceans are remarkably diverse, varying in both phenotypes by several orders of magnitude, with notable differences between the two extant suborders, Mysticeti and Odontoceti. We analyzed the evolutionary history of brain and body mass, and relative brain size measured by the encephalization quotient (EQ), using a data set of extinct and extant taxa to capture temporal variation in the mode and direction of evolution. Our results suggest that cetacean brain and body mass evolved under strong directional trends to increase through time, but decreases in EQ were widespread. Mysticetes have significantly lower EQs than odontocetes due to a shift in brain:body allometry following the divergence of the suborders, caused by rapid increases in body mass in Mysticeti and a period of body mass reduction in Odontoceti. The pattern in Cetacea contrasts with that in primates, which experienced strong trends to increase brain mass and relative brain size, but not body mass. We discuss what these analyses reveal about the convergent evolution of large brains, and highlight that until recently the most encephalized mammals were odontocetes, not primates.

Reconsidering the evolution of brain, cognition, and behavior in birds and mammals

Despite decades of research, some of the most basic issues concerning the extraordinarily complex brains and behavior of birds and mammals, such as the factors responsible for the diversity of brain size and composition, are still unclear. This is partly due to a number of conceptual and methodological issues. Determining species and group differences in brain composition requires accounting for the presence of taxon-cerebrotypes and the use of precise statistical methods. The role of allometry in determining brain variables should be revised. In particular, bird and mammalian brains appear to have evolved in response to a variety of selective pressures influencing both brain size and composition. “Brain” and “cognition” are indeed meta-variables, made up of the variables that are ecologically relevant and evolutionarily selected. External indicators of species differences in cognition and behavior are limited by the complexity of these differences. Indeed, behavioral differences between species and individuals are caused by cognitive and affective components. Although intra-species variability forms the basis of species evolution, some of the mechanisms underlying individual differences in brain and behavior appear to differ from those between species. While many issues have persisted over the years because of a lack of appropriate data or methods to test them; several fallacies, particularly those related to the human brain, reflect scientists' preconceptions. The theoretical framework on the evolution of brain, cognition, and behavior in birds and mammals should be reconsidered with these biases in mind.

Hidden Markov models for evolution and comparative genomics analysis

The problem of reconstruction of ancestral states given a phylogeny and data from extant species arises in a wide range of biological studies. The continuous-time Markov model for the discrete states evolution is generally used for the reconstruction of ancestral states. We modify this model to account for a case when the states of the extant species are uncertain. This situation appears, for example, if the states for extant species are predicted by some program and thus are known only with some level of reliability; it is common for bioinformatics field. The main idea is formulation of the problem as a hidden Markov model on a tree (tree HMM, tHMM), where the basic continuous-time Markov model is expanded with the introduction of emission probabilities of observed data (e.g. prediction scores) for each underlying discrete state. Our tHMM decoding algorithm allows us to predict states at the ancestral nodes as well as to refine states at the leaves on the basis of quantitative comparative genomics. The test on the simulated data shows that the tHMM approach applied to the continuous variable reflecting the probabilities of the states (i.e. prediction score) appears to be more accurate then the reconstruction from the discrete states assignment defined by the best score threshold. We provide examples of applying our model to the evolutionary analysis of N-terminal signal peptides and transcription factor binding sites in bacteria. The program is freely available at http://bioinf.fbb.msu.ru/~nadya/tHMM and via web-service at http://bioinf.fbb.msu.ru/treehmmweb.

Brain reorganization, not relative brain size, primarily characterizes anthropoid brain evolution

Comparative analyses of primate brain evolution have highlighted changes in size and internal organization as key factors underlying species diversity. It remains, however, unclear (i) how much variation in mosaic brain reorganization versus variation in relative brain size contributes to explaining the structural neural diversity observed across species, (ii) which mosaic changes contribute most to explaining diversity, and (iii) what the temporal origin, rates and processes are that underlie evolutionary shifts in mosaic reorganization for individual branches of the primate tree of life. We address these questions by combining novel comparative methods that allow assessing the temporal origin, rate and process of evolutionary changes on individual branches of the tree of life, with newly available data on volumes of key brain structures (prefrontal cortex, frontal motor areas and cerebrocerebellum) for a sample of 17 species (including humans). We identify patterns of mosaic change in brain evolution that mirror brain systems previously identified by electrophysiological and anatomical tract-tracing studies in non-human primates and functional connectivity MRI studies in humans. Across more than 40 Myr of anthropoid primate evolution, mosaic changes contribute more to explaining neural diversity than changes in relative brain size, and different mosaic patterns are differentially selected for when brains increase or decrease in size. We identify lineage-specific evolutionary specializations for all branches of the tree of life covered by our sample and demonstrate deep evolutionary roots for mosaic patterns associated with motor control and learning.

Functional divergence of the brain-size regulating gene MCPH1 during primate evolution and the origin of humans

BACKGROUND

One of the key genes that regulate human brain size, MCPH1 has evolved under strong Darwinian positive selection during the evolution of primates. During this evolution, the divergence of MCPH1 protein sequences among primates may have caused functional changes that contribute to brain enlargement.

RESULTS

To test this hypothesis, we used co-immunoprecipitation and reporter gene assays to examine the activating and repressing effects of MCPH1 on a set of its down-stream genes and then compared the functional outcomes of a series of mutant MCPH1 proteins that carry mutations at the human- and great-ape-specific sites. The results demonstrate that the regulatory effects of human MCPH1 and rhesus macaque MCPH1 are different in three of eight down-stream genes tested (p73, cyclinE1 and p14ARF), suggesting a functional divergence of MCPH1 between human and non-human primates. Further analyses of the mutant MCPH1 proteins indicated that most of the human-specific mutations could change the regulatory effects on the down-stream genes. A similar result was also observed for one of the four great-ape-specific mutations.

CONCLUSIONS

Collectively, we propose that during primate evolution in general and human evolution in particular, the divergence of MCPH1 protein sequences under Darwinian positive selection led to functional modifications, providing a possible molecular mechanism of how MCPH1 contributed to brain enlargement during primate evolution and human origin.

Brain size of Homo floresiensis and its evolutionary implications

The extremely small endocranial volume (ECV) of LB1, the type specimen of Homo floresiensis, poses a challenge in our understanding of human brain evolution. Some researchers hypothesize dramatic dwarfing of relative brain size from Homo erectus presumably without significant decrease in intellectual function, whereas others expect a lesser degree of brain diminution from a more primitive, small-brained form of hominin currently undocumented in eastern Asia. However, inconsistency in the published ECVs for LB1 (380-430 cc), unclear human intraspecific brain-body size scaling and other uncertainties have hampered elaborative modelling of its brain size reduction. In this study, we accurately determine the ECV of LB1 using high-resolution micro-CT scan. The ECV of LB1 thus measured, 426 cc, is larger than the commonly cited figure in previous studies (400 cc). Coupled with brain-body size correlation in Homo sapiens calculated based on a sample from 20 worldwide modern human populations, we construct new models of the brain size reduction in the evolution of H. floresiensis. The results show a more significant contribution of scaling effect than previously claimed.

Parallel episodes of phyletic dwarfism in callitrichid and cheirogaleid primates

The Callitrichidae are the smallest anthropoids, whereas the Cheirogaleidae include the smallest of all primates. Using species-level analyses, we show that these are derived conditions; both neonatal and adult body mass decreased in a gradual, phyletic manner in parallel across callitrichids, and across cheirogaleids. We identify lineages with particularly rapid decreases and highlight the pygmy marmoset, Callithrix pygmaea, as a phenotypic outlier. The life-history traits associated with body-mass reduction in each clade suggest that the convergent evolution of small body size was achieved by changes in different ontogenetic stages. Body-size reduction in callitrichids appears to be almost exclusively due to alterations in prenatal growth rate, whereas body-size reduction in cheirogaleids may have been largely due to reduced duration of growth phases. Finally, we use these results to discuss some of the debates surrounding the evolution of Homo floresiensis and suggest potential parallels between the evolution of H. floresiensis and callitrichids.

Genetic architecture supports mosaic brain evolution and independent brain-body size regulation

The mammalian brain consists of distinct parts that fulfil different functions. Finlay and Darlington have argued that evolution of the mammalian brain is constrained by developmental programs, suggesting that different brain parts are not free to respond individually to selection and evolve independent of other parts or overall brain size. However, comparisons among mammals with matched brain weights often reveal greater differences in brain part size, arguing against strong developmental constraints. Here, we test these hypotheses using a quantitative genetic approach involving over 10,000 mice. We identify independent loci for size variation in seven key parts of the brain, and observe that brain parts show low or no phenotypic correlation, as is predicted by a mosaic scenario. We also demonstrate that variation in brain size is independently regulated from body size. The allometric relations seen at higher phylogenetic levels are thus unlikely to be the product of strong developmental constraints.