A genomic hotspot of diversifying selection and structural change in the hoary bat (Lasiurus cinereus)

Background

Previous work found that numerous genes positively selected within the hoary bat (Lasiurus cinereus) lineage are physically clustered in regions of conserved synteny. Here I further validate and expand on those finding utilizing an updated L. cinereus genome assembly and additional bat species as well as other tetrapod outgroups.

Methods

A chromosome-level assembly was generated by chromatin-contact mapping and made available by DNAZoo (www.dnazoo.org). The genomic organization of orthologous genes was extracted from annotation data for multiple additional bat species as well as other tetrapod clades for which chromosome-level assemblies were available from the National Center for Biotechnology Information (NCBI). Tests of branch-specific positive selection were performed for L. cinereus using PAML as well as with the HyPhy package for comparison.

Results

Twelve genes exhibiting significant diversifying selection in the L. cinereus lineage were clustered within a 12-Mb genomic window; one of these (Trpc4) also exhibited diversifying selection in bats generally. Ten of the 12 genes are landmarks of two distinct blocks of ancient synteny that are not linked in other tetrapod clades. Bats are further distinguished by frequent structural rearrangements within these synteny blocks, which are rarely observed in other Tetrapoda. Patterns of gene order and orientation among bat taxa are incompatible with phylogeny as presently understood, implying parallel evolution or subsequent reversals. Inferences of positive selection were found to be robust to alternative phylogenetic topologies as well as a strong shift in background nucleotide composition in some taxa.

Discussion

This study confirms and further localizes a genomic hotspot of protein-coding divergence in the hoary bat, one that also exhibits an increased tempo of structural change in bats compared with other mammals. Most genes in the two synteny blocks have elevated expression in brain tissue in humans and model organisms, and genetic studies implicate the selected genes in cranial and neurological development, among other functions.

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 hierarchical radiation of phyllostomid bats as revealed by adaptive molar morphology

Adaptive radiations are bursts in biodiversity that generate new evolutionary lineages and phenotypes. However, because they typically occur over millions of years, it is unclear how their macroevolutionary dynamics vary through time and among groups of organisms. Phyllostomid bats radiated extensively for diverse diets-from insects to vertebrates, fruit, nectar, and blood-and we use their molars as a model system to examine the dynamics of adaptive radiations. Three-dimensional shape analyses of lower molars of Noctilionoidea (Phyllostomidae and close relatives) indicate that different diet groups exhibit distinct morphotypes. Comparative analyses further reveal that phyllostomids are a striking example of a hierarchical radiation; phyllostomids' initial, higher-level diversification involved an "early burst" in molar morphological disparity as lineages invaded new diet-affiliated adaptive zones, followed by subsequent lower-level diversifications within adaptive zones involving less dramatic morphological changes. We posit that strong selective pressures related to initial shifts to derived diets may have freed molars from morpho-functional constraints associated with the ancestral molar morphotype. Then, lineages with derived diets (frugivores and nectarivores) diversified within broad adaptive zones, likely reflecting finer-scale niche partitioning. Importantly, the observed early burst pattern is only evident when examining molar traits that are strongly linked to diet, highlighting the value of ecomorphological traits in comparative studies. Our results support the hypothesis that adaptive radiations are commonly hierarchical and involve different tempos and modes at different phylogenetic levels, with early bursts being more common at higher levels.

Sample Size and Geometric Morphometrics Methodology Impact the Evaluation of Morphological Variation

Geometric morphometrics has had a profound impact on our understanding of morphological evolution. However, factors such as sample size and the views and elements selected for two-dimensional geometric morphometric (2DGM) analyses, which are often dictated by specimen availability and time rather than study design, may affect the outcomes of those analyses. Leveraging large intraspecific sample sizes (n > 70) for two bat species, Lasiurus borealis and Nycticeius humeralis, we evaluate the impact of sample size on calculations of mean shape, shape variance, and centroid size. Additionally, we assessed the concordance of multiple skull 2D views with one another and characterized morphological variation in skull shape in L. borealis and N. humeralis, as well as a closely related species, Lasiurus seminolus. Given that L. seminolus is a morphologically cryptic species with L. borealis, we assessed whether differences in skull shape and in 2DGM approach would allow species discrimination. We found that reducing sample size impacted mean shape and increased shape variance, that shape differences were not consistent across views or skull elements, and that trends shown by the views and elements were not all strongly associated with one another. Further, we found that L. borealis and L. seminolus were statistically different in shape using 2DGM in all views and elements. These results underscore the importance of selecting appropriate sample sizes, 2D views, and elements based on the hypothesis being tested. While there is likely not a generalizable sample size or 2D view that can be employed given the wide variety of research questions and systems evaluated using 2DGM, a generalizable solution to issues with 2DGM presented here is to run preliminary analyses using multiple views, elements, and sample sizes, thus ensuring robust conclusions.

Ontogeny of cranial musculoskeletal anatomy and its relationship to allometric increase in bite force in an insectivorous bat (Eptesicus fuscus)

Bite force is a performance metric commonly used to link cranial morphology with dietary ecology, as the strength of forces produced by the feeding apparatus largely constrains the foods an individual can consume. At a macroevolutionary scale, there is evidence that evolutionary changes in the anatomical elements involved in producing bite force have contributed to dietary diversification in mammals. Much less is known about how these elements change over postnatal ontogeny. Mammalian diets drastically shift over ontogeny-from drinking mother's milk to feeding on adult foods-presumably with equally drastic changes in the morphology of the feeding apparatus and bite performance. Here, we investigate ontogenetic morphological changes in the insectivorous big brown bat (Eptesicus fuscus), which has an extreme, positive allometric increase in bite force during development. Using contrast-enhanced micro-computed tomography scans of a developmental series from birth to adult morphology, we quantified skull shape and measured skeletal and muscular parameters directly related to bite force production. We found pronounced changes in the skull over ontogeny, including a large increase in the volume of the temporalis and masseter muscles, and an expansion of the skull dome and sagittal crest that would serve to increase the temporalis attachment area. These changes indicate that development of the jaw adductors play an important role in the development of biting performance of these bats. Notably, static bite force increases with positive allometry with respect to all anatomical measures examined, suggesting that modifications in biting dynamics and/or improved motor coordination also contribute to increases in biting performance.

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.

Diversification of the ruminant skull along an evolutionary line of least resistance

Clarifying how microevolutionary processes scale to macroevolutionary patterns is a fundamental goal in evolutionary biology, but these analyses, requiring comparative datasets of population-level variation, are limited. By analyzing a previously published dataset of 2859 ruminant crania, we find that variation within and between ruminant species is biased by a highly conserved mammalian-wide allometric pattern, CREA (craniofacial evolutionary allometry), where larger species have proportionally longer faces. Species with higher morphological integration and species more biased toward CREA have diverged farther from their ancestors, and Ruminantia as a clade diversified farther than expected in the direction of CREA. Our analyses indicate that CREA acts as an evolutionary "line of least resistance" and facilitates morphological diversification due to its alignment with the browser-grazer continuum. Together, our results demonstrate that constraints at the population level can produce highly directional patterns of phenotypic evolution at the macroevolutionary scale. Further research is needed to explore how CREA has been exploited in other mammalian clades.

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 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.

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.

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.

Quantifying the link between craniodental morphology and diet in the Soricidae using geometric morphometrics

Dietary adaptations have often been associated with heightened taxonomic diversity. Yet, one of the most species-rich mammalian families, the Soricidae, is often considered to be ecologically and morphologically relatively homogenous. Here, we use geometric morphometrics to capture skull and dentary morphology in a broad sample of shrew species and test the hypothesis that morphological variation among shrew species reflects adaptations to food hardness. Our analyses demonstrate that morphology is associated with dietary ecology. Species that consume hard food items are larger and have specific morphological adaptions including an anteroposteriorly expanded parietal, an anteroposteriorly short and dorsoventrally tall rostrum, a mediolaterally wide palate, buccolingually wide cheek teeth, a large coronoid process and a dorsoventrally short jaw joint. The masseter muscle does not appear to play an important role in the strong bite force of shrews and the dentary is a better indicator of ecology than the skull. Our phylogenetic flexible discriminant function analysis suggests that the evolutionary history of shrews has shaped their morphology, canalizing dietary adaptations and enabling functional equivalence whereby different morphologies achieve similar dietary performances. Our work makes possible future studies of niche partitioning among sympatric species as well as the investigation of the diet of extinct soricids.

Divergent morphological responses to millennia of climate change in two species of bats from Hall's Cave, Texas, USA

How species will respond to ongoing and future climate change is one of the most important questions facing biodiversity scientists today. The fossil record provides unparalleled insight into past ecological and evolutionary responses to climate change, but the resource remains virtually untapped for many organisms. We use geometric morphometrics and a 25,000 year fossil record to quantify changes in body size and mandible shape through time and across climate regimes for two bat species present in Quaternary paleontological deposits of central Texas: Myotis velifer, a bat distributed throughout the Southwestern US and Mexico that is still found in central Texas today, and Eptesicus fuscus, a bat widely distributed throughout North America that has been extirpated in central Texas. Because of ecogeographic rules like Bergmann's rule, which posits that endotherms are larger in colder environments, we hypothesized that both species were larger during cooler time intervals. Additionally, we hypothesized that both species would show variation in dental morphology across the studied sequence as a response to climate change. While we found a decrease in centroid size-a proxy for --body size-through time for both species, we could not establish a clear relationship between centroid size and temperature alone. However, we did find that specimens from drier environments were significantly larger than those from wetter ones. Furthermore, we found significant dental shape variation between environments reflecting different temperature levels for both species. Yet only M. velifer exhibited significant variation between environments of varying precipitation levels. This result was surprising because present-day populations of E. fuscus are highly variable across both temperature and precipitation gradients. We determined that the morphological change experienced by M. velifer through time, and between warmer and cooler temperatures, was associated with the coronoid process, condylar process, and the mandibular symphysis. These parts play a pivotal role in bite force, so changes in these features might relate to changes in diet. We show that long-term datasets derived from fossil material provide invaluable insight not only into the validity of ecogeographic rules, but also into the adaptive capacities of extant taxa when faced with environmental changes. Our results highlight diverging responses to a variety of climate factors that are relevant to consider in biodiversity research given ongoing global change.

The evolutionary diversity of locomotor innovation in rodents is not linked to proximal limb morphology

Rodents are the most species-rich order within Mammalia and have evolved disparate morphologies to accommodate numerous locomotor niches, providing an excellent opportunity to understand how locomotor innovation can drive speciation. To evaluate the connection between the evolutionary success of rodents and the diversity of rodent locomotor ecologies, we used a large dataset of proximal limb CT scans from across Myomorpha and Geomyoidea to examine internal and external limb shape. Only fossorial rodents displayed a major reworking of their proximal limbs in either internal or external morphology, with other locomotor modes plotting within a generalist morphospace. Fossorial rodents were also the only locomotor mode to consistently show increased rates of humerus/femur morphological evolution. We propose that these rodent clades were successful at spreading into ecological niches due to high behavioral plasticity and small body sizes, allowing them to modify their locomotor mode without requiring major changes to their proximal limb morphology.

Quantifying shape and ecology in avian pedal claws: The relationship between the bony core and keratinous sheath

Terrestrial tetrapods use their claws to interact with their environments in a plethora of ways. Birds in particular have developed a diversity of claw shapes since they are often not bound to terrestrial locomotion and have heterogeneous body masses ranging several orders of magnitude. Numerous previous studies have hypothesized a connection between pedal claw shape and ecological mode in birds, yet have generated conflicting results, spanning from clear ecological groupings based on claw shape to a complete overlap of ecological modes. The majority of these studies have relied on traditional morphometric arc measurements of keratinous sheaths and have variably accounted for likely confounding factors such as body mass and phylogenetic relatedness. To better address the hypothesized relationship between ecology and claw shape in birds, we collected 580 radiographs allowing visualization of the bony core and keratinous sheath shape in 21 avian orders. Geometric morphometrics was used to quantify bony core and keratinous sheath shape and was compared to results using traditional arc measurements. Neither approach significantly separates bird claws into coarse ecological categories after integrating body size and phylogenetic relatedness; however, some separation between ecological groups is evident and we find a gradual shift from the claw shape of ground-dwelling birds to those of predatory birds. Further, the bony claw core and keratinous sheath are significantly correlated, and the degree of functional integration does not differ across ecological groups. Therefore, it is likely possible to compare fossil bony cores with extant keratinous sheaths after applying corrections. Finally, traditional metrics and geometric morphometric shape are significantly, yet loosely correlated. Based on these results, future workers are encouraged to use geometric morphometric approaches to study claw geometry and account for confounding factors such as body size, phylogeny, and individual variation prior to predicting ecology in fossil taxa.