Role of ecology in shaping external nasal morphology in bats and implications for olfactory tracking

Echolocation and dietary adaptations mediate brain-endocast covariation in bats

Bats exhibit remarkable ecological diversity, reflected in different species' sensory, cognitive and behavioral ecology. Bat brain volume has been linked to powered flight, laryngeal echolocation, and dietary transitions. Given the developmental trajectories and functional demands the skull and brain share, the bat skull-brain complex represents a unique means to better understand evolutionary processes and trade-offs. We assessed the brain-endocast correspondence across bats, considering whether changes in correspondence reflect ecological adaptations. We demonstrate that estimates of brain volume from both methods showed similar allometric trajectories, apart from those for cerebral cortex. Our results reveal a significant effect of diet and echolocation on brain-endocast correspondence of the cerebral cortex and olfactory bulbs, respectively. We suggest that shifts in the brain-endocast correspondence of the olfactory bulbs indicate an evolutionary trade-off between olfaction and echolocation. Our study offers a different perspective for future comparative neuroanatomical studies involving extinct and living species in museum collections.

Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in Plantago Plastomes

Repeats can mediate rearrangements and recombination in plant mitochondrial genomes and plastid genomes. While repeat accumulations are linked to heightened evolutionary rates and complex structures in specific lineages, debates persist regarding the extent of their influence on sequence and structural evolution. In this study, 75 Plantago plastomes were analyzed to investigate the relationships between repeats, nucleotide substitution rates, and structural variations. Extensive repeat accumulations were associated with significant rearrangements and inversions in the large inverted repeats (IRs), suggesting that repeats contribute to rearrangement hotspots. Repeats caused infrequent recombination that potentially led to substoichiometric shifting, supported by long-read sequencing. Repeats were implicated in elevating evolutionary rates by facilitating localized hypermutation, likely through DNA damage and repair processes. This study also observed a decrease in nucleotide substitution rates for loci translocating into IRs, supporting the role of biased gene conversion in maintaining lower substitution rates. Combined with known parallel changes in mitogenomes, it is proposed that potential dysfunction in nuclear-encoded genes associated with DNA replication, recombination, and repair may drive the evolution of Plantago organellar genomes. These findings contribute to understanding how repeats impact organellar evolution and stability, particularly in rapidly evolving plant lineages.

Evolution of olfactory receptor superfamily in bats based on high throughput molecular modelling

The origin of flight and laryngeal echolocation in bats is likely to have been accompanied by evolutionary changes in other aspects of their sensory biology. Of all sensory modalities in bats, olfaction is perhaps the least well understood. Olfactory receptors (ORs) function in recognizing odour molecules, with crucial roles in evaluating food, as well as in processing social information. Here we compare OR repertoire sizes across taxa and apply a new pipeline that integrates comparative genome data with protein structure modelling and then we employ molecular docking techniques with small molecules to analyse OR functionality based on binding energies. Our results suggest a sharp contraction in odorant recognition of the functional OR repertoire during the origin of bats, consistent with a reduced dependence on olfaction. We also compared bat lineages with contrasting different ecological characteristics and found evidence of differences in OR gene expansion and contraction, and in the composition of ORs with different tuning breadths. The strongest binding energies of ORs in non-echolocating fruit-eating bats were seen to correspond to ester odorants, although we did not detect a quantitative advantage of functional OR repertoires in these bats compared with echolocating insectivorous species. Overall, our findings based on molecular modelling and computational docking suggest that bats have undergone olfactory evolution linked to dietary adaptation. Our results from extant and ancestral bats help to lay the groundwork for targeted experimental functional tests in the future.

Soft tissues influence nasal airflow in diapsids: Implications for dinosaurs

The nasal passage performs multiple functions in amniotes, including olfaction and thermoregulation. These functions would have been present in extinct animals as well. However, fossils preserve only low-resolution versions of the nasal passage due to loss of soft-tissue structures after death. To test the effects of these lower resolution models on interpretations of nasal physiology, we performed a broadly comparative analysis of the nasal passages in extant diapsid representatives, e.g., alligator, turkey, ostrich, iguana, and a monitor lizard. Using computational fluid dynamics, we simulated airflow through 3D reconstructed models of the different nasal passages and compared these soft-tissue-bounded results to similar analyses of the same airways under the lower-resolution limits imposed by fossilization. Airflow patterns in these bony-bounded airways were more homogeneous and slower flowing than those of their soft-tissue counterparts. These data indicate that bony-bounded airway reconstructions of extinct animal nasal passages are far too conservative and place overly restrictive physiological limitations on extinct species. In spite of the diverse array of nasal passage shapes, distinct similarities in airflow were observed, including consistent areas of nasal passage constriction such as the junction of the olfactory region and main airway. These nasal constrictions can reasonably be inferred to have been present in extinct taxa such as dinosaurs.

Skull Shape Variations in the Eidolon helvum (African Fruit Bat) Based on Geographical Location

The shape and size of a skull provides insight into the age, breed and gender of the animal. Skull shape variations have been reported in different animals, with some theories linking these variations to evolution and/or migration. This study assessed the variations observed in the skull shape, size and gross morphometrics of two groups of the Eidolon helvum obtained from two geographical regions in Nigeria (south and north). All skulls were rostro-caudally elongated, having a dolichocephalic appearance. The skulls from the north had a distinct dome shape, with a more prominent zygomatic process, absence of a 'diastema' and an extra upper molar, while the southern skulls showed a more dorsally flattened skull and a less prominent zygomatic process. The shape of the sagittal crest was different in the two groups, while there was the presence of an accessory infraorbital foramen in some of the southern skulls. The southern skulls lacked the palatine foramen. The lacrimal foramen was observed to be more caudally placed in the southern skulls. Values for most linear measurements were higher in the northern skulls, although statistically significant difference was not present in all. The value for the neurocranial volume was considerably higher in the northern skulls (4.41 ± 0.28 mls) relative to the southern skulls (2.0 ± 0.27 mls). Statistically significant differences were not observed between males and females (within regions). Data obtained from this study may find application in evolution and migration studies, wildlife medicine and surgery and comparative and forensic anatomy.

Aeroscapes and the Sensory Ecology of Olfaction in a Tropical Dry Forest

Aeroscapes—dynamic patterns of air speed and direction—form a critical component of landscape ecology by shaping numerous animal behaviors, including movement, foraging, and social and/or reproductive interactions. Aeroecology is particularly critical for sensory ecology: air is the medium through which many sensory signals and cues propagate, inherently linking sensory perception to variables such as air speed and turbulence. Yet, aeroscapes are seldom explicitly considered in studies of sensory ecology and evolution. A key first step towards this goal is to describe the aeroscapes of habitats. Here, we quantify the variation in air movement in two successional stages (early and late) of a tropical dry forest in Costa Rica. We recorded air speeds every 10 seconds at five different heights simultaneously. Average air speeds and turbulence increased with height above the ground, generally peaked midday, and were higher overall at the early successional forest site. These patterns of lower air speed and turbulence at ground level and overnight have important implications for olfactory foraging niches, as chemotaxis is most reliable when air movement is low and steady. We discuss our results in the context of possible selective pressures and observed variation in the foraging ecology, behaviors, and associated morphologies of resident vertebrates, with a focus on mammals. However, these data also have relevance to researchers studying socioecology, invertebrate biology, plant evolution, community ecology and more. Further investigation into how animals use different forest types, canopy heights and partition activities across different times of day will further inform our understanding of how landscape and sensory ecology are interrelated. Finally, we emphasize the timeliness of monitoring aeroecology as global wind patterns shift with climate change and human disturbance alters forest structure, which may have important downstream consequences for biological conservation.

How to Accurately Delineate Morphologically Conserved Taxa and Diagnose Their Phenotypic Disparities: Species Delimitation in Cryptic Rhinolophidae (Chiroptera)

Systematics and taxonomy are the backbone of all components of biology and ecology, yet cryptic species present a major challenge for accurate species identification. This is especially problematic as they represent a substantial portion of undiscovered biodiversity, and have implications for not only species conservation, but even assaying potential risk of zoonotic spillover. Here, we use integrative approaches to delineate potential cryptic species in horseshoe bats (Rhinolophidae), evaluate the phenotypic disparities between cryptic species, and identify key traits for their identification. We tested the use of multispecies coalescent models (MSC) using Bayesian Phylogenetic and Phylogeography (BPP) and found that BPP was useful in delineating potential cryptic species, and consistent with acoustic traits. Our results show that around 40% of Asian rhinolophid species are potentially cryptic and have not been formally described. In order to avoid potential misidentification and allow species to be accurately identified, we identified quantitative noseleaf sella and acoustic characters as the most informative traits in delineating between potential cryptic species in Rhinolophidae. This highlights the physical differences between cryptic species that are apparent in noseleaf traits which often only qualitatively described but rarely measured. Each part of the noseleaf including the sella, lateral lappets, and lancet furrows, play roles in focusing acoustic beams and thus, provide useful characteristics to identify cryptic Rhinolophus species. Finally, species delimitation for cryptic species cannot rely on genetic data alone, but such data should be complemented by other evidence, including phenotypic, acoustic data, and geographic distributions to ensure accurate species identification and delineation.

Molecular diet analysis of neotropical bats based on fecal DNA metabarcoding

Bat communities in the Neotropics are some of the most speciose assemblages of mammals on Earth, with regions supporting more than 100 sympatric species with diverse feeding ecologies. Because bats are small, nocturnal, and volant, it is difficult to directly observe their feeding habits, which has resulted in their classification into broadly defined dietary guilds (e.g., insectivores, carnivores, and frugivores). Apart from these broad guilds, we lack detailed dietary information for many species and therefore have only a limited understanding of interaction networks linking bats and their diet items. In this study, we used DNA metabarcoding of plants, arthropods, and vertebrates to investigate the diets of 25 bat species from the tropical dry forests of Lamanai, Belize. Our results report some of the first detection of diet items for the focal bat taxa, adding rich and novel natural history information to the field of bat ecology. This study represents a comprehensive first effort to apply DNA metabarcoding to bat diets at Lamanai and provides a useful methodological framework for future studies testing hypotheses about coexistence and niche differentiation in the context of modern high-throughput molecular data.

Phylogenetic Patterns in Mouth Posture and Echolocation Emission Behavior of Phyllostomid Bats

While phyllostomid bats show an impressive range of feeding habits, most of them emit highly similar echolocation calls. Due to the presence of an often prominent noseleaf, it has long been assumed that all phyllostomids emit echolocation calls exclusively through the nostrils rather than through the mouth. However, photo evidence documents also phyllostomid bats flying with an opened mouth. We hypothesized that all phyllostomid species emit echolocation calls only through the nostrils and therefore fly consistently with a closed mouth, and that observations of an open mouth should be a rare and random behavior among individuals and species. Using a high-speed camera and standardized conditions in a flight cage, we screened 40 phyllostomid species. Behavior varied distinctly among the species and mouth posture shows a significant phylogenetic signal. Bats of the frugivorous subfamilies Rhinophyllinae and Carolliinae, the nectarivorous subfamilies Glossophaginae and Lonchophyllinae, and the sanguivorous subfamily Desmodontinae all flew consistently with open mouths. So did the animalivorous subfamilies Glyphonycterinae, Micronycterinae and Phyllostominae, with the notable exception of species in the omnivorous genus Phyllostomus, which consistently flew with mouths closed. Bats from the frugivorous subfamily Stenodermatinae also flew exclusively with closed mouths with the single exception of the genus Sturnira, which is the sister clade to all other stenodermatine species. Further, head position angles differed significantly between bats echolocating with their mouth closed and those echolocating with their mouths opened, with closed-mouth phyllostomids pointing only the nostrils in the direction of flight and open-mouth phyllostomids pointing both the nostrils and mouth gape in the direction of flight. Ancestral trait reconstruction showed that the open mouth mode is the ancestral state within the Phyllostomidae. Based on the observed behavioral differences, we suggest that phyllostomid bats are not all nasal emitters as previously thought and discuss possible reasons. Further experiments, such as selectively obstructing sound emission through nostrils or mouth, respectively, will be necessary to clarify the actual source, plasticity and ecological relevance of sound emission of phyllostomid bats flying with their mouths open.

Olfactory tracking strategies in a neotropical fruit bat

Many studies have characterized olfactory-tracking behaviors in animals, and it has been proposed that search strategies may be generalizable across a wide range of species. Olfaction is important for fruit- and nectar-feeding bats, but it is uncertain whether existing olfactory search models can predict the strategies of flying mammals that emit echolocation pulses through their nose. Quantitative assessments of how well echolocating bats track and localize odor sources are lacking, so we developed a behavioral assay to characterize the olfactory detection and tracking behavior of crawling northern yellow-shouldered bats (Sturnira parvidens), a common neotropical frugivore. Trained bats were presented with a choice between control and banana-odor-infused solutions in a series of experiments that confirmed that bats are able to locate a reward based on odor cues alone and examined the effect of odor concentration on olfactory search behaviors. Decision distance (the distance from which bats made their change in direction before directly approaching the target) was distinctly bimodal, with an observed peak that coincided with an inflection point in the odor concentration gradient. We observed two main search patterns that are consistent with both serial sampling and learned route-following strategies. These results support the hypothesis that bats can combine klinotaxis with spatial awareness of experimental conditions to locate odor sources, similar to terrestrial mammals. Contrary to existing models, bats did not display prominent head-scanning behaviors during their final approach, which may be due to constraints of nasal-emitted biosonar for orientation.

Phylogeny and foraging behaviour shape modular morphological variation in bat humeri

Bats show a remarkable ecological diversity that is reflected both in dietary and foraging guilds (FGs). Cranial ecomorphological adaptations linked to diet have been widely studied in bats, using a variety of anatomical, computational and mathematical approaches. However, foraging-related ecomorphological adaptations and the concordance between cranial and postcranial morphological adaptations remain unexamined in bats and limited to the interpretation of traditional aerodynamic properties of the wing (e.g. wing loading [WL] and aspect ratio [AR]). For this reason, the postcranial ecomorphological diversity in bats and its drivers remain understudied. Using 3D virtual modelling and geometric morphometrics (GMM), we explored the phylogenetic, ecological and biological drivers of humeral morphology in bats, evaluating the presence and magnitude of modularity and integration. To explore decoupled patterns of variation across the bone, we analysed whole-bone shape, diaphyseal and epiphyseal shape. We also tested whether traditional aerodynamic wing traits correlate with humeral shape. By studying 37 species from 20 families (covering all FGs and 85% of dietary guilds), we found similar patterns of variation in whole-bone and diaphyseal shape and unique variation patterns in epiphyseal shape. Phylogeny, diet and FG significantly correlated with shape variation at all levels, whereas size only had a significant effect on epiphyseal morphology. We found a significant phylogenetic signal in all levels of humeral shape. Epiphyseal shape significantly correlated with wing AR. Statistical support for a diaphyseal-epiphyseal modular partition of the humerus suggests a functional partition of shape variability. Our study is the first to show within-structure modular morphological variation in the appendicular skeleton of any living tetrapod. Our results suggest that diaphyseal shape correlates more with phylogeny, whereas epiphyseal shape correlates with diet and FG.