Flying primates? Megabats have the advanced pathway from eye to midbrain

Where Do Core Thalamocortical Axons Terminate in Mammalian Neocortex When There Is No Cytoarchitecturally Distinct Layer 4?

Although the mammalian cerebral cortex is most often described as a hexalaminar structure, there are cortical areas (primary motor cortex) and species (elephants, cetaceans, and hippopotami), where a cytoarchitecturally indistinct, or absent, layer 4 is noted. Thalamocortical projections from the core, or first order, thalamic system terminate primarily in layers 4/inner 3. We explored the termination sites of core thalamocortical projections in cortical areas and in species where there is no cytoarchitecturally distinct layer 4 using the immunolocalization of vesicular glutamate transporter 2, a known marker of core thalamocortical axon terminals, in 31 mammal species spanning the eutherian radiation. Several variations from the canonical cortical column outline of layer 4 and core thalamocortical inputs were noted. In shrews/microchiropterans, layer 4 was present, but many core thalamocortical projections terminated in layer 1 in addition to layers 4 and inner 3. In primate primary visual cortex, the sublaminated layer 4 was associated with a specialized core thalamocortical projection pattern. In primate primary motor cortex, no cytoarchitecturally distinct layer 4 was evident and the core thalamocortical projections terminated throughout layer 3. In the African elephant, cetaceans, and river hippopotamus, no cytoarchitecturally distinct layer 4 was observed and core thalamocortical projections terminated primarily in inner layer 3 and less densely in outer layer 3. These findings are contextualized in terms of cortical processing, perception, and the evolutionary trajectory leading to an indistinct or absent cortical layer 4.

Escaping the nocturnal bottleneck, and the evolution of the dorsal and ventral streams of visual processing in primates

Early mammals were small and nocturnal. Their visual systems had regressed and they had poor vision. After the extinction of the dinosaurs 66 mya, some but not all escaped the 'nocturnal bottleneck' by recovering high-acuity vision. By contrast, early primates escaped the bottleneck within the age of dinosaurs by having large forward-facing eyes and acute vision while remaining nocturnal. We propose that these primates differed from other mammals by changing the balance between two sources of visual information to cortex. Thus, cortical processing became less dependent on a relay of information from the superior colliculus (SC) to temporal cortex and more dependent on information distributed from primary visual cortex (V1). In addition, the two major classes of visual information from the retina became highly segregated into magnocellular (M cell) projections from V1 to the primate-specific temporal visual area (MT), and parvocellular-dominated projections to the dorsolateral visual area (DL or V4). The greatly expanded P cell inputs from V1 informed the ventral stream of cortical processing involving temporal and frontal cortex. The M cell pathways from V1 and the SC informed the dorsal stream of cortical processing involving MT, surrounding temporal cortex, and parietal-frontal sensorimotor domains. This article is part of the theme issue 'Systems neuroscience through the lens of evolutionary theory'.

Nuclear organization of catecholaminergic neurons in the brains of a lar gibbon and a chimpanzee

Using tyrosine hydroxylase immunohistochemistry, we describe the nuclear parcellation of the catecholaminergic system in the brains of a lar gibbon (Hylobates lar) and a chimpanzee (Pan troglodytes). The parcellation of catecholaminergic nuclei in the brains of both apes is virtually identical to that observed in humans and shows very strong similarities to that observed in mammals more generally, particularly other primates. Specific variations of this system in the apes studied include an unusual high-density cluster of A10dc neurons, an enlarged retrorubral nucleus (A8), and an expanded distribution of the neurons forming the dorsolateral division of the locus coeruleus (A4). The additional A10dc neurons may improve dopaminergic modulation of the extended amygdala, the enlarged A8 nucleus may be related to the increased use of communicative facial expressions in the hominoids compared to other primates, while the expansion of the A4 nucleus appears to be related to accelerated evolution of the cerebellum in the hominoids compared to other primates. In addition, we report the presence of a compact division of the locus coeruleus proper (A6c), as seen in other primates, that is not present in other mammals apart from megachiropteran bats. The presence of this nucleus in primates and megachiropteran bats may reflect homology or homoplasy, depending on the evolutionary scenario adopted. The fact that the complement of homologous catecholaminergic nuclei is mostly consistent across mammals, including primates, is advantageous for the selection of model animals for the study of specific dysfunctions of the catecholaminergic system in humans.

Retrospective analysis of ocular disease in a population of captive pteropodid bats, 2003-2020

OBJECTIVE

To perform retrospective analysis of captive pteropodid bats presented to the University of Florida for ocular or adnexal disease from 2003-2020.

ANIMALS STUDIED

Twenty-four individuals from seven species were included.

PROCEDURES

Records were analyzed for disease process, methods of treatment, and surgical techniques and complications.

RESULTS

The most frequently reported abnormality was corneal disease (79%), followed by cataracts (54%), and uveitis (42%). Corneal disease was primarily attributed to either trauma or exposure keratitis secondary to buphthalmia. The majority of uveitis appeared to be lens-induced. Five cases (21%) of glaucoma were reported, all of which accompanied lens luxation. Of the seven enucleations performed, six had post-operative complications (85.7%), including swelling at the surgical site, seroma formation, and bacterial infection. There was no significant relationship between age and trauma, age and cataract formation, sex and trauma, or species and cataract formation.

CONCLUSIONS

The most common underlying cause of ocular pathology in these cases was trauma. While the bats tolerated topical and systemic treatment well, individual temperament must be taken into account when developing treatment plans, and prevention of injury is the most effective management strategy.

Microchiropterans have a diminutive cerebral cortex, not an enlarged cerebellum, compared to megachiropterans and other mammals

Small echolocating bats are set apart from most other mammals by their relatively large cerebellum, a feature that has been associated to echolocation, as it is presumed to indicate a relatively enlarged number of neurons in the cerebellum in comparison to other brain structures. Here we quantify the neuronal composition of the cerebral cortex, cerebellum and remaining brain structures of seven species of large Pteropodid bats (formerly classified as megachiropterans), one of which echolocates, and six species of small bats (formerly classified as microchiropterans), all of which echolocate. This chiropteran data is compared to 60 mammalian species in our dataset to determine whether the relatively large cerebellum of the small echolocating bats, and possibly that of the echolocating Pteropodid, contains a relatively enlarged number of neurons. We find no evidence that the distribution of neurons differs between microchiropterans and megachiropterans, but our data indicate that microchiropterans, like the smallest shrew in our dataset, have diminutive cerebral cortices, which makes the cerebellum appear relatively large. We propose that, in agreement with the diminutive brain size of the earliest fossil mammals, this is a plesiomorphic, not a derived, feature of microchiropteran brains. The results of this study also reveal important neural characteristics related to the phylogenetic affinities and relationships of the chiropterans.

Distribution, number, and certain neurochemical identities of infracortical white matter neurons in the brains of three megachiropteran bat species

A large population of infracortical white matter neurons, or white matter interstitial cells (WMICs), are found within the subcortical white matter of the mammalian telencephalon. We examined WMICs in three species of megachiropterans, Megaloglossus woermanni, Casinycteris argynnis, and Rousettus aegyptiacus, using immunohistochemical and stereological techniques. Immunostaining for neuronal nuclear marker (NeuN) revealed substantial numbers of WMICs in each species-M. woermanni 124,496 WMICs, C. argynnis 138,458 WMICs, and the larger brained R. aegyptiacus having an estimated WMIC population of 360,503. To examine the range of inhibitory neurochemical types we used antibodies against parvalbumin, calbindin, calretinin, and neural nitric oxide synthase (nNOS). The calbindin and nNOS immunostained neurons were the most commonly observed, while those immunoreactive for calretinin and parvalbumin were sparse. The proportion of WMICs exhibiting inhibitory neurochemical profiles was ~26%, similar to that observed in previously studied primates. While for the most part the WMIC population in the megachiropterans studied was similar to that observed in other mammals, the one feature that differed was the high proportion of WMICs immunoreactive to calbindin, whereas in primates (macaque monkey, lar gibbon and human) the highest proportion of inhibitory WMICs contain calretinin. Interestingly, there appears to be an allometric scaling of WMIC numbers with brain mass. Further quantitative comparative work across more mammalian species will reveal the developmental and evolutionary trends associated with this infrequently studied neuronal population.

Origins of Functional Organization in the Visual Cortex

How are the complex maps for orientation selectivity (OS) created in the primary visual cortex (V1)? Rodents and rabbits have a random distribution of OS preferences across V1 while in cats, ferrets, and all primates cells with similar OS preferences cluster together into relatively wide cortical columns. Given other clear similarities in the organization of the visual pathways, why is it that maps coding OS preferences are so radically different? Prominent models have been created of cortical OS mapping that incorporate Hebbian plasticity, intracortical interactions, and the properties of growing axons. However, these models suggest that the maps arise primarily through intracortical interactions. Here we focus on several other features of the visual system and brain that may influence V1 structure. These are: eye divergence, the total number of cells in V1, the thalamocortical networks, the topography of the retina and phylogeny. We outline the evidence for and against these factors contributing to map formation. One promising theory is that the central-to-peripheral ratio (CP ratio) of retinal cell density can be used to predict whether or not a species has pinwheel maps. Animals with high CP ratios (>7) have orientation columns while those with low CP ratios (<4) have random OS maps. The CP ratio is related to the total number of cells in cortex, which also appears to be a reasonable contributing factor. However, while these factors correlate with map structure to some extent, there is a gray area where certain species do not fit elegantly into the theory. A problem with the existing literature is that OS maps have been investigated in only a small number of mammals, from a small fraction of the mammalian phylogenetic tree. We suggest four species (agouti, fruit bat, sheep, and wallaby) that have a range of interesting characteristics, which sit at intermediate locations between primates and rodents, that make them good targets for filling in the missing gaps in the literature. We make predictions about the map structures of these species based on the organization of their brains and visual systems and, in doing so, set possible paths for future research.

Bat research in Australasia – in memory of Les Hall, part 2

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Reference values for selected ophthalmic diagnostic tests in two species of microchiroptera bats (Artibeus lituratus and Anoura caudifer)

OBJECTIVE

To establish reference values for ophthalmic tests in two bat species. BATS: Fourteen bats including seven great fruit-eating bats (Artibeus lituratus) and seven tailed tailless bats (Anoura caudifer).

PROCEDURES

Normal values for following ophthalmic tests were investigated as follows: (a) aqueous tear production using the standardized endodontic paper point tear test (EPPTT), (b) rebound tonometry, and (c) horizontal palpebral fissure length.

RESULTS

Aqueous tear production was 2.53 ± 1.65 mm/min for A lituratus and 1.89 ± 0.62 for A caudifer. Intraocular pressure measured in the upright position was 11.0 ± 3.28 mm Hg for A lituratus and 7.28 ± 2.70 for A caudifer. Horizontal palpebral fissure length was 5.04 ± 0.45 mm for A lituratus and 3.92 ± 0.51 for A caudifer.

CONCLUSIONS

The data obtained in the present study may serve as a reference for ophthalmic parameters and help practitioners in the diagnosis and management of eye diseases in bats, as well for future investigations about microchiroptera bats.

Functional Shifts in Bat Dim-Light Visual Pigment Are Associated with Differing Echolocation Abilities and Reveal Molecular Adaptation to Photic-Limited Environments

Bats are excellent models for studying the molecular basis of sensory adaptation. In Chiroptera, a sensory trade-off has been proposed between the visual and auditory systems, though the extent of this association has yet to be fully examined. To investigate whether variation in visual performance is associated with echolocation, we experimentally assayed the dim-light visual pigment rhodopsin from bat species with differing echolocation abilities. While spectral tuning properties were similar among bats, we found that the rate of decay of their light-activated state was significantly slower in a nonecholocating bat relative to species that use distinct echolocation strategies, consistent with a sensory trade-off hypothesis. We also found that these rates of decay were remarkably slower compared with those of other mammals, likely indicating an adaptation to dim light. To examine whether functional changes in rhodopsin are associated with shifts in selection intensity upon bat Rh1 sequences, we implemented selection analyses using codon-based likelihood clade models. While no shifts in selection were identified in response to diverse echolocation abilities of bats, we detected a significant increase in the intensity of evolutionary constraint accompanying the diversification of Chiroptera. Taken together, this suggests that substitutions that modulate the stability of the light-activated rhodopsin state were likely maintained through intensified constraint after bats diversified, being finely tuned in response to novel sensory specializations. Our study demonstrates the power of combining experimental and computational approaches for investigating functional mechanisms underlying the evolution of complex sensory adaptations.

The role of ecological factors in shaping bat cone opsin evolution

Bats represent one of the largest and most striking nocturnal mammalian radiations, exhibiting many visual system specializations for performance in light-limited environments. Despite representing the greatest ecological diversity and species richness in Chiroptera, Neotropical lineages have been undersampled in molecular studies, limiting the potential for identifying signatures of selection on visual genes associated with differences in bat ecology. Here, we investigated how diverse ecological pressures mediate long-term shifts in selection upon long-wavelength (Lws) and short-wavelength (Sws1) opsins, photosensitive cone pigments that form the basis of colour vision in most mammals, including bats. We used codon-based likelihood clade models to test whether ecological variables associated with reliance on visual information (e.g. echolocation ability and diet) or exposure to varying light environments (e.g. roosting behaviour and foraging habitat) mediated shifts in evolutionary rates in bat cone opsin genes. Using additional cone opsin sequences from newly sequenced eye transcriptomes of six Neotropical bat species, we found significant evidence for different ecological pressures influencing the evolution of the cone opsins. While Lws is evolving under significantly lower constraint in highly specialized high-duty cycle echolocating lineages, which have enhanced sonar ability to detect and track targets, variation in Sws1 constraint was significantly associated with foraging habitat, exhibiting elevated rates of evolution in species that forage among vegetation. This suggests that increased reliance on echolocation as well as the spectral environment experienced by foraging bats may differentially influence the evolution of different cone opsins. Our study demonstrates that different ecological variables may underlie contrasting evolutionary patterns in bat visual opsins, and highlights the suitability of clade models for testing ecological hypotheses of visual evolution.

Auditory opportunity and visual constraint enabled the evolution of echolocation in bats

Substantial evidence now supports the hypothesis that the common ancestor of bats was nocturnal and capable of both powered flight and laryngeal echolocation. This scenario entails a parallel sensory and biomechanical transition from a nonvolant, vision-reliant mammal to one capable of sonar and flight. Here we consider anatomical constraints and opportunities that led to a sonar rather than vision-based solution. We show that bats' common ancestor had eyes too small to allow for successful aerial hawking of flying insects at night, but an auditory brain design sufficient to afford echolocation. Further, we find that among extant predatory bats (all of which use laryngeal echolocation), those with putatively less sophisticated biosonar have relatively larger eyes than do more sophisticated echolocators. We contend that signs of ancient trade-offs between vision and echolocation persist today, and that non-echolocating, phytophagous pteropodid bats may retain some of the necessary foundations for biosonar.

The organization of melanopsin-immunoreactive cells in microbat retina

Intrinsically photosensitive retinal ganglion cells (ipRGCs) respond to light and play roles in non-image forming vision, such as circadian rhythms, pupil responses, and sleep regulation, or image forming vision, such as processing visual information and directing eye movements in response to visual clues. The purpose of the present study was to identify the distribution, types, and proportion of melanopsin-immunoreactive (IR) cells in the retina of a nocturnal animal, i.e., the microbat (Rhinolophus ferrumequinum). Three types of melanopsin-IR cells were observed in the present study. The M1 type had dendritic arbors that extended into the OFF sublayer of the inner plexiform layer (IPL). M1 soma locations were identified either in the ganglion cell layer (GCL, M1c; 21.00%) or in the inner nuclear layer (INL, M1d; 5.15%). The M2 type had monostratified dendrites in the ON sublayer of the IPL and their cell bodies lay in the GCL (M2; 5.79%). The M3 type was bistratified cells with dendrites in both the ON and OFF sublayers of the IPL. M3 soma locations were either in the GCL (M3c; 26.66%) or INL (M3d; 4.69%). Additionally, some M3c cells had curved dendrites leading up towards the OFF sublayer of the IPL and down to the ON sublayer of the IPL (M3c-crv; 7.67%). Melanopsin-IR cells displayed a medium soma size and medium dendritic field diameters. There were 2-5 primary dendrites and sparsely branched dendrites with varicosities. The total number of the neurons in the GCL was 12,254.17 ± 660.39 and that of the optic nerve axons was 5,179.04 ± 208.00 in the R. ferrumequinum retina. The total number of melanopsin-IR cells was 819.74 ± 52.03. The ipRGCs constituted approximately 15.83% of the total RGC population. This study demonstrated that the nocturnal microbat, R. ferrumequinum, has a much higher density of melanopsin-IR cells than documented in diurnal animals.

The Distribution of Ki-67 and Doublecortin-Immunopositive Cells in the Brains of Three Strepsirrhine Primates: Galago demidoff, Perodicticus potto, and Lemur catta

This study investigated the pattern of adult neurogenesis throughout the brains of three prosimian primate species using immunohistochemical techniques for endogenous markers of this neural process. Two species, Galago demidoff and Perodicticus potto, were obtained from wild populations in the primary rainforest of central Africa, while one species, Lemur catta, was captive-bred. Two brains from each species, perfusion-fixed with 4% paraformaldehyde, were sectioned (50 µm section thickness) in sagittal and coronal planes. Using Ki-67 and doublecortin (DCX) antibodies, proliferating cells and immature neurons were identified in the two canonical neurogenic sites of mammals, the subventricular zone of the lateral ventricle (SVZ) giving rise to the rostral migratory stream (RMS), and the subgranular zone of the dentate gyrus of the hippocampus. In addition a temporal migratory stream (TMS), emerging from the temporal horn of the lateral ventricle to supply the piriform cortex and adjacent brain regions with new neurons, was also evident in the three prosimian species. While no Ki-67-immunoreactive cells were observed in the cerebellum, DCX-immunopositive cells were observed in the cerebellar cortex of all three species. These findings are discussed in a phylogenetic context.

Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species

Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.

Megachiropteran bats profoundly unique from microchiropterans in climbing and walking locomotion: Evolutionary implications

Understandably, most locomotor analyses of bats have focused on flight mechanics and behaviors. However, we investigated nonflight locomotion in an effort to glean deeper insights into the evolutionary history of bats. We used high-speed video (300 Hz) to film and compare walking and climbing mechanics and kinematics between several species of the suborders Megachiroptera (Pteropodidae) versus Microchiroptera (Vespertilionidae and Phyllostomatidae). We found fundamentally distinctive behaviors, functional abilities, and performance outcomes between groups, but nearly homogeneous outcomes within groups. Megachiropterans exhibited climbing techniques and skills not found in microchiropterans and which aligned with other fully arboreal mammals. Megachiropterans climbed readily when placed in a head-up posture on a vertical surface, showed significantly greater ability than microchiropterans to abduct and extend the reach of their limbs, and climbed at a greater pace by using a more aggressive ipsilateral gait, at times being supported by only a single contact point. In addition, megachiropterans showed little ability to employ basic walking mechanics when placed on the ground, also a pattern observed in some highly adapted arboreal mammals. Conversely, microchiropterans resisted climbing vertical surfaces in a head-up posture, showed significantly less extension of their limbs, and employed a less-aggressive, slower contralateral gait with three points of contact. When walking, microchiropterans used the same gait they did when climbing which is representative of basic tetrapod terrestrial mechanics. Curiously, megachiropterans cycled their limbs significantly faster when climbing than when attempting to walk, whereas microchiropterans cycled their limbs at significantly faster rates when walking than when climbing. We contend that nonflight locomotion mechanics give a deep evolutionary view into the ancestral es locomotor platform on which flight was built in each of these groups.

FLOW-CYTOMETRIC ANALYSES OF NUCLEAR DNA CONTENT IN FOUR FAMILIES OF NEOTROPICAL BATS

Flow-cytometric analyses of 29 species of microchiropteran bats representing four families and 20 genera revealed that bats possess only 79% (5.43 pg) of the DNA content of a "typical" mammal (e.g., Mus musculus strain C57BL; 7 pg). Chiroptera, the second largest order of mammals, is thus an exception to the prevailing view that mammals possess a minimum nuclear DNA content of 7 pg. Limitations on cell size resulting from a high metabolic rate may have constrained evolution of DNA content and could explain why the extensive heterochromatic additions that are common in some groups of mammals are absent in bats. Chromosomes of bats have been well studied; detailed chromosomal banding data are available for nearly all the species used in this investigation. However, no significant correlations were found between DNA content and karyotypic characteristics such as 2n, fundamental number, and rate or pattern of chromosomal evolution.

The Distribution of Ki-67 and Doublecortin Immunopositive Cells in the Brains of Three Microchiropteran Species, Hipposideros fuliginosus, Triaenops persicus, and Asellia tridens

This study uses Ki-67 and doublecortin (DCX) immunohistochemistry to delineate potential neurogenic zones, migratory pathways, and terminal fields associated with adult neurogenesis in the brains of three microchiropterans. As with most mammals studied to date, the canonical subgranular and subventricular neurogenic zones were observed. Distinct labeling of newly born cells and immature neurons within the dentate gyrus of the hippocampus was observed in all species. A distinct rostral migratory stream (RMS) that appears to split around the medial aspect of the caudate nucleus was observed. These two rostral stream divisions appear to merge at the rostroventral corner of the caudate nucleus to turn and enter the olfactory bulb, where a large terminal field of immature neurons was observed. DCX immunolabeled neurons were observed mostly in the rostral neocortex, but a potential migratory stream to the neocortex was not identified. A broad swathe of newly born cells and immature neurons was found between the caudoventral division of the RMS and the piriform cortex. In addition, occasional immature neurons were observed in the amygdala and DCX-immunopositive axons were observed in the anterior commissure. While the majority of these features have been found in several mammal species, the large number of DCX immunolabeled cells found between the RMS and the piriform cortex and the presence of DCX immunostained axons in the anterior commissure are features only observed in microchiropterans and insectivores to date. In the diphyletic scenario of chiropteran evolution, these observations align the microchiropterans with the insectivores. Anat Rec, 299:1548-1560, 2016. © 2016 Wiley Periodicals, Inc.

Organization of cholinergic, catecholaminergic, serotonergic and orexinergic nuclei in three strepsirrhine primates: Galago demidoff, Perodicticus potto and Lemur catta

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Cholinergic, catecholaminergic, serotonergic and orexinergic systems in the brains of strepsirrhine primates are described.

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All species show a similar global pattern of nuclear organization of these systems.

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For these systems there appears to be a primate-typical organization.

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Certain variations indicate a phylogenetic relationship between primates and megachiropterans.

The nuclear organization of the cholinergic, catecholaminergic, serotonergic and orexinergic systems in the brains of three species of strepsirrhine primates is presented. We aimed to investigate the nuclear complement of these neural systems in comparison to those of simian primates, megachiropterans and other mammalian species. The brains were coronally sectioned and immunohistochemically stained with antibodies against choline acetyltransferase, tyrosine hydroxylase, serotonin and orexin-A. The nuclei identified were identical among the strepsirrhine species investigated and identical to previous reports in simian primates. Moreover, a general similarity to other mammals was found, but specific differences in the nuclear complement highlighted potential phylogenetic interrelationships. The central feature of interest was the structure of the locus coeruleus complex in the primates, where a central compactly packed core (A6c) of tyrosine hydroxylase immunopositive neurons was surrounded by a shell of less densely packed (A6d) tyrosine hydroxylase immunopositive neurons. This combination of compact and diffuse divisions of the locus coeruleus complex is only found in primates and megachiropterans of all the mammalian species studied to date. This neural character, along with variances in a range of other neural characters, supports the phylogenetic grouping of primates with megachiropterans as a sister group.

Divergence of dim-light vision among bats (order: Chiroptera) as estimated by molecular and electrophysiological methods

Dim-light vision is present in all bats, but is divergent among species. Old-World fruit bats (Pteropodidae) have fully developed eyes; the eyes of insectivorous bats are generally degraded, and these bats rely on well-developed echolocation. An exception is the Emballonuridae, which are capable of laryngeal echolocation but prefer to use vision for navigation and have normal eyes. In this study, integrated methods, comprising manganese-enhanced magnetic resonance imaging (MEMRI), f-VEP and RNA-seq, were utilized to verify the divergence. The results of MEMRI showed that Pteropodidae bats have a much larger superior colliculus (SC)/ inferior colliculus (IC) volume ratio (3:1) than insectivorous bats (1:7). Furthermore, the absolute visual thresholds (log cd/m(2)•s) of Pteropodidae (-6.30 and -6.37) and Emballonuridae (-3.71) bats were lower than those of other insectivorous bats (-1.90). Finally, genes related to the visual pathway showed signs of positive selection, convergent evolution, upregulation and similar gene expression patterns in Pteropodidae and Emballonuridae bats. Different results imply that Pteropodidae and Emballonuridae bats have more developed vision than the insectivorous bats and suggest that further research on bat behavior is warranted.

The marmoset monkey as a model for visual neuroscience

The common marmoset (Callithrix jacchus) has been valuable as a primate model in biomedical research. Interest in this species has grown recently, in part due to the successful demonstration of transgenic marmosets. Here we examine the prospects of the marmoset model for visual neuroscience research, adopting a comparative framework to place the marmoset within a broader evolutionary context. The marmoset's small brain bears most of the organizational features of other primates, and its smooth surface offers practical advantages over the macaque for areal mapping, laminar electrode penetration, and two-photon and optical imaging. Behaviorally, marmosets are more limited at performing regimented psychophysical tasks, but do readily accept the head restraint that is necessary for accurate eye tracking and neurophysiology, and can perform simple discriminations. Their natural gaze behavior closely resembles that of other primates, with a tendency to focus on objects of social interest including faces. Their immaturity at birth and routine twinning also makes them ideal for the study of postnatal visual development. These experimental factors, together with the theoretical advantages inherent in comparing anatomy, physiology, and behavior across related species, make the marmoset an excellent model for visual neuroscience.

Sensory rewiring in an echolocator: genome-wide modification of retinogenic and auditory genes in the bat Myotis davidii

Bats comprise 20% of all mammalian species and display a number of characteristics, including true flight, echolocation, and a heightened ability to resist viral load that uniquely position this group for comparative genomic studies. Here we searched for evidence of genomic variation consistent with sensory rewiring through bat evolution. We focused on two species with divergent sensory preferences. Myotis davidii is a bat species that echolocates and possesses dim- but not daylight-adapted vision whereas the black flying fox (Pteropus alecto) has highly developed day vision but does not echolocate. Using the naked mole rat as a reference, we found five functional genes (CYP1A2, RBP3, GUCY2F, CRYBB1, and GRK7) encoding visual proteins that have degenerated into pseudogenes in M. davidii but not P. alecto. In a second approach genome-wide codon usage bias (CUB) was compared between the two bat species. This CUB ranking systematically enriched for vision-related (CLN8, RD3, IKZF1, LAMC3, CRX, SOX8, VAX2, HPS1, RHO, PRPH2, and SOX9) and hearing-related (TPRN, TMIE, SLC52A3, OTOF, WFS1, SOD1, TBX18, MAP1A, OTOS, GPX1, and USH1G) machinery in M. davidii but not P. alecto. All vision and hearing genes selectively enriched in M. davidii for which orthologs could be identified also were more biased in the echolocating M. lucifugus than the nonecholocating P. vampyrus. We suggest that the existence of codon bias in vision- and hearing-related genes in a species that has evolved echolocation implies CUB is part of evolution’s toolkit to rewire sensory systems. We propose that the two genetic changes (pseudogene formation and CUB) collectively paint a picture of that incorporates a combination of destruction and gain-of-function. Together, they help explain how natural selection has reduced physiological costs associated with the development of a smaller eye poorly adapted to day vision but that also contribute to enhanced dim light vision and the hearing adaptations consonant with echolocation.

Mitochondrial genome of the black flying fox, Pteropus alecto (Chiroptera: Megachiroptera: Pteropodidae)

In this article we report the complete mitochondrial genome of black flying fox, Pteropus alecto, with the sequence length of 16,739 bp for the first time. The mitogenome contained a total of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. The base composition was A (33.1%), G (14.5%), C (27.2%) and T (25.2%), indicating that the percentage of A and T (58.3%) was higher than that of G and C. Most of these genes were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes. The mitochondrial genome analyzed here will provide new genetic information to study the evolution of bats.

Adult neurogenesis in eight Megachiropteran species

The present study evaluated, using immunohistochemical methods, the presence and characteristics of proliferating and newly generated neurons in the brain of eight wild-caught adult Megachiropteran species. For the neurogenic patterns observed, direct homologies are evident in other mammalian species; however, there were several distinctions in the presence or absence of proliferating and immature neurons, and migratory streams that provide important clues regarding the use of the brain in the analysis of Chiropteran phylogenetic affinities. In all eight species studied, numerous Ki-67- and doublecortin (DCX)-immunopositive cells were identified in the subventricular zone (SVZ). These cells migrated to the olfactory bulb through a Primate-like rostral migratory stream (RMS) that is composed of dorsal and ventral substreams which merge before entering the olfactory bulb. Some cells were observed emerging from the RMS coursing caudally and dorsally to the rostral neocortex. In the dentate gyrus of all species, Ki-67- and DCX-expressing cells were observed in the granular cell layer and hilus. Similar to Primates, proliferating cells and immature neurons were identified in the SVZ of the temporal horn of Megachiropterans. These cells migrated to the rostral and caudal piriform cortex through a Primate-like temporal migratory stream. Sparsely distributed Ki-67-immunopositive, but DCX-immunonegative, cells were identified in the tectum, brainstem and cerebellum. The observations from this study add to a number of neural characteristics that phylogenetically align Megachiropterans to Primates.

Bats and bat-borne diseases: a perspective on Australian megabats

Bats are the second most species rich and abundant group of mammals and display an array of unique characteristics but are also among the most poorly studied mammals. They fill an important ecological niche and have diversified into a wide range of habitats. In recent years, bats have been implicated as reservoirs for some of the most highly pathogenic emerging and re-emerging infectious diseases reported to date, including SARS-like coronavirus, Ebola, Hendra and Nipah viruses. The ability of bats to harbour these viruses in the absence of clinical signs of disease has resulted in a resurgence of interest in bat biology and virus–host interactions. Interest in bats, in Australia in particular, has intensified following the identification of several novel bat-borne viruses from flying-foxes, including Hendra virus, which is capable of spillover from bats to horses and subsequently to humans with potentially fatal consequences. As we continue to encroach on the natural habitats of bats, a better understanding of bat biology, ecology and virus–host interactions has never before been so critical. In this review, we focus on the biology of Australian pteropid bats and the pathogens they harbour, summarising current knowledge of bat-borne diseases, bat ecology, ethology and immunology.

Rethinking primate origins again

In 1974, Cartmill introduced the theory that the earliest primate adaptations were related to their being visually oriented predators active on slender branches. Given more recent data on primate-like marsupials, nocturnal prosimians, and early fossil primates, and the context in which these primates first appeared, this theory has been modified. We hypothesize that our earliest primate relatives were likely exploiting the products of co-evolving angiosperms, along with insects attracted to fruits and flowers, in the slender supports of the terminal branch milieu. This has been referred to as the primate/angiosperm co-evolution theory. Cartmill subsequently posited that: "If the first euprimates had grasping feet and blunt teeth adapted for eating fruit, but retained small divergent orbits…" then the angiosperm coevolution theory would have support. The recent discovery of Carpolestes simpsoni provides this support. In addition, new field data on small primate diets, and a new theory concerning the visual adaptations of primates, have provided further evidence supporting the angiosperm coevolution theory.

Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals

Although great progress has been made in resolving the relationships of placental mammals, the position of several clades in Laurasiatheria remain controversial. In this study, we performed a phylogenetic analysis of 97 orthologs (46,152 bp) for 15 taxa, representing all laurasiatherian orders. Additionally, phylogenetic trees of laurasiatherian mammals with draft genome sequences were reconstructed based on 1608 exons (2,175,102 bp). Our reconstructions resolve the interordinal relationships within Laurasiatheria and corroborate the clades Scrotifera, Fereuungulata, and Cetartiodactyla. Furthermore, we tested alternative topologies within Laurasiatheria, and among alternatives for the phylogenetic position of Perissodactyla, a sister-group relationship with Cetartiodactyla receives the highest support. Thus, Pegasoferae (Perissodactyla + Carnivora + Pholidota + Chiroptera) does not appear to be a natural group. Divergence time estimates from these genes were compared with published estimates for splits within Laurasiatheria. Our estimates were similar to those of several studies and suggest that the divergences among these orders occurred within just a few million years.

Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification

Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.

The two suborders of chiropterans have the canonical heavy-chain immunoglobulin (Ig) gene repertoire of eutherian mammals

Bats comprise 20% of all mammals, yet little is known about their immune system and virtually nothing about their immunoglobulin genes. We show that four different bat species transcribe genes encoding IgM, IgE, IgA and IgG subclasses, the latter which have diversified after speciation; the canonical pattern for eutherian mammals. IgD transcripts were only recovered from insectivorous bats and were comprised of CH1, CH3 and two hinge exons; the second hinge exon was fused to CH3. IgA in all species resembles human IgA2 with the putative cysteine forming the bridge to the light chain found at position 77. Sequence comparisons yielded no evidence for a diphyletic origin of the suborders. Bats show no close similarity to another mammalian order; the strongest association was with carnivores. Data reveal that CH diversity and VDJ and CDR3 organization are similar to other eutherian mammals, although the expressed VH3 family repertoire was unusually diverse.