Morphological innovation, diversification and invasion of a new adaptive zone

Maxillary morphology of chimpanzees: Captive versus wild environments

Morphological studies typically avoid using osteological samples that derive from captive animals because it is assumed that their morphology is not representative of wild populations. Rearing environments indeed differ between wild and captive individuals. For example, mechanical properties of the diets provided to captive animals can be drastically different from the food present in their natural habitats, which could impact cranial morphology and dental health. Here, we examine morphological differences in the maxillae of wild versus captive chimpanzees (Pan troglodytes) given the prominence of this species in comparative samples used in human evolution research and the key role of the maxilla in such studies. Size and shape were analysed using three-dimensional geometric morphometric methods based on computed tomography scans of 94 wild and 30 captive specimens. Captive individuals have on average larger and more asymmetrical maxillae than wild chimpanzees, and significant differences are present in their maxillary shapes. A large proportion of these shape differences are attributable to static allometry, but wild and captive specimens still differ significantly from each other after allometric size adjustment of the shape data. Levels of shape variation are higher in the captive group, while the degree of size variation is likely similar in our two samples. Results are discussed in the context of ontogenetic growth trajectories, changes in dietary texture, an altered social environment, and generational differences. Additionally, sample simulations show that size and shape differences between chimpanzees and bonobos (Pan paniscus) are exaggerated when part of the wild sample is replaced with captive chimpanzees. Overall, this study confirms that maxillae of captive chimpanzees should not be included in morphological or taxonomic analyses when the objective is to characterise the species.

Once upon a fly: The biogeographical odyssey of Labrundinia (Chironomidae, Tanypodinae), an aquatic non-biting midge towards diversification

Labrundinia is a highly recognizable lineage in the Pentaneurini tribe (Diptera, Chironomidae). The distinct predatory free-swimming larvae of this genus are typically present in unpolluted aquatic environments, such as small streams, ponds, lakes, and bays. They can be found on the bottom mud, clinging to rocks and wood, and dwelling among aquatic vegetation. Labrundinia has been extensively studied in ecological research and comprises 39 species, all but one of which has been described from regions outside the Palearctic. Earlier phylogenetic studies have suggested that the initial diversification of the genus likely occurred in the Neotropical Region, with its current presence in the Nearctic Region and southern South America being the result of subsequent dispersal events. Through the integration of molecular and morphological data in a calibrated phylogeny, we reveal a complex and nuanced evolutionary history for Labrundinia, providing insights into its biogeographical and diversification patterns. In this comprehensive study, we analyze a dataset containing 46 Labrundinia species, totaling 10,662 characters, consisting of 10,616 nucleotide sites and 46 morphological characters. The molecular data was generated mainly by anchored enrichment hybrid methods. Using this comprehensive dataset, we inferred the phylogeny of the group based on a total evidence matrix. Subsequently, we employed the generated tree for time calibration and further analysis of biogeography and diversification patterns. Our findings reveal multiple dispersal events out of the Neotropics, where the group originated in the late Cretaceous approximately 72 million years ago (69-78 Ma). We further reveal that the genus experienced an early burst of diversification rates during the Paleocene, which gradually decelerated towards the present-day. We also find that the Neotropics have played a pivotal role in the evolution of Labrundinia by serving as both a cradle and a museum. By "cradle," we mean that the region has been a hotspot for the origin and diversification of new Labrundinia lineages, while "museum" refers to the region's ability to preserve ancestral lineages over extended periods. In summary, our findings indicate that the Neotropics have been a key source of genetic diversity for Labrundinia, resulting in the development of distinctive adaptations and characteristics within the genus. This evidence highlights the crucial role that these regions have played in shaping the evolutionary trajectory of Labrundinia.

Facing the facts: adaptive trade-offs along body size ranges determine mammalian craniofacial scaling

The mammalian cranium (skull without lower jaw) is representative of mammalian diversity and is thus of particular interest to mammalian biologists across disciplines. One widely retrieved pattern accompanying mammalian cranial diversification is referred to as 'craniofacial evolutionary allometry' (CREA). This posits that adults of larger species, in a group of closely related mammals, tend to have relatively longer faces and smaller braincases. However, no process has been officially suggested to explain this pattern, there are many apparent exceptions, and its predictions potentially conflict with well-established biomechanical principles. Understanding the mechanisms behind CREA and causes for deviations from the pattern therefore has tremendous potential to explain allometry and diversification of the mammalian cranium. Here, we propose an amended framework to characterise the CREA pattern more clearly, in that 'longer faces' can arise through several kinds of evolutionary change, including elongation of the rostrum, retraction of the jaw muscles, or a more narrow or shallow skull, which all result in a generalised gracilisation of the facial skeleton with increased size. We define a standardised workflow to test for the presence of the pattern, using allometric shape predictions derived from geometric morphometrics analysis, and apply this to 22 mammalian families including marsupials, rabbits, rodents, bats, carnivores, antelopes, and whales. Our results show that increasing facial gracility with size is common, but not necessarily as ubiquitous as previously suggested. To address the mechanistic basis for this variation, we then review cranial adaptations for harder biting. These dictate that a more gracile cranium in larger species must represent a structural sacrifice in the ability to produce or withstand harder bites, relative to size. This leads us to propose that facial gracilisation in larger species is often a product of bite force allometry and phylogenetic niche conservatism, where more closely related species tend to exhibit more similar feeding ecology and biting behaviours and, therefore, absolute (size-independent) bite force requirements. Since larger species can produce the same absolute bite forces as smaller species with less effort, we propose that relaxed bite force demands can permit facial gracility in response to bone optimisation and alternative selection pressures. Thus, mammalian facial scaling represents an adaptive by-product of the shifting importance of selective pressures occurring with increased size. A reverse pattern of facial 'shortening' can accordingly also be found, and is retrieved in several cases here, where larger species incorporate novel feeding behaviours involving greater bite forces. We discuss multiple exceptions to a bite force-mediated influence on facial proportions across mammals which lead us to argue that ecomorphological specialisation of the cranium is likely to be the primary driver of facial scaling patterns, with some developmental constraints as possible secondary factors. A potential for larger species to have a wider range of cranial functions when less constrained by bite force demands might also explain why selection for larger sizes seems to be prevalent in some mammalian clades. The interplay between adaptation and constraint across size ranges thus presents an interesting consideration for a mechanistically grounded investigation of mammalian cranial allometry.

The Role of (Co)variation in Shaping the Response to Selection in New World Leaf-Nosed Bats

AbstractUnderstanding and predicting the evolutionary responses of complex morphological traits to selection remains a major challenge in evolutionary biology. Because traits are genetically correlated, selection on a particular trait produces both direct effects on the distribution of that trait and indirect effects on other traits in the population. The correlations between traits can strongly impact evolutionary responses to selection and may thus impose constraints on adaptation. Here, we used museum specimens and comparative quantitative genetic approaches to investigate whether the covariation among cranial traits facilitated or constrained the response to selection during the major dietary transitions in one of the world's most ecologically diverse mammalian families-the phyllostomid bats. We reconstructed the set of net selection gradients that would have acted on each cranial trait during the major transitions to feeding specializations and decomposed the selection responses into their direct and indirect components. We found that for all transitions, most traits capturing craniofacial length evolved toward adaptive directions owing to direct selection. Additionally, we showed instances of dietary transitions in which the complex interaction between the patterns of covariation among traits and the strength and direction of selection either constrained or facilitated evolution. Our work highlights the importance of considering the within-species covariation estimates to quantify evolvability and to disentangle the relative contribution of variational constraints versus selective causes for observed patterns.

Phylogenetic, morphological and niche differentiation unveil new species limits for the big brown bat (Eptesicus fuscus)

Phylogeographic accounts of mammals across fragmented landscapes show high levels of genetic, morphological and ecological variation. The big brown bat (Eptesicus fuscus) widely spans mainland landmasses from Canada to Ecuador and Colombia, and the insular Caribbean through The Bahamas and Greater and Lesser Antilles. Given the distribution of E. fuscus, we hypothesized that insular lineages could represent a different species aided by isolation. We assessed species limits by capitalizing on available mitochondrial and genomic data. Novel morphological and spatial datasets were produced to examine limits phenotypically and whether ecological niches could be associated with differences between groups. Phylogenetics strongly supported the Caribbean as unique compared to the mainland. Genomic data indicated high levels of genetic structure within the Caribbean and no detectable admixture of the Caribbean with continental lineages. Similarly, the Caribbean group shows high phenotypic disparity, and niche models revealed differences in habitat suitability between groups, concordant with the phylogenetic results. This study uncovered signals of divergence supporting the Caribbean clade of E. fuscus as unique through an integrative framework. We endorse re-evaluating the taxonomic status of Caribbean big brown bats as Eptesicus dutertreus. This recognition can help promote local conservation plans for insular lineages of big brown bats.

Uncovering the mosaic evolution of the carnivoran skeletal system

The diversity of vertebrate skeletons is often attributed to adaptations to distinct ecological factors such as diet, locomotion, and sensory environment. Although the adaptive evolution of skull, appendicular skeleton, and vertebral column is well studied in vertebrates, comprehensive investigations of all skeletal components simultaneously are rarely performed. Consequently, we know little of how modes of evolution differ among skeletal components. Here, we tested if ecological and phylogenetic effects led to distinct modes of evolution among the cranial, appendicular and vertebral regions in extant carnivoran skeletons. Using multivariate evolutionary models, we found mosaic evolution in which only the mandible, hindlimb and posterior (i.e. last thoracic and lumbar) vertebrae showed evidence of adaptation towards ecological regimes whereas the remaining skeletal components reflect clade-specific evolutionary shifts. We hypothesize that the decoupled evolution of individual skeletal components may have led to the origination of distinct adaptive zones and morphologies among extant carnivoran families that reflect phylogenetic hierarchies. Overall, our work highlights the importance of examining multiple skeletal components simultaneously in ecomorphological analyses. Ongoing work integrating the fossil and palaeoenvironmental record will further clarify deep-time drivers that govern the carnivoran diversity we see today and reveal the complexity of evolutionary processes in multicomponent systems.

Cochlea development shapes bat sensory system evolution

Sensory organs must develop alongside the skull within which they are largely encased, and this relationship can manifest as the skull constraining the organs, organs constraining the skull, or organs constraining one another in relative size. How this interplay between sensory organs and the developing skull plays out during the evolution of sensory diversity; however, remains unknown. Here, we examine the developmental sequence of the cochlea, the organ responsible for hearing and echolocation, in species with distinct diet and echolocation types within the ecologically diverse bat super-family Noctilionoidea. We found the size and shape of the cochlea largely correlates with skull size, with exceptions of Pteronotus parnellii, whose high duty cycle echolocation (nearly constant emission of sound pulses during their echolocation process allowing for detailed information gathering, also called constant frequency echolocation) corresponds to a larger cochlear and basal turn, and Monophyllus redmani, a small-bodied nectarivorous bat, for which interactions with other sensory organs restrict cochlea size. Our findings support the existence of developmental constraints, suggesting that both developmental and anatomical factors may act synergistically during the development of sensory systems in noctilionoid bats.

Ecomorphology and sensory biology of bats

This special issue of The Anatomical Record is inspired by and dedicated to Professor Kunwar P. Bhatnagar, whose lifelong interests in biology, and long career studying bats, inspired many and advanced our knowledge of the world's only flying mammals. The 15 articles included here represent a broad range of investigators, treading topics familiar to Prof. Bhatnagar, who was interested in seemingly every aspect of bat biology. Key topics include broad themes of bat development, sensory systems, and specializations related to flight and diet. These articles paint a complex picture of the fascinating adaptations of bats, such as rapid fore limb development, ear morphologies relating to echolocation, and other enhanced senses that allow bats to exploit niches in virtually every part of the world. In this introduction, we integrate and contextualize these articles within the broader story of bat ecomorphology, providing an overview of each of the key themes noted above. This special issue will serve as a springboard for future studies both in bat biology and in the broader world of mammalian comparative anatomy and ecomorphology.

Neuronal scaling in the olfactory system of bats

Comparative studies are a common way to address large-scale questions in sensory biology. For studies that investigate olfactory abilities, the most commonly used metric is olfactory bulb size. However, recent work has called into question the broad-scale use of olfactory bulb size. In this paper, we use three neuroanatomical measures with a more mechanistic link to olfactory function (number of olfactory sensory neurons (OSNs), number of mitral cells (MCs), and number of glomeruli) to ask how species with different diets may differ with respect to olfactory ability. We use phyllostomid bats as our study system because behavioral and physiological work has shown that fruit- and nectar-feeding phyllostomids rely on odors for detecting, localizing, and assessing potential foods, while insect-eating species do not. Therefore, we predicted that fruit- and nectar-feeding bats would have larger numbers of these three neuroanatomical measures than insect-eating species. In general, our results supported the predictions. We found that fruit-eaters had greater numbers of OSNs and glomeruli than insect-eaters, but we found no difference between groups in number of MCs. We also examined the allometric relationship between the three neuroanatomical variables and olfactory bulb volume, and we found isometry in all cases. These findings lend support to the notion that neuroanatomical measures can offer valuable insights into comparative olfactory abilities, and suggest that the size of the olfactory bulb may be an informative parameter to use at the whole-organism level.

Ecomorphological correlates of inner and middle ear anatomy within phyllostomid bats

Echolocation is the primary sense used by most bats to navigate their environment. However, the influence of echolocating behaviors upon the morphology of the auditory apparatus remains largely uninvestigated. While it is known that middle ear ossicle size scales positively with body mass across mammals, and that peak call frequency scales negatively with body mass among bats, there are still large gaps in our understanding of the degree to which allometry or ecology influences the morphology of the chiropteran auditory apparatus. To investigate this, we used μCT datasets to quantify three morphological components of the inner and middle ear: ossicle size, ossicle shape, and cochlear spirality. These data were collected across 27 phyllostomid species, spanning a broad range of body sizes, habitats, and dietary categories, and the relationships between these variables and ear morphology were assessed using a comparative phylogenetic approach. Ossicle size consistently scaled with strong negative allometry relative to body mass. Cochlear spirality was significantly (p = .025) associated with wing aspect ratio (a proxy for habitat use) but was not associated with body mass. From a morphological perspective, the malleus and incus exhibited some variation in kind with diet and call frequency, while stapes morphology is more closely tied to body size. Future work will assess these relationships within other chiropteran lineages, and investigate potential morphological differences in the middle and inner ear of echolocating-vs-non-echolocating taxa.

An updated synthesis of and outstanding questions in the olfactory and vomeronasal systems in bats: Genetics asks questions only anatomy can answer

The extensive diversity observed in bat nasal chemosensory systems has been well-documented at the histological level. Understanding how this diversity evolved and developing hypotheses as to why particular patterns exist require a phylogenetic perspective, which was first outlined in the work of anatomist Kunwar Bhatnagar. With the onset of genetics and genomics, it might be assumed that the puzzling patterns observed in the morphological data have been clarified. However, there is still a widespread mismatch of genetic and morphological correlations among bat chemosensory systems. Novel genomic evidence has set up new avenues to explore that demand more evidence from anatomical structures. Here, we outline the progress that has been made in both morphological and molecular studies on the olfactory and vomeronasal systems in bats since the work of Bhatnagar. Genomic data of olfactory and vomeronasal receptors demonstrate the strong need for further morphological sampling, with a particular focus on receiving brain regions, glands, and ducts.

Origins and evolution of biological novelty

Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.

Reed bamboos drive skull shape evolution in bush frogs of the Western Ghats, Peninsular India

Reed bamboo is a major ecological and economic resource for many animals, including humans. Nonetheless, the influence of this plant's evolutionary role on the morphology of animal species remains unexplored. Here, we investigated the significance of bamboo habitats as ecological opportunities in shaping the skull morphology of bush frogs (Raorchestes) from the Western Ghats, Peninsular India. We applied a three-dimensional (3D) geometric morphometric approach to capture the skull shape of 55 species of bush frogs. We visualized the skull shape variables in phylomorphospace with principal component analysis and performed phylogenetic generalized least-squares analysis to assess the impact of cranial size (evolutionary allometry) and habitat (bamboo or non-bamboo) on cranial shape. We quantified the morphological disparity between bamboo and non-bamboo bush frogs' skull shape, and employed RRphylo, a phylogenetic ridge regression method, to access the evolutionary rate and rate shifts of skull shape change. The phylomorphospace delineated bamboo and non-bamboo bush frogs. While cranial shape exhibited a significant but smaller association with size, its association with habitat type was non-significant. We detected, however, significant differences in skull shape between the two frog groups, with bamboo frogs showing higher morphological disparity and a remarkable shift in the evolutionary rate of skull shape diversification. These findings underscore the role of reed bamboo in the evolution of skull shape in the radiation of frogs, endemic to the Western Ghats. We demonstrate that the association between the members of two distinct endemic clades (bamboo reeds and bamboo frogs) is the outcome of a deep-time ecological opportunity that dates back to the Miocene.

Beaks promote rapid morphological diversification along distinct evolutionary trajectories in labrid fishes (Eupercaria: Labridae)

The upper and lower jaws of some wrasses (Eupercaria: Labridae) possess teeth that have been coalesced into a strong durable beak that they use to graze on hard coral skeletons, hard-shelled prey, and algae, allowing many of these species to function as important ecosystem engineers in their respective marine habitats. While the ecological impact of the beak is well understood, questions remain about its evolutionary history and the effects of this innovation on the downstream patterns of morphological evolution. Here we analyze 3D cranial shape data in a phylogenetic comparative framework and use paleoclimate modeling to reconstruct the evolution of the labrid beak across 205 species. We find that wrasses evolved beaks three times independently, once within odacines and twice within parrotfishes in the Pacific and Atlantic Oceans. We find an increase in the rate of shape evolution in the Scarus+Chlorurus+Hipposcarus (SCH) clade of parrotfishes likely driven by the evolution of the intramandibular joint. Paleoclimate modeling shows that the SCH clade of parrotfishes rapidly morphologically diversified during the middle Miocene. We hypothesize that possession of a beak in the SCH clade coupled with favorable environmental conditions allowed these species to rapidly morphologically diversify.

Disentangling Mechanical and Sensory Modules in the Radiation of Noctilionoid Bats

AbstractWith diverse mechanical and sensory functions, the vertebrate cranium is a complex anatomical structure whose shifts between modularity and integration, especially in mechanical function, have been implicated in adaptive diversification. Yet how mechanical and sensory systems and their functions coevolve, as well as how their interrelationship contributes to phenotypic disparity, remain largely unexplored. To examine the modularity, integration, and evolutionary rates of sensory and mechanical structures within the head, we analyzed hard and soft tissue scans from ecologically diverse bats in the superfamily Noctilionoidea, a clade that ranges from insectivores and carnivores to frugivores and nectarivores. We identified eight regions that evolved in a coordinated fashion, thus recognizable as evolutionary modules: five associated with bite force and three linked to olfactory, visual, and auditory systems. Interrelationships among these modules differ between Neotropical leaf-nosed bats (family Phyllostomidae) and other noctilionoids. Consistent with the hypothesis that dietary transitions begin with changes in the capacity to detect novel food items followed by adaptations to process them, peak rates of sensory module evolution predate those of some mechanical modules. We propose that the coevolution of structures influencing bite force, olfaction, vision, and hearing constituted a structural opportunity that allowed the phyllostomid ancestor to take advantage of existing ecological opportunities and contributed to the clade's remarkable radiation.

An integrative approach to understanding diversity patterns and assemblage rules in Neotropical bats

Understanding the mechanisms shaping species composition of assemblages is critical for incorporating ecological and evolutionary perspectives into biodiversity conservation. Thus, we quantified the relative support of community assembly mechanisms by assessing how species richness relates to the functional and phylogenetic biodiversity of Neotropical bat assemblages. We assessed the association of functional diversity for functional categories and phylogenetic diversity with species richness for 20 assemblages of Neotropical bats. In addition, we contrasted functional and phylogenetic diversity against null models to determine the mechanisms that structure the assemblages. We hypothesize functional/phylogenetic overdispersion for high species sites and a positive relationship between those dimensions of diversity and richness. Functional divergence increased with species richness, indicating that the variability in ecological attributes among abundant bats increases as the assemblages contain more species. Taxa were more distantly related as richness increases, but distances among closely related species remained constant. We found a consistent tendency of clustering of functional traits in site assemblages, particularly in abundant species. We proposed competition between clades as a possible mechanism modulating the community structure in Neotropical bat assemblages. Our results suggest that decreasing overlap in functional traits between abundant species could promote coexistence with rare species that can buffer ecosystem function due to species loss.

Shark mandible evolution reveals patterns of trophic and habitat-mediated diversification

Environmental controls of species diversity represent a central research focus in evolutionary biology. In the marine realm, sharks are widely distributed, occupying mainly higher trophic levels and varied dietary preferences, mirrored by several morphological traits and behaviours. Recent comparative phylogenetic studies revealed that sharks present a fairly uneven diversification across habitats, from reefs to deep-water. We show preliminary evidence that morphological diversification (disparity) in the feeding system (mandibles) follows these patterns, and we tested hypotheses linking these patterns to morphological specialisation. We conducted a 3D geometric morphometric analysis and phylogenetic comparative methods on 145 specimens representing 90 extant shark species using computed tomography models. We explored how rates of morphological evolution in the jaw correlate with habitat, size, diet, trophic level, and taxonomic order. Our findings show a relationship between disparity and environment, with higher rates of morphological evolution in reef and deep-water habitats. Deep-water species display highly divergent morphologies compared to other sharks. Strikingly, evolutionary rates of jaw disparity are associated with diversification in deep water, but not in reefs. The environmental heterogeneity of the offshore water column exposes the importance of this parameter as a driver of diversification at least in the early part of clade history.

Reconstructing the dietary habits and trophic positions of the Longipterygidae (Aves: Enantiornithes) using neontological and comparative morphological methods

The Longipterygidae are a unique clade among the enantiornithines in that they exhibit elongate rostra (≥60% total skull length) with dentition restricted to the distal tip of the rostrum, and pedal morphologies suited for an arboreal lifestyle (as in other enantiornithines). This suite of features has made interpretations of this group’s diet and ecology difficult to determine due to the lack of analogous taxa that exhibit similar morphologies together. Many extant bird groups exhibit rostral elongation, which is associated with several disparate ecologies and diets (e.g., aerial insectivory, piscivory, terrestrial carnivory). Thus, the presence of rostral elongation in the Longipterygidae only somewhat refines trophic predictions of this clade. Anatomical morphologies do not function singularly but as part of a whole and thus, any dietary or ecological hypothesis regarding this clade must also consider other features such as their unique dentition. The only extant group of dentulous volant tetrapods are the chiropterans, in which tooth morphology and enamel thickness vary depending upon food preference. Drawing inferences from both avian bill proportions and variations in the dental morphology of extinct and extant taxa, we provide quantitative data to support the hypothesis that the Longipterygidae were animalivorous, with greater support for insectivory.

By a whisker: the sensory role of vibrissae in hovering flight in nectarivorous bats

Whiskers are important tactile structures widely used across mammals for a variety of sensory functions, but it is not known how bats-representing about a fifth of all extant mammal species-use them. Nectar-eating bats typically have long vibrissae (long, stiff hairs) arranged in a forward-facing brush-like formation that is not present in most non-nectarivorous bats. They also commonly use a unique flight strategy to access their food-hovering flight. Here we investigated whether these species use their vibrissae to optimize their feeding by assisting fine flight control. We used behavioural experiments to test if bats' flight trajectory into the flower changed after vibrissa removal, and phylogenetic comparative methods to test whether vibrissa length is related to nectarivory. We found that bat flight trajectory was altered after vibrissae removal and that nectarivorous bats possess longer vibrissae than non-nectivorous species, providing evidence of an additional source of information in bats' diverse sensory toolkit.

Environmentally driven phenotypic convergence and niche conservatism accompany speciation in hoary bats

Species that are geographically widespread may exist across environmentally heterogeneous landscapes that could influence patterns of occupation and phylogeographic structure. Previous studies have suggested that geographic range size should be positively correlated with niche breadth, allowing widespread species to sustain viable populations over diverse environmental gradients. We examined the congruence of phenotypic and phylogenetic divergence with the environmental factors that help maintain species level diversity in the geographically widespread hoary bats (Lasiurus cinereus sensu lato) across their distribution. Genetic sequences were analyzed using multiple phylogenetic and species delimitation methods, and phenotypic data were analyzed using supervised and unsupervised machine learning approaches. Spatial data from environmental, geographic, and topographic features were analyzed in a multiple regression analysis to determine their relative effect on phenotypic diversity. Ecological niches of each hoary bat species were examined in environmental space to quantify niche overlap, equivalency, and the magnitude of niche differentiation. Phylogenetic and species delimitation analyses support existence of three geographically structured species of hoary bat, each of which is phenotypically distinct. However, the Hawaiian hoary bat is morphologically more similar to the South American species than to the North American species despite a closer phylogenetic relationship to the latter. Multiple regression and niche analyses revealed higher environmental similarities between the South American and Hawaiian species. Hoary bats thus exhibit a pattern of phenotypic variation that disagrees with well-supported genetic divergences, instead indicating phenotypic convergence driven by similar environmental features and relatively conserved niches occupied in tropical latitudes.

Wings of fringed fruit-eating bats (Artibeus fimbriatus) are highly integrated biological aerofoils from perspectives of secondary sexual dimorphism, allometry and modularity

Phenotypic variability is ubiquitous. This is especially true in bats, where families such as Phyllostomidae encompass as much phenotypic variability as some entire orders of mammals. Typically, phenotypic variability is characterized based on cranial morphology, with studies of other functionally important aspects of the phenotype, such as legs, feet and wings, being less frequent. We examined patterns of secondary sexual dimorphism and allometry of wing elements of the fringed fruit-eating bat (Artibeus fimbriatus) and examined, for the first time, the modularity of bat wings. Patterns were based on 13 wing measurements taken from 21 females and 15 males from eastern Paraguay. From a multivariate perspective, A. fimbriatus exhibited significant secondary sexual dimorphism. Females were larger than males for all 13 wing characteristics, with significant differences involving the last phalanx of the fourth and fifth digits. Female wings were also relatively larger than male wings from a multivariate perspective, as was the last phalanx of the fourth and fifth digits, after adjusting for wing size based on forearm length. Wing elements were highly variable regarding allometric relationships, with some exhibiting no allometric patterns and others exhibiting isometry or hyperallometry, depending on the element. Wings exhibited significant modularity, with metacarpals, proximal phalanges and distal phalanges each representing a discrete module. The wings of A. fimbriatus exhibit substantive patterns of dimorphism, allometry and modularity. Although the big mother hypothesis is a strong theoretical construct to explain wing dimorphism, there is not yet any sound theoretical basis for the patterns of allometry and modularity of the wing. Further investigation is required to understand the determinants of variation in wing morphology.

The evolution of head size hypoallometry: Biomechanical implications and brain investment as a possible cause

Species' mean relative head size decreases with increasing species mean body size in paper wasps, which may have important implications for biomechanics in these flying animals. Here we quantify the allometric relationship (log/log slope) of head size to body size in paper wasps. We sampled species in two genera (Agelaia and Polybia) to test whether head/body allometry was consistent among genera. Head mass/total mass relationships were significantly hypoallometric (log/log slopes ∼0.90) and statistically similar between Agelaia and Polybia. We reanalyzed previously published multi-genus data to calculate the slope of head/body allometry, and to compare two different aspects of head size: the allometry of head mass which could impact weight distribution along the longitudinal axis of the body, and the allometry of head volume which could impact fluid resistance and mobility. The multi-genus data set yielded a similar estimate for the slope of head mass allometry (∼0.90), but the slope of head volume allometry was significantly shallower (∼0.80): relative head volume increases faster than relative head mass as total size decreases. We suggest the demands of brain housing affect the greater investment in head size and head weight in smaller species. Relative brain size is greater for smaller-bodied species within clades (Haller's rule), and brain volume had a significantly lower allometric slope than both head mass and head volume. Relatively large brains may require increased relative head size in smaller-bodied species. Brain housing may represent a basic developmental constraint on head size and head weight, and brain allometry could consequently impact the relationships of body shape and body mass distribution to body size.

Exploitation of an ancestral pheromone biosynthetic pathway contributes to diversification in Heliconius butterflies

During courtship, male butterflies of many species produce androconial secretions containing male sex pheromones (MSPs) that communicate species identity and affect female choice. MSPs are thus likely candidates as reproductive barriers, yet their role in speciation remains poorly studied. Although Heliconius butterflies are a model system in speciation, their MSPs have not been investigated from a macroevolutionary perspective. We use GC/MS to characterize male androconial secretions in 33 of the 69 species in the Heliconiini tribe. We found these blends to be species-specific, consistent with a role in reproductive isolation. We detected a burst in blend diversification rate at the most speciose genus, Heliconius; a consequence of Heliconius and Eueides species using a fatty acid (FA) metabolic pathway to unlock more complex blends than basal Heliconiini species, whose secretions are dominated by plant-like metabolites. A comparison of 10 sister species pairs demonstrates a striking positive correlation between blend dissimilarity and range overlap, consistent with character displacement or reinforcement in sympatry. These results demonstrate for the first time that MSP diversification can promote reproductive isolation across this group of butterflies, showcasing how implementation of an ancestral trait, the co-option of the FA metabolic pathway for pheromone production, can facilitate rapid speciation.

Revised phylogeny from complete mitochondrial genomes of phyllostomid bats resolves subfamilial classification

Classically, molecular phylogenetic trees of Phyllostomidae have been inferred using a combination of a few mitochondrial and nuclear markers. However, there is still uncertainty in the relationships, especially among deep clades within the family. In this study, we provide newly sequenced complete mitochondrial genomes from 26 bat species, including genomes of 23 species reported here for the first time. By carefully analysing these genomes using maximum likelihood and Bayesian methods and different ingroup and outgroup samples, partition schemes and data types, we investigated the robustness and sensitivity of our phylogenetic results. The optimal topologies were those inferred from the complete data matrix of nucleotides, with complex and highly parameterized substitution models and partition schemes. Our results show a statistically robust picture of the evolutionary relationships between phyllostomid subfamilies and clarify hitherto uncertain relationships of Lonchorhininae and Macrotinae.

Estimating bite force in extinct dinosaurs using phylogenetically predicted physiological cross-sectional areas of jaw adductor muscles

I present a Bayesian phylogenetic predictive modelling (PPM) framework that allows the prediction of muscle parameters (physiological cross-sectional area, A _Phys) in extinct archosaurs from skull width (W _Sk) and phylogeny. This approach is robust to phylogenetic uncertainty and highly versatile given its ability to base predictions on simple, readily available predictor variables. The PPM presented here has high prediction accuracy (up to 95%), with downstream biomechanical modelling yielding bite force estimates that are in line with previous estimates based on muscle parameters from reconstructed muscles. This approach does not replace muscle reconstructions but one that provides a powerful means to predict A _Phys from skull geometry and phylogeny to the same level of accuracy as that measured from reconstructed muscles in species for which soft tissue data are unavailable or difficult to obtain.

Evolutionary transitions in diet influence the exceptional diversification of a lizard adaptive radiation

Background

Diet is a key component of a species ecological niche and plays critical roles in guiding the trajectories of evolutionary change. Previous studies suggest that dietary evolution can influence the rates and patterns of species diversification, with omnivorous (animal and plant, ‘generalist’) diets slowing down diversification compared to more restricted (‘specialist’) herbivorous and carnivorous diets. This hypothesis, here termed the “dietary macroevolutionary sink” hypothesis (DMS), predicts that transitions to omnivorous diets occur at higher rates than into any specialist diet, and omnivores are expected to have the lowest diversification rates, causing an evolutionary sink into a single type of diet. However, evidence for the DMS hypothesis remains conflicting. Here, we present the first test of the DMS hypothesis in a lineage of ectothermic tetrapods—the prolific Liolaemidae lizard radiation from South America.

Results

Ancestral reconstructions suggest that the stem ancestor was probably insectivorous. The best supported trait model is a diet-dependent speciation rate, with independent extinction rates. Herbivory has the highest net diversification rate, omnivory ranks second, and insectivory has the lowest. The extinction rate is the same for all three diet types and is much lower than the speciation rates. The highest transition rate was from omnivory to insectivory, and the lowest transition rates were between insectivory and herbivory.

Conclusions

Our findings challenge the core prediction of the DMS hypothesis that generalist diets represent an ‘evolutionary sink’. Interestingly, liolaemid lizards have rapidly and successfully proliferated across some of the world’s coldest climates (at high elevations and latitudes), where species have evolved mixed arthropod-plant (omnivore) or predominantly herbivore diets. This longstanding observation is consistent with the higher net diversification rates found in both herbivory and omnivory. Collectively, just like the evolution of viviparity has been regarded as a ‘key adaptation’ during the liolaemid radiation across cold climates, our findings suggest that transitions from insectivory to herbivory (bridged by omnivory) are likely to have played a role as an additional key adaptation underlying the exceptional diversification of these reptiles across extreme climates.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02028-3.

Bat Dentitions: A Model System for Studies at The Interface of Development, Biomechanics, and Evolution

The evolution of complex dentitions was a major innovation in mammals that facilitated the expansion into new dietary niches that imposed selection for tight form-function relationships. Teeth allow mammals to ingest and process food items by applying forces produced by a third-class lever system composed by the jaw adductors, the cranium, and the mandible. Physical laws determine changes in jaw adductor (biting) forces at different bite point locations along the mandible (outlever), thus individual teeth are expected to experience different mechanical regimes during feeding. If the mammal dentition exhibits functional adaptations to mandible feeding biomechanics, then teeth are expected to have evolved to develop mechanically-advantageous sizes, shapes, and positions. Here, we present bats as a model system to test this hypothesis and, more generally, for integrative studies of mammal dental diversity. We combine a field-collected dataset of bite forces along the tooth row with data on dental and mandible morphology across 30 bat species. We (1) describe, for the first time, bite force trends along the tooth row of bats, (2) use phylogenetic comparative methods to investigate relationships among bite force patterns, tooth and mandible morphology, and (3) hypothesize how these biting mechanics patterns may relate to the developmental processes controlling tooth formation. We find that bite force variation along the tooth row is consistent with predictions from lever mechanics models, with most species having the greatest bite force at the first lower molar. The cross-sectional shape of the mandible body is strongly associated with the position of maximum bite force along the tooth row, likely reflecting mandibular adaptations to varying stress patterns among species. Further, dental dietary adaptations seem to be related to bite force variation along molariform teeth, with insectivorous species exhibiting greater bite force more anteriorly, narrower teeth and mandibles, and frugivores/omnivores showing greater bite force more posteriorly, wider teeth and mandibles. As these craniodental traits are linked through development, dietary specialization appears to have shaped intrinsic mechanisms controlling traits relevant to feeding performance.

Broad-scale gradients of resource utilization by phyllostomid bats in Atlantic Forest: patterns of dietary overlap, turnover and the efficacy of ecomorphological approaches

Identifying mechanisms that promote coexistence at the local level is enigmatic for many organisms. Numerous studies have indirectly demonstrated that biotic interactions may not cause deterministic patterns reflective of the coexistence of interacting bat species. Nonetheless, demonstration of the partitioning of resources by phyllostomid bats by directly examining diet matrices may illuminate a mechanism of coexistence. I examined the dietary overlap of phyllostomid bats across 23 sites in the Atlantic Forest of South America. I also examined components of beta diversity (turnover and nestedness) of resources among species as well as the degree to which morphology can act as a surrogate for dietary similarity in each community. Bats exhibited high overlap. Nonetheless, dietary beta diversity was more related to turnover than nestedness of items suggesting substantive species-specific affinities. Niche breath and dietary overlap were positively related to the number of species and the number of resources consumed in communities. Accordingly, changes in richness across Atlantic Forest may be facilitated by increases in resources available at the community level. There were positive, yet weak relationships between morphological and dietary distance. The relationship between morphology and diet was invariant relative to geography, species richness, number of dietary resources, average diet breadth and average dietary overlap indicating that in the Atlantic Forest morphology is a consistent surrogate of dietary relationships of species. Atlantic Forest is one of the most anthropogenically modified tropical forests in the world. This in combination with distinct climatic seasonality likely causes higher dietary overlap, weaker ecomorphological relationships and persistence of only the most general bat species.

Chromosome Painting in Lonchorhina aurita Sheds Light onto the Controversial Phylogenetic Position of Sword-Nosed Bats (Chiroptera, Phyllostomidae)

The subfamily Lonchorhininae encompasses 6 species of sword-nosed bats (Lonchorhina) and is one of the most problematic lineages in the Neotropical leaf-nosed bats (Phyllostomidae) phylogeny. There are at least 5 different hypotheses to explain when the subfamily diverged from the remaining phyllostomids, but none with robust statistical support. Here, we generated a chromosome painting homology map of Lonchorhina aurita karyotype (2n = 32 and FN = 60) using whole-chromosome probes of Macrotus californicus (MCA; 2n = 40 and FN = 60). We placed the karyotype changes of L. aurita in a phylogenetic context to discuss the most likely branching position of Lonchorhininae based on karyotypic evolution. We show that L. aurita has a derived karyotype with 24 segments homologous to the 20 MCA chromosomes used as probes. Comparative analyses between 7 published painted bats species across 4 phyllostomid subfamilies (Macrotinae, Phyllostominae, Glossophaginae, and Lonchophyllinae) revealed that one inversion (MCA 4inv) and one fusion (MCA 17 + 18) are shared derived features between the karyotypes of L. aurita and species of Phyllostominae not yet observed in other bats. Our data show that chromosomal homology maps may contribute with new insights into a long-standing phylogenetic debate that has endured for decades.

The structure of tropical bat-plant interaction networks during an extreme El Niño-Southern Oscillation event

Interaction network structure reflects the ecological mechanisms acting within biological communities, which are affected by environmental conditions. In tropical forests, higher precipitation usually increases fruit production, which may lead frugivores to increase specialization, resulting in more modular and less nested animal–plant networks. In these ecosystems, El Niño is a major driver of precipitation, but we still lack knowledge of how species interactions change under this influence. To understand bat–plant network structure during an extreme El Niño‐Southern Oscillation event, we determined the links between plantivorous bat species and the plants they consume by DNA barcoding seeds and pulp in bat faeces. These interactions were recorded in the dry forest and rainforest of Costa Rica, during the dry and the wet seasons of an extreme El Niño year. From these we constructed seasonal and whole‐year bat–plant networks and analysed their structures and dissimilarities. In general, networks had low nestedness, had high modularity, and were dominated by one large compartment which included most species and interactions. Contrary to our expectations, networks were less nested and more modular in drier conditions, both in the comparison between forest types and between seasons. We suggest that increased competition, when resources are scarce during drier seasons and habitats, lead to higher resource partitioning among bats and thus higher modularity. Moreover, we have found similar network structures between dry and rainforests during El Niño and non‐El Niño years. Finally, most interaction dissimilarity among networks occurred due to interaction rewiring among species, potentially driven by seasonal changes in resource availability.

A novel intramandibular joint facilitates feeding versatility in the sixbar distichodus

The intramandibular joint (IMJ) is a secondary point of movement between the two major bones of the lower jaw. It has independently evolved in several groups of teleost fishes, each time representing a departure from related species in which the mandible functions as a single structure rotating only at the quadratomandibular joint (QMJ). In this study, we examine kinematic consequences of the IMJ novelty in a freshwater characiform fish, the herbivorous Distichodus sexfasciatus. We combine traditional kinematic approaches with trajectory-based analysis of motion shapes to compare patterns of prey capture movements during substrate biting, the fish's native feeding mode, and suction of prey from the water column. We find that the IMJ enables complex jaw motions and contributes to feeding versatility by allowing the fish to modulate its kinematics in response to different prey and to various scenarios of jaw-substrate interaction. Implications of the IMJ include context-dependent movements of lower versus upper jaws, enhanced lower jaw protrusion, and the ability to maintain contact between the teeth and substrate throughout the jaw closing or biting phase of the motion. The IMJ in D. sexfasciatus appears to be an adaptation for removing attached benthic prey, consistent with its function in other groups that have evolved the joint. This study builds on our understanding of the role of the IMJ during prey capture and provides insights into broader implications of the innovative trait.

Evolutionary innovations in Antarctic brittle stars linked to glacial refugia

The drivers behind evolutionary innovations such as contrasting life histories and morphological change are central questions of evolutionary biology. However, the environmental and ecological contexts linked to evolutionary innovations are generally unclear. During the Pleistocene glacial cycles, grounded ice sheets expanded across the Southern Ocean continental shelf. Limited ice-free areas remained, and fauna were isolated from other refugial populations. Survival in Southern Ocean refugia could present opportunities for ecological adaptation and evolutionary innovation. Here, we reconstructed the phylogeographic patterns of circum-Antarctic brittle stars Ophionotus victoriae and O. hexactis with contrasting life histories (broadcasting vs brooding) and morphology (5 vs 6 arms). We examined the evolutionary relationship between the two species using cytochrome c oxidase subunit I (COI) data. COI data suggested that O. victoriae is a single species (rather than a species complex) and is closely related to O. hexactis (a separate species). Since their recent divergence in the mid-Pleistocene, O. victoriae and O. hexactis likely persisted differently throughout glacial maxima, in deep-sea and Antarctic island refugia, respectively. Genetic connectivity, within and between the Antarctic continental shelf and islands, was also observed and could be linked to the Antarctic Circumpolar Current and local oceanographic regimes. Signatures of a probable seascape corridor linking connectivity between the Scotia Sea and Prydz Bay are also highlighted. We suggest that survival in Antarctic island refugia was associated with increase in arm number and a switch from broadcast spawning to brooding in O. hexactis, and propose that it could be linked to environmental changes (such as salinity) associated with intensified interglacial-glacial cycles.

Functional differences in echolocation call design in an adaptive radiation of bats

All organisms have specialized systems to sense their environment. Most bat species use echolocation for navigation and foraging, but which and how ecological factors shaped echolocation call diversity remains unclear for the most diverse clades, including the adaptive radiation of neotropical leaf-nosed bats (Phyllostomidae). This is because phyllostomids emit low-intensity echolocation calls and many inhabit dense forests, leading to low representation in acoustic surveys. We present a field-collected, echolocation call dataset spanning 35 species and all phyllostomid dietary guilds. We analyze these data under a phylogenetic framework to test the hypothesis that echolocation call design and parameters are specialized for the acoustic demands of different diets, and investigate the contributions of phylogeny and body size to echolocation call diversity. We further link call parameters to dietary ecology by contrasting minimum detectable prey size estimates (MDPSE) across species. We find phylogeny and body size explain a substantial proportion of echolocation call parameter diversity, but most species can be correctly assigned to taxonomic (61%) or functional (77%) dietary guilds based on call parameters. This suggests a degree of acoustic ecological specialization, albeit with interspecific similarities in call structure. Theoretical MDPSE are greatest for omnivores and smallest for insectivores. Omnivores significantly differ from other dietary guilds in MDPSE when phylogeny is not considered, but there are no differences among taxonomic dietary guilds within a phylogenetic context. Similarly, predators of non-mobile/non-evasive prey and predators of mobile/evasive prey differ in estimated MDPSE when phylogeny is not considered. Phyllostomid echolocation call structure may be primarily specialized for overcoming acoustic challenges of foraging in dense habitats, and then secondarily specialized for the detection of food items according to functional dietary guilds. Our results give insight into the possible ecological mechanisms shaping the diversity of sensory systems, and their reciprocal influence on resource use.

Skull Morphology, Bite Force, and Diet in Insectivorous Bats from Tropical Dry Forests in Colombia

In Neotropical bats, studies on bite force have focused mainly on differences in trophic ecology, and little is known about whether factors other than body size generate interspecific differences in bite force amongst insectivorous bats and, consequently, in their diets. We tested if bite force is related to skull morphology and also to diet in an assemblage of Neotropical insectivorous bats from tropical dry forests in the inter-Andean central valley in Colombia. It is predicted that the preference of prey types among insectivorous species is based on bite force and cranial characteristics. We also evaluated whether skull morphology varies depending on the species and sex. Cranial measurements and correlations between morphological variation and bite force were examined for 10 insectivorous bat species. We calculated the size-independent mechanical advantage for the mandibular (jaw) lever system. In all species, bite force increased with length of the skull and the jaw more than other cranial measurements. Obligate insectivorous species were morphologically different from the omnivorous Noctilio albiventris, which feeds primarily on insects, but also consumes fish and fruits. Our results show that bite force and skull morphology are closely linked to diets in Neotropical insectivorous bats and, consequently, these traits are key to the interactions within the assemblage and with their prey.

The influence of divergent reproductive strategies in shaping modularity and morphological evolution in mammalian jaws

Marsupial neonates are born at an earlier developmental stage than placental mammals, but the rapid development of their forelimbs and cranial skeleton allows them to climb to the pouch, begin suckling and complete their development ex utero. The mechanical environment in which marsupial neonates develop is vastly different from that of placental neonates, which exhibit a more protracted development of oral muscles and bones. This difference in reproductive strategy has been theorized to constrain morphological evolution in the oral region of marsupials. Here, we use 3D morphometrics to characterize one of these oral bones, the lower jaw (dentary), and assess modularity (pattern of covariation among traits), morphological disparity and rates of morphological evolution in two clades of carnivorous mammals: the marsupial Dasyuromorphia and placental fissiped Carnivora. We find that dasyuromorph dentaries have fewer modules than carnivorans and exhibit tight covariation between the angular and coronoid processes, the primary attachment sites for jaw-closing muscles. This pattern of modularity may result from the uniform action of muscles on the developing mandible during suckling. Carnivorans are free from this constraint and exhibit a pattern of modularity that more strongly reflects genetic and developmental signals of trait covariation. Alongside differences in modularity, carnivorans exhibit greater disparity and faster rates of morphological evolution compared with dasyuromorphs. Taken together, this suggests dasyuromorphs have retained a signal of trait covariation that reflects the outsized influence of muscular force during early development, a feature that may have impacted the ability of marsupial carnivores to explore specialized regions of morphospace.

Foraging strategies, craniodental traits, and interaction in the bite force of Neotropical frugivorous bats (Phyllostomidae: Stenodermatinae)

Bats in the family Phyllostomidae exhibit great diversity in skull size and morphology that reflects the degree of resource division and ecological overlap in the group. In particular, the subfamily Stenodermatinae has high morphological diversification associated with cranial and mandibular traits that are associated with the ability to consume the full range of available fruits (soft and hard).We analyzed craniodental traits and their relationship to the bite force in 343 specimens distributed in seven species of stenodermatine bats with two foraging strategies: nomadic and sedentary frugivory. We evaluated 19 traits related to feeding and bite force in live animals by correcting bite force with body size.We used a generalized linear model (GLM) and post hoc tests to determine possible relationships and differences between cranial traits, species, and sex. We also used Blomberg's K to measure the phylogenetic signal and phylogenetic generalized least-squares (PGLS) to ensure the phylogenetic independence of the traits.We found that smaller nomadic species, A. anderseni and A. phaeotis , have a similar bite force to the large species A. planirostris and A. lituratus; furthermore, P. helleri registered a bite force similar to that of the sedentary bat, S. giannae. Our study determined that all the features of the mandible and most of the traits of the skull have a low phylogenetic signal. Through the PGLS, we found that the diet and several cranial features (mandibular toothrow length, dentary length, braincase breadth, mastoid breadth, greatest length of skull, condylo-incisive length, and condylo-canine length) determined bite force performance among Stenodermatiane.Our results reinforce that skull size is a determining factor in the bite force, but also emphasize the importance of its relationships with morphology, ecology, and phylogeny of the species, which gives us a better understanding of the evolutionary adaptions of this highly diverse Neotropical bat group.

Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution

Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sources including blood, nectar, and fruit. To assess whether dietary diversification in this group was accompanied by molecular adaptations for changing metabolic demands, we sequenced 89 transcriptomes across 58 species and combined these with published data to compare ∼13,000 protein coding genes across 66 species. We tested for positive selection on focal lineages, including those inferred to have undergone dietary shifts. Unexpectedly, we found a broad signature of positive selection in the ancestral phyllostomid branch, spanning genes implicated in the metabolism of all major macronutrients, yet few positively selected genes at the inferred switch to plantivory. Branches corresponding to blood- and nectar-based diets showed selection in loci underpinning nitrogenous waste excretion and glycolysis, respectively. Intriguingly, patterns of selection in metabolism genes were mirrored by those in loci implicated in craniofacial remodeling, a trait previously linked to phyllostomid dietary specialization. Finally, we show that the null model of the widely-used branch-site test is likely to be misspecified, with the implication that the test is too conservative and probably under-reports true cases of positive selection. Our findings point to a complex picture of adaptive radiation, in which the evolution of new dietary specializations has been facilitated by early adaptations combined with the generation of new genetic variation.

Positive Selection and Gene Expression Analyses from Salivary Glands Reveal Discrete Adaptations within the Ecologically Diverse Bat Family Phyllostomidae

The leaf-nosed bats (Phyllostomidae) are outliers among chiropterans with respect to the unusually high diversity of dietary strategies within the family. Salivary glands, owing to their functions and high ultrastructural variability among lineages, are proposed to have played an important role during the phyllostomid radiation. To identify genes underlying salivary gland functional diversification, we sequenced submandibular gland transcriptomes from phyllostomid species representative of divergent dietary strategies. From the assembled transcriptomes, we performed an array of selection tests and gene expression analyses to identify signatures of adaptation. Overall, we identified an enrichment of immunity-related gene ontology terms among 53 genes evolving under positive selection. Lineage-specific selection tests revealed several endomembrane system genes under selection in the vampire bat. Many genes that respond to insulin were under selection and differentially expressed genes pointed to modifications of amino acid synthesis pathways in plant-visitors. Results indicate salivary glands have diversified in various ways across a functional diverse clade of mammals in response to niche specializations.

Inter- and intra-specific variation in hair cortisol concentrations of Neotropical bats

Quantifying hair cortisol has become popular in wildlife ecology for its practical advantages for evaluating stress. Before hair cortisol levels can be reliably interpreted, however, it is key to first understand the intrinsic factors explaining intra- and inter-specific variation. Bats are an ecologically diverse group of mammals that allow studying such variation. Given that many bat species are threatened or have declining populations in parts of their range, minimally invasive tools for monitoring colony health and identifying cryptic stressors are needed to efficiently direct conservation efforts. Here we describe intra- and inter-specific sources of variation in hair cortisol levels in 18 Neotropical bat species from Belize and Mexico. We found that fecundity is an important ecological trait explaining inter-specific variation in bat hair cortisol. Other ecological variables such as colony size, roost durability and basal metabolic rate did not explain hair cortisol variation among species. At the individual level, females exhibited higher hair cortisol levels than males and the effect of body mass varied among species. Overall, our findings help validate and accurately apply hair cortisol as a monitoring tool in free-ranging bats.

Complex macroevolutionary dynamics underly the evolution of the crocodyliform skull

All modern crocodyliforms (alligators, crocodiles and the gharial) are semi-aquatic generalist carnivores that are relatively similar in cranial form and function. However, this homogeneity represents just a fraction of the variation that once existed in the clade, which includes extinct herbivorous and marine forms with divergent skull structure and function. Here, we use high-dimensional three-dimensional geometric morphometrics to quantify whole-skull morphology across modern and fossil crocodyliforms to untangle the factors that shaped the macroevolutionary history and relatively low phenotypic variation of this clade through time. Evolutionary modelling demonstrates that the pace of crocodyliform cranial evolution is initially high, particularly in the extinct Notosuchia, but slows near the base of Neosuchia, with a late burst of rapid evolution in crown-group crocodiles. Surprisingly, modern crocodiles, especially Australian, southeast Asian, Indo-Pacific species, have high rates of evolution, despite exhibiting low variation. Thus, extant lineages are not in evolutionary stasis but rather have rapidly fluctuated within a limited region of morphospace, resulting in significant convergence. The structures related to jaw closing and bite force production (e.g. pterygoid flange and quadrate) are highly variable, reinforcing the importance of function in driving phenotypic variation. Together, these findings illustrate that the apparent conservativeness of crocodyliform skulls betrays unappreciated complexity in their macroevolutionary dynamics.

Inter- and intraspecific variation in the Artibeus species complex demonstrates size and shape partitioning among species

Neotropical leaf-nosed bats (family Phyllostomidae) are one of the most diverse mammalian families and Artibeus spp. is one of the most speciose phyllostomid genera. In spite of their species diversity, previous work on Artibeus crania using linear morphometrics has uncovered limited interspecific variation. This dearth of shape variation suggests that differences in cranial morphology are not contributing to niche partitioning across species, many of which are often found in sympatry. Using two-dimensional geometric morphometric methods on crania from eleven species from the Artibeus species complex, the current study demonstrates substantial cranial interspecific variation, sexual size and shape dimorphism, and intraspecific geographic variation. The majority of species were shown to have a unique size and shape, which suggests that each species may be taking advantage of slightly different ecological resources. Further, both sexual size and shape dimorphism were significant in the Artibeus species complex. Male and female Artibeus are known to have sex specific foraging strategies, with males eating near their roosts and females feeding further from their roosts. The presence of cranial sexual dimorphism in the Artibeus species complex, combined with previous work showing that different fruit size and hardness is correlated with different cranial shapes in phyllostomids, indicates that the males and females may be utilizing different food resources, leading to divergent cranial morphotypes. Additional field studies will be required to confirm this emergent hypothesis. Finally, significant geographical shape variation was found in a large intraspecific sample of Artibeus lituratus crania. However, this variation was not correlated with latitude and instead may be linked to local environmental factors. Additional work on ecology and behavior in the Artibeus species complex underlying the morphological variation uncovered in this study will allow for a better understanding of how the group has reached its present diversity.

Large-scale genome sampling reveals unique immunity and metabolic adaptations in bats

Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species, one generated in this study, encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defence receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defence response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance antiviral immune response while dampening inflammatory signalling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.

Head and mandible shapes are highly integrated yet represent two distinct modules within and among worker subcastes of the ant genus Pheidole

Ants use their mandibles for a wide variety of tasks related to substrate manipulation, brood transport, food processing, and colony defense. Due to constraints involved in colony upkeep, ants evolved a remarkable diversity of mandibular forms, often related to specific roles such as specialized hunting and seed milling. Considering these varied functional demands, we focused on understanding how the mandible and head shape vary within and between Pheidole subcastes. Using x-ray microtomography and 3D geometric morphometrics, we tested whether these structures are integrated and modular, and how ecological predictors influenced these features. Our results showed that mandible and head shape of majors and minor workers tend to vary from robust to slender, with some more complex changes related to the mandibular base. Additionally, we found that head and mandible shapes are characterized by a high degree of integration, but with little correlation with feeding and nesting habits. Our results suggest that a combination of structural (allometric) constraints and the behavioral flexibility conferred by subcaste dimorphism might largely buffer selective pressures that would otherwise lead to a fine-tuning between ecological conditions and morphological adaptation.

Functional correlates of skull shape in Chiroptera: feeding and echolocation adaptations

Morphological, functional, and behavioral adaptations of bats are among the most diverse within mammals. A strong association between bat skull morphology and feeding behavior has been suggested previously. However, morphological variation related to other drivers of adaptation, in particular echolocation, remains understudied. We assessed variation in skull morphology with respect to ecology (diet and emission type) and function (bite force, masticatory muscles and echolocation characteristics) using geometric morphometrics and comparative methods. Our study suggests that variation in skull shape of 10 bat families is the result of adaptations to broad dietary categories and sound emission types (oral or nasal). Skull shape correlates with echolocation parameters only in a subsample of insectivorous species, possibly because they (almost) entirely rely on this sensory system for locating and capturing prey. Insectivores emitting low frequencies are characterized by a ventrally tilted rostrum, a trait not associated with feeding parameters. This result questions the validity of a trade-off between feeding and echolocation function. Our study advances understanding of the relationship between skull morphology and specific features of echolocation and suggests that evolutionary constraints due to echolocation may differ between different groups within the Chiroptera.

Find the food first: An omnivorous sensory morphotype predates biomechanical specialization for plant based diets in phyllostomid bats

The role of mechanical morphologies in the exploitation of novel niche space is well characterized; however, the role of sensory structures in unlocking new niches is less clear. Here, we investigate the relationship between the evolution of sensory structures and diet during the radiation of noctilionoid bats. With a broad range of foraging ecologies and a well-supported phylogeny, noctilionoids constitute an ideal group for studying this relationship. We used diffusible iodine-based contrast enhanced computed tomography scans of 44 noctilionoid species to analyze relationships between the relative volumes of three sensory structures (olfactory bulbs, orbits, and cochleae) and diet. We found a positive relationship between frugivory and both olfactory and orbit size. However, we also found a negative relationship between nectarivory and cochlea size. Ancestral state estimates suggest that larger orbits and olfactory bulbs were present in the common ancestor of family Phyllostomidae, but not in other noctilionoid. This constellation of traits indicates a shift toward omnivory at the base of Phyllostomidae, predating their radiation into an exceptionally broad range of dietary niches. This is consistent with a scenario in which changes in sensory systems associated with foraging and feeding set the stage for subsequent morphological modification and diversification.

Sensory adaptations reshaped intrinsic factors underlying morphological diversification in bats

Background

Morphological evolution may be impacted by both intrinsic (developmental, constructional, physiological) and extrinsic (ecological opportunity and release) factors, but can intrinsic factors be altered by adaptive evolution and, if so, do they constrain or facilitate the subsequent diversification of biological form? Bats underwent deep adaptive divergences in skull shape as they evolved different sensory modes; here we investigate the potential impact of this process on two intrinsic factors that underlie morphological variation across organisms, allometry, and modularity.

Results

We use comparative phylogenetic and morphometric approaches to examine patterns of evolutionary allometry and modularity across a 3D geometric morphometric dataset spanning all major bat clades. We show that allometric relationships diverge between echolocators and visually oriented non-echolocators and that the evolution of nasal echolocation reshaped the modularity of the bat cranium.

Conclusions

Shifts in allometry and modularity may have significant consequences on the diversification of anatomical structures, as observed in the bat skull.