Behavioural leads in evolution: evidence from the fossil record

Measuring the replicability of our own research

In the study of transgenic mouse models of neurodevelopmental and neurodegenerative disorders, we use batteries of tests to measure deficits in behaviour and from the results of these tests, we make inferences about the mental states of the mice that we interpret as deficits in "learning", "memory", "anxiety", "depression", etc. This paper discusses the problems of determining whether a particular transgenic mouse is a valid mouse model of disease X, the problem of background strains, and the question of whether our behavioural tests are measuring what we say they are. The problem of the reliability of results is then discussed: are they replicable between labs and can we replicate our results in our own lab? This involves the study of intra- and inter- experimenter reliability. The variables that influence replicability and the importance of conducting a complete behavioural phenotype: sensory, motor, cognitive and social emotional behaviour are discussed. Then the thorny question of failure to replicate is examined: Is it a curse or a blessing? Finally, the role of failure in research and what it tells us about our research paradigms is examined.

Fluctuating climate and dietary innovation drove ratcheted evolution of proboscidean dental traits

Identification of the selective forces that shaped adaptive phenotypes generally relies on current habitat and function, but these may differ from the context in which adaptations arose. Moreover, the fixation of adaptive change in a fluctuating environment and the mechanisms of long-term trends are still poorly understood, as is the role of behaviour in triggering these processes. Time series of fossils can provide evidence on these questions, but examples of individual lineages with adequate fossil and proxy data over extended periods are rare. Here, we present new data on proboscidean dental evolution in East Africa over the past 26 million years, tracking temporal patterns of morphological change in relation to proxy evidence of diet, vegetation and climate (aridity). We show that behavioural experimentation in diet is correlated with environmental context, and that major adaptive change in dental traits followed the changes in diet and environment but only after acquisition of functional innovations in the masticatory system. We partition traits by selective agent, showing that the acquisition of high, multiridged molars was primarily a response to an increase in open, arid environments with high dust accumulation, whereas enamel folding was more associated with the amount of grass in the diet. We further show that long-term trends in these features proceeded in a ratchet-like mode, alternating between directional change at times of high selective pressure and stasis when the selective regime reversed. This provides an explanation for morphology adapted to more extreme conditions than current usage (Liem's Paradox). Our study illustrates how, in fossil series with adequate stratigraphic control and proxy data, environmental and behavioural factors can be mapped on to time series of morphological change, illuminating the mode of acquisition of an adaptive complex.

The ecology and evolution of key innovations

The idea of 'key innovations' has long been influential in theoretical and empirical approaches to understanding adaptive diversification. Despite originally revolving around traits inducing major ecological shifts, the key innovation concept itself has evolved, conflating lineage diversification with trait-dependent ecological shifts. In this opinion article we synthesize the history of the term, clarify the relationship between key innovations and adaptive radiation, and propose a return to the original concept of key innovations: the evolution of organismal features which permit a species to occupy a previously inaccessible ecological state. Ultimately, we suggest an integrative approach to studying key innovations, necessitating experimental approaches of form and function, natural history studies of resource use, and phylogenetic comparative perspectives.

Sexual selection promotes giraffoid head-neck evolution and ecological adaptation

The long neck of the giraffe has been held as a classic example of adaptive evolution since Darwin's time. Here we report on an unusual fossil giraffoid, Discokeryx xiezhi, from the early Miocene, which has an unusual disk-shaped headgear and the most complicated head-neck joints in known mammals. The distinctive morphology and our finite element analyses indicate an adaptation for fierce head-butting behavior. Tooth enamel isotope data suggest that D. xiezhi occupied a niche different from that of other herbivores, comparable to the characteristic high-level browsing niche of modern giraffes. The study shows that giraffoids exhibit a higher headgear diversity than other ruminants and that living in specific ecological niches may have fostered various intraspecific combat behaviors that resulted in extreme head-neck morphologies in different giraffoid lineages.

Nine Levels of Explanation : A Proposed Expansion of Tinbergen's Four-Level Framework for Understanding the Causes of Behavior

Tinbergen's classic "On Aims and Methods of Ethology" (Zeitschrift für Tierpsychologie, 20, 1963) proposed four levels of explanation of behavior, which he thought would soon apply to humans. This paper discusses the need for multilevel explanation; Huxley and Mayr's prior models, and others that followed; Tinbergen's differences with Lorenz on "the innate"; and Mayr's ultimate/proximate distinction. It synthesizes these approaches with nine levels of explanation in three categories: phylogeny, natural selection, and genomics (ultimate causes); maturation, sensitive period effects, and routine environmental effects (intermediate causes); and hormonal/metabolic processes, neural circuitry, and eliciting stimuli (proximate causes), as a respectful extension of Tinbergen's levels. The proposed classification supports and builds on Tinbergen's multilevel model and Mayr's ultimate/proximate continuum, adding intermediate causes in accord with Tinbergen's emphasis on ontogeny. It requires no modification of Standard Evolutionary Theory or The Modern Synthesis, but shows that much that critics claim was missing was in fact part of Neo-Darwinian theory (so named by J. Mark Baldwin in The American Naturalist in 1896) all along, notably reciprocal causation in ontogeny, niche construction, cultural evolution, and multilevel selection. Updates of classical examples in ethology are offered at each of the nine levels, including the neuroethological and genomic findings Tinbergen foresaw. Finally, human examples are supplied at each level, fulfilling his hope of human applications as part of the biology of behavior. This broad ethological framework empowers us to explain human behavior-eventually completely-and vindicates the idea of human nature, and of humans as a part of nature.

A Dual Role for Behavior in Evolution and Shaping Organismal Selective Environments

The hypothesis that evolved behaviors play a determining role in facilitating and impeding the evolution of other traits has been discussed for more than 100 years with little consensus beyond an agreement that the ideas are theoretically plausible in accord with the Modern Synthesis. Many recent reviews of the genomic, epigenetic, and developmental mechanisms underpinning major behavioral transitions show how facultative expression of novel behaviors can lead to the evolution of obligate behaviors and structures that enhance behavioral function. Phylogenetic and genomic studies indicate that behavioral traits are generally evolutionarily more labile than other traits and that they help shape selective environments on the latter traits. Adaptive decision-making to encounter resources and avoid stress sources requires specific sensory inputs, which behaviorally shape selective environments by determining those features of the external world that are biologically relevant. These recent findings support the hypothesis of a dual role for behavior in evolution and are consistent with current evolutionary theory.

Working out the bipedal walking expenditure of energy based on foot morphology of different hominid genera: Implications for foot evolution

Among the Hominidae family of primates, Homo is characterized by more economical bipedal walking. Over the course of evolution towards bipedalism, the foot becomes the only organ directly interacting with substrate and likely influence the bipedal walking economy. However, working out the energy expenditure in bipedal walking from the specific aspect of foot morphology is still challenging, which hinders the understanding of the evolution of both hominid feet and economical bipedal walking. Here we present a functional model to quantitatively assess bipedal walking expenditure of energy from hominid foot morphology. According to our results, the feet of Homo are most suited to economical bipedal walking among hominids. However, the genus whose feet possess second best ability for economical bipedal walking is not our closest relative Pan, but is Gorilla. Using phylogenetically informed morphometric analyses, we further infer the evolutionary changes of hominid foot morphology and investigate the corresponding variation of bipedal walking expenditure. Our results reveal the economical bipedal walking benefits from the morphological changes of human foot after descending from the last common ancestor of hominids. Conversely, the foot morphologies of great apes reflect selections for other locomotor modes, at cost of larger energy expenditure in bipedal walking.

Morphological evolution in relationship to sidewinding, arboreality and precipitation in snakes of the family Viperidae

Compared with other squamates, snakes have received relatively little ecomorphological investigation. We examined morphometric and meristic characters of vipers, in which both sidewinding locomotion and arboreality have evolved multiple times. We used phylogenetic comparative methods that account for intraspecific variation (measurement error models) to determine how morphology varied in relationship to body size, sidewinding, arboreality and mean annual precipitation (which we chose over other climate variables through model comparison). Some traits scaled isometrically; however, head dimensions were negatively allometric. Although we expected sidewinding specialists to have different body proportions and more vertebrae than non-sidewinding species, they did not differ significantly for any trait after correction for multiple comparisons. This result suggests that the mechanisms enabling sidewinding involve musculoskeletal morphology and/or motor control, that viper morphology is inherently conducive to sidewinding (‘pre-adapted’) or that behaviour has evolved faster than morphology. With body size as a covariate, arboreal vipers had long tails, narrow bodies and lateral compression, consistent with previous findings for other arboreal snakes, plus reduced posterior body tapering. Species from wetter environments tended to have longer tails, wider heads and reduced anterior tapering. This study adds to the growing evidence that, despite superficial simplicity, snakes have evolved various morphological specializations in relationship to behaviour and ecology.

Reconstructing the ancestral phenotypes of great apes and humans (Homininae) using subspecies-level phylogenies

Owing to their close affinity, the African great apes are of interest in the study of human evolution. Although numerous researchers have described the ancestors we share with these species with reference to extant great apes, few have done so with phylogenetic comparative methods. One obstacle to the application of these techniques is the within-species phenotypic variation found in this group. Here, we leverage this variation, modelling common ancestors using ancestral state reconstructions (ASRs) with reference to subspecies-level trait data. A subspecies-level phylogeny of the African great apes and humans was estimated from full-genome mitochondrial DNA sequences and used to implement ASRs for 14 continuous traits known to vary between great ape subspecies. Although the inclusion of within-species phenotypic variation increased the phylogenetic signal for our traits and improved the performance of our ASRs, whether this was done through the inclusion of subspecies phylogeny or through the use of existing methods made little difference. Our ASRs corroborate previous findings that the last common ancestor of humans, chimpanzees and bonobos was a chimp-like animal, but also suggest that the last common ancestor of humans, chimpanzees, bonobos and gorillas was an animal unlike any extant African great ape.

Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift

Polar bear (Ursus maritimus) and brown bear (Ursus arctos) are recently diverged species that inhabit vastly differing habitats. Thus, analysis of the polar bear and brown bear genomes represents a unique opportunity to investigate the evolutionary mechanisms and genetic underpinnings of rapid ecological adaptation in mammals. Copy number (CN) differences in genomic regions between closely related species can underlie adaptive phenotypes and this form of genetic variation has not been explored in the context of polar bear evolution. Here, we analyzed the CN profiles of 17 polar bears, 9 brown bears, and 2 black bears (Ursus americanus). We identified an average of 318 genes per individual that showed evidence of CN variation (CNV). Nearly 200 genes displayed species-specific CN differences between polar bear and brown bear species. Principal component analysis of gene CN provides strong evidence that CNV evolved rapidly in the polar bear lineage and mainly resulted in CN loss. Olfactory receptors composed 47% of CN differentiated genes, with the majority of these genes being at lower CN in the polar bear. Additionally, we found significantly fewer copies of several genes involved in fatty acid metabolism as well as AMY1B, the salivary amylase-encoding gene in the polar bear. These results suggest that natural selection shaped patterns of CNV in response to the transition from an omnivorous to primarily carnivorous diet during polar bear evolution. Our analyses of CNV shed light on the genomic underpinnings of ecological adaptation during polar bear evolution.

Intraspecific brain size variation between coexisting sunfish ecotypes

Variation in spatial complexity and foraging requirements between habitats can impose different cognitive demands on animals that may influence brain size. However, the relationship between ecologically related cognitive performance and brain size is not well established. We test whether variation in relative brain size and brain region size is associated with habitat use within a population of pumpkinseed sunfish composed of different ecotypes that inhabit either the structurally complex shoreline littoral habitat or simpler open-water pelagic habitat. Sunfish using the littoral habitat have on average 8.3% larger brains than those using the pelagic habitat. We found little difference in the proportional sizes of five brain regions between ecotypes. The results suggest that cognitive demands on sunfish may be reduced in the pelagic habitat given no habitat-specific differences in body condition. They also suggest that either a short divergence time or physiological processes may constrain changes to concerted, global modifications of brain size between sunfish ecotypes.

Multiproxy evidence for leaf-browsing and closed habitats in extinct proboscideans (Mammalia, Proboscidea) from Central Chile

The multiproxy approach represents a novel methodology and a unique opportunity to obtain a more detailed view of ancient resource use. Our multiproxy study, carried out on gomphotheres from Chile, widens potential occupied habitats to closed-canopy forests. This habitat variability supports the hypothesis that the diet of gomphotheres appears to be more constrained by resource availability than by the potential dietary range. We strongly recommend the use of a multiproxy approach, where morphology analyses are complemented by other sources of information. This approach prevents misleading conclusions about the origin of the proxy’s signal from arising, such as a leaf-browsing diet inferred from the dental calculus and microwear not necessarily being indicative of humidity.

Proboscideans are so-called ecosystem engineers and are considered key players in hypotheses about Late Pleistocene megafaunal extinctions. However, knowledge about the autoecology and chronology of the proboscideans in South America is still open to debate and raises controversial views. Here, we used a range of multiproxy approaches and new radiocarbon datings to study the autoecology of Chilean gomphotheres, the only group of proboscideans to reach South America during the Great American Biotic Interchange (∼3.1 to 2.7 million years before present). As part of this study, we analyzed stable isotopes, dental microwear, and dental calculus microfossils on gomphothere molars from 30 Late Pleistocene sites (31° to 42°S). These proxies provided different scales of temporal resolution, which were then combined to assess the dietary and habitat patterns of these proboscideans. The multiproxy study suggests that most foraging took place in relatively closed environments. In Central Chile, there is a positive correlation between lower δ¹³C values and an increasing consumption of arboreal/scrub elements. Analyses of dental microwear and calculus microfossils have verified these leaf-browsing feeding habits. From a comparative perspective, the dietary pattern of South American gomphotheres appears to be constrained more by resource availability than by the potential dietary range of the individual taxa. This multiproxy study is aimed at increasing knowledge of the life history of gomphotheres and thus follows an issue considered one of the greatest challenges for paleontology in South America, recently pointed out by the need to thoroughly understand the role of ecological engineers before making predictions about the consequences of ecosystem defaunation.

A grazing Gomphotherium in Middle Miocene Central Asia, 10 million years prior to the origin of the Elephantidae

Feeding preference of fossil herbivorous mammals, concerning the coevolution of mammalian and floral ecosystems, has become of key research interest. In this paper, phytoliths in dental calculus from two gomphotheriid proboscideans of the middle Miocene Junggar Basin, Central Asia, have been identified, suggesting that Gomphotherium connexum was a mixed feeder, while the phytoliths from G. steinheimense indicates grazing preference. This is the earliest-known proboscidean with a predominantly grazing habit. These results are further confirmed by microwear and isotope analyses. Pollen record reveals an open steppic environment with few trees, indicating an early aridity phase in the Asian interior during the Mid-Miocene Climate Optimum, which might urge a diet remodeling of G. steinheimense. Morphological and cladistic analyses show that G. steinheimense comprises the sister taxon of tetralophodont gomphotheres, which were believed to be the general ancestral stock of derived "true elephantids"; whereas G. connexum represents a more conservative lineage in both feeding behavior and tooth morphology, which subsequently became completely extinct. Therefore, grazing by G. steinheimense may have acted as a behavior preadaptive for aridity, and allowing its lineage evolving new morphological features for surviving later in time. This study displays an interesting example of behavioral adaptation prior to morphological modification.

Digital reconstruction of the mandible of an adult Lesothosaurus diagnosticus with insight into the tooth replacement process and diet

Fragmentary caudal ends of the left and right mandible assigned to Lesothosaurus diagnosticus, an early ornithischian, was recently discovered in the continental red bed succession of the upper Elliot Formation (Lower Jurassic) at Likhoele Mountain (Mafeteng District) in Lesotho. Using micro-CT scanning, this mandible could be digitally reconstructed in 3D. The replacement teeth within the better preserved (left) dentary were visualised. The computed tomography dataset suggests asynchronous tooth replacement in an individual identified as an adult on the basis of bone histology. Clear evidence for systematic wear facets created by attrition is lacking. The two most heavily worn teeth are only apically truncated. Our observations of this specimen as well as others do not support the high level of dental wear expected from the semi-arid palaeoenvironment in which Lesothosaurus diagnosticus lived. Accordingly, a facultative omnivorous lifestyle, where seasonality determined the availability, quality, and abundance of food is suggested. This would have allowed for adaptability to episodes of increased environmental stress.

Evolution of kin recognition mechanisms in a fish

Both selection and phylogenetic history can influence the evolution of phenotypic traits. Here we used recently characterized variation in kin recognition mechanisms among six guppy populations to explore the phylogenetic history of this trait. Guppies can use two different kin recognition mechanisms: either phenotype matching, in which individuals are identified based on comparison with a recognition template, or familiarity, in which individuals are remembered based on previous interactions. Across the six populations, we identified four transitions in recognition mechanism: phenotype matching evolved once and was subsequently lost in a single population, whereas familiarity evolved twice. Based on a molecular clock, these transitions occurred among populations that had diverged on a timescale of hundreds of thousands of years, which is two orders of magnitude faster than previously documented transitions in recognition mechanisms. A randomization test provided no evidence that recognition mechanisms were constrained by phylogeny, suggesting that recognition mechanisms have the capacity to evolve rapidly, although the specific selection pressures that may be contributing to variation in recognition mechanisms across populations remain unknown.

Novelty and Innovation in the History of Life

The history of life as documented by the fossil record encompasses evolutionary diversifications at scales ranging from the Ediacaran-Cambrian explosion of animal life and the invasion of land by vascular plants, insects and vertebrates to the diversification of flowering plants over the past 100 million years and the radiation of horses. Morphological novelty and innovation has been a recurrent theme. The architects of the modern synthesis of evolutionary theory made three claims about evolutionary novelty and innovation: first, that all diversifications in the history of life represent adaptive radiations; second, that adaptive radiations are driven principally by ecological opportunity rather than by the supply of new morphological novelties, thus the primary questions about novelty and innovation focus on their ecological and evolutionary success; and third, that the rate of morphological divergence between taxa was more rapid early in the history of a clade but slowed over time as ecological opportunities declined. These claims have strongly influenced subsequent generations of evolutionary biologists, yet over the past two decades each has been challenged by data from the fossil record, by the results of comparative phylogenetic analyses and through insights from evolutionary developmental biology. Consequently a broader view of novelty and innovation is required. An outstanding issue for future work is identifying the circumstances associated with different styles of diversification and whether their frequency has changed through the history of life.

DNA Dispose, but Subjects Decide. Learning and the Extended Synthesis

Adaptation by means of natural selection depends on the ability of populations to maintain variation in heritable traits. According to the Modern Synthesis this variation is sustained by mutations and genetic drift. Epigenetics, evodevo, niche construction and cultural factors have more recently been shown to contribute to heritable variation, however, leading an increasing number of biologists to call for an extended view of speciation and evolution. An additional common feature across the animal kingdom is learning, defined as the ability to change behavior according to novel experiences or skills. Learning constitutes an additional source for phenotypic variation, and change in behavior may induce long lasting shifts in fitness, and hence favor evolutionary novelties. Based on published studies, I demonstrate how learning about food, mate choice and habitats has contributed substantially to speciation in the canonical story of Darwin's finches on the Galapagos Islands. Learning cannot be reduced to genetics, because it demands decisions, which requires a subject. Evolutionary novelties may hence emerge both from shifts in allelic frequencies and from shifts in learned, subject driven behavior. The existence of two principally different sources of variation also prevents the Modern Synthesis from self-referring explanations.