Molecular evidence regarding the origin of echolocation and flight in bats

Correlated evolution between body size and echolocation in bats (order Chiroptera)

BACKGROUND

Body size and echolocation call frequencies are related in bats. However, it is unclear if this allometry applies to the entire clade. Differences have been suggested between nasal and oral emitting bats, as well as between some taxonomic families. Additionally, the scaling of other echolocation parameters, such as bandwidth and call duration, needs further testing. Moreover, it would be also interesting to test whether changes in body size have been coupled with changes in these echolocation parameters throughout bat evolution. Here, we test the scaling of peak frequency, bandwidth, and call duration with body mass using phylogenetically informed analyses for 314 bat species. We specifically tested whether all these scaling patterns differ between nasal and oral emitting bats. Then, we applied recently developed Bayesian statistical techniques based on large-scale simulations to test for the existence of correlated evolution between body mass and echolocation.

RESULTS

Our results showed that echolocation peak frequencies, bandwidth, and duration follow significant allometric patterns in both nasal and oral emitting bats. Changes in these traits seem to have been coupled across the laryngeal echolocation bats diversification. Scaling and correlated evolution analyses revealed that body mass is more related to peak frequency and call duration than to bandwidth. We exposed two non-exclusive kinds of mechanisms to explain the link between size and each of the echolocation parameters.

CONCLUSIONS

The incorporation of Bayesian statistics based on large-scale simulations could be helpful for answering macroevolutionary patterns related to the coevolution of traits in bats and other taxonomic groups.

Echoes through time: amazing inferences from a fossil bat

Sister to the Chiroptera crown-clade, the 50 million year old Vielasia sigei is suggested to have used laryngeal echolocation based on morphometric analyses. We discuss how Vielasia's discovery influences our understanding of the evolution of echolocation in bats and the insights fossils provide to the lives of extinct species.

A 50-million-year-old, three-dimensionally preserved bat skull supports an early origin for modern echolocation

Bats are among the most recognizable, numerous, and widespread of all mammals. But much of their fossil record is missing, and bat origins remain poorly understood, as do the relationships of early to modern bats. Here, we describe a new early Eocene bat that helps bridge the gap between archaic stem bats and the hyperdiverse modern bat radiation of more than 1,460 living species. Recovered from ∼50 million-year-old cave sediments in the Quercy Phosphorites of southwestern France, Vielasia sigei's remains include a near-complete, three-dimensionally preserved skull-the oldest uncrushed bat cranium yet found. Phylogenetic analyses of a 2,665 craniodental character matrix, with and without 36.8 kb of DNA sequence data, place Vielasia outside modern bats, with total evidence tip-dating placing it sister to the crown clade. Vielasia retains the archaic dentition and skeletal features typical of early Eocene bats, but its inner ear shows specializations found in modern echolocating bats. These features, which include a petrosal only loosely attached to the basicranium, an expanded cochlea representing ∼25% basicranial width, and a long basilar membrane, collectively suggest that the kind of laryngeal echolocation used by most modern bats predates the crown radiation. At least 23 individuals of V. sigei are preserved together in a limestone cave deposit, indicating that cave roosting behavior had evolved in bats by the end of the early Eocene; this period saw the beginning of significant global climate cooling that may have been an evolutionary driver for bats to first congregate in caves.

A molecular phylogeny for all 21 families within Chiroptera (bats)

Bats, members of the Chiroptera order, rank as the second most diverse group among mammals. Recent molecular systematic studies on bats have successfully classified 21 families within two suborders: Yinpterochiroptera and Yangochiroptera. Nevertheless, the phylogeny within these 21 families has remained a subject of controversy. In this study, we have employed a balanced approach to establish a robust family-level phylogenetic hypothesis for bats, utilizing a more comprehensive molecular dataset. This dataset includes representative species from all 21 bat families, resulting in a reduced level of missing genetic information. The resulting phylogenetic tree comprises 21 lineages that are strongly supported, each corresponding to one of the bat families. Our findings support to place the Emballonuroidea superfamily as the basal lineage of Yangochiroptera, and that Myzopodidae should be situated as a basal lineage of Emballonuroidea, forming a sister relationship with the clade consisting of Nycteridae and Emballonuridae. Finally, we have conducted dating analyses on this newly resolved phylogenetic tree, providing divergence times for each bat family. Collectively, our study has employed a relatively comprehensive molecular dataset to establish a more robust phylogeny encompassing all 21 bat families. This improved phylogenetic framework will significantly contribute to our understanding of evolutionary processes, ecological roles, disease dynamics, and biodiversity conservation in the realm of bats.

A new shrew mole species of the genus Uropsilus (Eulipotyphla: Talpidae) from northwestern Vietnam

A new medium-sized shrew mole species of the genus Uropsilus from Mount Fansipan, Hoang Lien National Park, Lao Cai Province, northwestern Vietnam is described based on morphological and molecular differences. Uropsilus fansipanensis sp. nov. is distinguished from the other Uropsilus species by the combination of the following features: the dorsum is lightly reddish-brown and venter is dark gray; the dark gray tail is long and slender, with a scattered white base and short bristle hairs; orbital process is oriented upwards posteriorly; lacrimal foramen is well developed and much larger than infraorbital foramen; the lower first premolar is approximately the same size as the lower third premolar. Genetic distances in terms of mitochondrial cytochrome b from other Uropsilus species presented pairwise divergences from 8.63 to 20.70%. To date, the new species is known to exist only in the type locality of Mt. Fansipan, a wet and cold temperate climate area with an upper montane forest at an elevation of approximately 2900 m, forming the southernmost distribution of the genus Uropsilus.

Integrative systematics and evolutionary history of Berylmys bowersi (Mammalia, Rodentia, Muridae)

The Bower's Berylmys (Berylmys bowersi) is one of the largest rodent species with a wide distribution range in southern China and the Indochinese Peninsula. The taxonomy and evolutionary history of the B. bowersi is still controversial and confusing. In this study, we used two mitochondrial (Cyt b and COI) and three nuclear (GHR, IRBP, and RAG1) genes to estimate the phylogeny, divergence times, and biogeographic history of B. bowersi. We also explored morphological variations among the specimens collected across China. Our phylogenetic analyses indicated that the traditional B. bowersi contains at least two species: B. bowersi and B. latouchei. Berylmys latouchei was considered a junior synonym of B. bowersi distributed in eastern China, which is confirmed to be distinguishable at specific level because of its larger size, relatively larger and whiter hind feet, and several cranial traits. The estimated split of B. bowersi and B. latouchei was at the early Pleistocene (ca. 2.00 Mya), which might be the outcome of the combined effects of climate change in the early Pleistocene and isolation by the Minjiang River. Our results highlight the Wuyi Mountains in northern Fujian, China, as a glacial refugia during the Pleistocene and call for more intensive surveys and systematic revisions of small mammals in eastern China.

Significant impact of redox regulation of estrogen-metabolizing proteins on cellular stress responses

The ultimate driving force, stress, promotes adaptability/evolution in proliferating organisms, transforming tumorigenic growth. Estradiol (E2) regulates both phenomena. In this study, bioinformatics-tools, site-directed-mutagenesis (human estrogen-sulfotransferase/hSULT1E1), HepG2 cells tested with N-acetyl-cysteine (NAC/thiol-inducer) or buthionine-sulfoxamine (BSO/thiol-depletory) were evaluated for hSULT1E1 (estradiol-sulphating/inactivating) functions. Reciprocal redox regulation of steroid sulfatase (STS, E2-desulfating/activating) results in the Cys-formylglycine transition by the formylglycine-forming enzyme (FGE). The enzyme sequences and structures were examined across the phylogeny. Motif/domain and the catalytic conserve sequences and protein-surface-topography (CASTp) were investigated. The E2 binding to SULT1E1 suggests that the conserved-catalytic-domain in this enzyme has critical Cysteine 83 at position. This is strongly supported by site-directed mutagenesis/HepG2-cell research. Molecular-docking and superimposition studies of E2 with the SULT1E1 of representative species and to STS reinforce this hypothesis. SULT1E1-STS are reciprocally activated in response to the cellular-redox-environment by the critical Cys of these two enzymes. The importance of E2 in organism/species proliferation and tissue tumorigenesis is highlighted.

Revalidation and expanded description of Mustela aistoodonnivalis (Mustelidae: Carnivora) based on a multigene phylogeny and morphology

The lacked-teeth pygmy weasel, Mustela aistoodonnivalis Wu & Kao, 1991, was originally described as being from Taibai Mountain and Zhashui county, Shaanxi, China. Subsequently, it was considered a subspecies or synonym of Mustela nivalis. In a faunal survey of northwestern Sichuan, eight specimens of M. aistoodonnivalis were collected. A molecular phylogenetic analysis of one mitochondrial and six nuclear genes clustered the specimens as a distinct clade and not with M. nivalis. Morphologically, the lack of the second lower molar differentiated them from M. nivalis, and genetic distances were typical of discrete species. These analyses confirmed that M. aistoodonnivalis is an independent species in the genus Mustela.

Genetic Characterization and Insular Habitat Enveloping of Endangered Leaf-Nosed Bat, Hipposideros nicobarulae (Mammalia: Chiroptera) in India: Phylogenetic Inference and Conservation Implication

The Nicobar leaf-nosed Bat (Hipposideros nicobarulae) was described in the early 20th century; however, its systematic classification has been debated for over 100 years. This endangered and endemic species has achieved species status through morphological data in the last 10 years. However, the genetic information and phylogenetic relationships of H. nicobarulae remain neglected. The generated mitochondrial cytochrome b gene (mtCytb) sequences (438 bp) of H. nicobarulae contains 53.42-53.65% AT composition and 1.82% variable sites. The studied species, H. nicobarulae maintains an 8.1% to 22.6% genetic distance from other Hipposideros species. The genetic divergence estimated in this study is congruent with the concept of gene speciation in bats. The Bayesian and Maximum-Likelihood phylogenies clearly discriminated all Hipposideros species and showed a sister relationship between H. nicobarulae and H. cf. antricola. Current mtCytb-based investigations of H. nicobarulae have confirmed the species status at the molecular level. Further, the MaxEnt-based species distribution modelling illustrates the most suitable habitat of H. nicobarulae (294 km²), of which the majority (171 km²) is located on Great Nicobar Island. The present study suggests rigorous sampling across the range, taxonomic coverage, the generation of multiple molecular markers (mitochondrial and nuclear), as well as more ecological information, which will help in understanding population genetic structure, habitat suitability, and the implementation of appropriate conservation action plans for H. nicobarulae and other Hipposideros species.

Correlated evolution of wing morphology and echolocation calls in bats

Introduction

Flight and echolocation are two crucial behaviors associated with niche expansion in bats. Previous researches have attempted to explain the interspecific divergence in flight morphology and echolocation vocalizations in some bat groups from the perspective of foraging ecology. However, the relationship between wing morphology and echolocation vocalizations of bats remains obscure, especially in a phylogenetic context.

Objectives

Here, we aimed to assess the correlated evolution of wing morphology and echolocation calls in bats within a phylogenetic comparative framework.

Methods

We integrated the information on search-phrase echolocation call duration, peak frequency, relative wing loading, aspect ratio, and foraging guilds for 152 bat species belonging to 15 families. We quantified the association among wing morphology, echolocation call parameters, and foraging guilds using phylogeny-based comparative analyses.

Results

Our analyses revealed that wing morphology and echolocation call parameters depended on families and exhibited a marked phylogenetic signal. Peak frequency of the call was negatively correlated with relative wing loading and aspect ratio. Call duration was positively correlated with relative wing loading and aspect ratio among open-space aerial foragers, edge-space aerial foragers, edge-space trawling foragers, and narrow-space gleaning foragers. Wing morphology, call duration, and peak frequency were predicted by foraging guilds.

Conclusion

These results demonstrate that adaptive response to foraging ecology has shaped the correlated evolution between flight morphology and echolocation calls in bats. Our findings expand the current knowledge regarding the link between morphology and vocalizations within the order Chiroptera.

First representative complete mitochondrial genome of the Taphozous melanopogon Temminck, 1841 (Chiroptera: Emballonuridae) from China

In this study, we present the first representative complete Taphozous melanopogon mitochondrial genome from China. Its mitochondrial genome was assembled and annotated using MitoZ. The genome is a circular molecule of 16,566 bp in length, including 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and a control region. Although maximum-likelihood and Bayesian inference phylogenetic trees indicate that the super family Emballonuridea forms a sister taxon with Noctilionidea instead of Vespertilionidea, mitochondrial genes provide only part of the phylogenetic information, and phylogenetic inferences utilizing nuclear genes are needed in future toward resolving phylogenetic relationship among Vespertilionidea, Noctilionidea, and Emballonuridea.

Evolution of inner ear neuroanatomy of bats and implications for echolocation

Phylogenomics of bats suggests that their echolocation either evolved separately in the bat suborders Yinpterochiroptera and Yangochiroptera, or had a single origin in bat ancestors and was later lost in some yinpterochiropterans^1-6. Hearing for echolocation behaviour depends on the inner ear, of which the spiral ganglion is an essential structure. Here we report the observation of highly derived structures of the spiral ganglion in yangochiropteran bats: a trans-otic ganglion with a wall-less Rosenthal's canal. This neuroanatomical arrangement permits a larger ganglion with more neurons, higher innervation density of neurons and denser clustering of cochlear nerve fascicles^7-13. This differs from the plesiomorphic neuroanatomy of Yinpterochiroptera and non-chiropteran mammals. The osteological correlates of these derived ganglion features can now be traced into bat phylogeny, providing direct evidence of how Yangochiroptera differentiated from Yinpterochiroptera in spiral ganglion neuroanatomy. These features are highly variable across major clades and between species of Yangochiroptera, and in morphospace, exhibit much greater disparity in Yangochiroptera than Yinpterochiroptera. These highly variable ganglion features may be a neuroanatomical evolutionary driver for their diverse echolocating strategies^4,14-17 and are associated with the explosive diversification of yangochiropterans, which include most bat families, genera and species.

Evolution of Complexity. Molecular Aspects of Preassembly

An extension of neo-Darwinism, termed preassembly, states that genetic material required for many complex traits, such as echolocation, was present long before emergence of the traits. Assembly of genes and gene segments had occurred over protracted time-periods within large libraries of non-coding genes. Epigenetic factors ultimately promoted transfers from noncoding to coding genes, leading to abrupt formation of the trait via de novo genes. This preassembly model explains many observations that to this present day still puzzle biologists: formation of super-complexity in the absence of multiple fossil precursors, as with bat echolocation and flowering plants; major genetic and physical alterations occurring in just a few thousand years, as with housecat evolution; lack of precursors preceding lush periods of species expansion, as in the Cambrian explosion; and evolution of costly traits that exceed their need during evolutionary times, as with human intelligence. What follows in this paper is a mechanism that is not meant to supplant neo-Darwinism; instead, preassembly aims to supplement current ideas when complexity issues leave them struggling.

The number of species of degus (genus Octodon) is currently underestimated: An appraisal of species limits and their phylogenetic relationships (Rodentia: Hystricomorpha: Octodontidae)

As currently understood, the genus Octodon contains five species degus, lunatus, bridgesii, pacificus, and ricardojeda. Previous phylogenetic studies suggest that genus specific diversity is underestimated. In order to evaluate the taxonomic diversity of Octodon, we implemented unilocus (cytochrome-b) and multilocus (cytochrome-b + 4 nuclear genes) species delimitation methods. Octodon degus was recovered as a sister of the other species of the genus. The unilocus bGMYC and mPTP methods, based on cytochrome-b sequences, delimits 11 and 7 candidate species respectively, and both methods fail to recognize O. pacificus from O. ricardojeda. Results of the multilocus analysis (BPP) vary as a function of the dataset used. When the five genes are used 11 species are delimited, while eight species are delimited when only the nuclear genes are used. Octodon bridgesii is shown as comprising at least two species (one on the Pacific coast and the typical form found on the Andean slopes), while O. ricardojeda may comprise two species (one on the Chilean side of the Andes and the other in Argentina). Likewise, both multilocus matrices recover O. pacificus as a distinct species. This shows that species diversity of Octodon is underestimated. Remarkably, many of the delimited species based on genetic data are morphologically differentiated in cranio-dental characteristics. However, a pair of species has not achieved morphological differentiation, being cryptic species. Finally, the incongruence between mitochondrial and nuclear phylogenies suggests that processes such as incomplete lineage sorting and/or introgression have been present during the radiation of the genus.

Making a bat: The developmental basis of bat evolution

Bats are incredibly diverse, both morphologically and taxonomically. Bats are the only mammalian group to have achieved powered flight, an adaptation that is hypothesized to have allowed them to colonize various and diverse ecological niches. However, the lack of fossils capturing the transition from terrestrial mammal to volant chiropteran has obscured much of our understanding of bat evolution. Over the last 20 years, the emergence of evo-devo in non-model species has started to fill this gap by uncovering some developmental mechanisms at the origin of bat diversification. In this review, we highlight key aspects of studies that have used bats as a model for morphological adaptations, diversification during adaptive radiations, and morphological novelty. To do so, we review current and ongoing studies on bat evolution. We first investigate morphological specialization by reviewing current knowledge about wing and face evolution. Then, we explore the mechanisms behind adaptive diversification in various ecological contexts using vision and dentition. Finally, we highlight the emerging work into morphological novelties using bat wing membranes.

Morphology and phylogeny of scalopine moles (Eulipotyphla: Talpidae: Scalopini) from the eastern Himalayas, with descriptions of a new genus and species

All scalopine moles are found in North America, except the Gansu mole (Scapanulus oweni), which is endemic to central-west China. In 2019, we collected two specimens of Scalopini on Mt Namjagbarwa in the eastern Himalayas, Tibet, China. We sequenced two mitochondrial (CYT B and 12S) and three nuclear (APOB, BRCA1 and RAG2) genes to estimate the phylogenetic relationships of the two moles, and also compared their morphology with other genera and species within the Scalopini. Both morphological and molecular analyses strongly suggest that the specimens represent a new monotypic genus and species, which are formally described here as Alpiscaptulus medogensis gen. et sp. nov. The dental formula of the new mole (44 teeth) is distinct from the Chinese Scapanulus oweni (36 teeth) and its hairy and pale brown tail is unique among species of the Scalopini. The Kimura-2-parameter (K2P) distances of CYT B between A. medogensis and the four recognized Scalopini genera range from 14.5% to 18.9%. A sister relationship between A. medogensis and Scapanulus oweni was strongly supported in the phylogenetic trees. The divergence between A. medogensis and Scapanulus oweni occurred in the mid-Miocene (c. 11.56 Mya), which corresponds with the rapid uplift of the Himalayan-Tibetan Plateau.

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.

The Life Hidden Inside Caves: Ecological and Economic Importance of Bat Guano

Bats are emblematic hosts of caves. These small flying mammals deserve special attention because their presence has a great economic and ecological impact; they introduce organic matter, the guano, in the ecosystem they live in. Indeed, “guano” (a Quechua word meaning “fertilizer”) is the accumulation of their fecal matter (excreta); its deposition can reach several meters. The composition of guano is influenced by the bat’s food. In addition to its role within the caves, the bat guano is exploited for various purposes; it is used as an effective fertilizer for the cultivation of plants because of having exceptionally high content of nitrogen, phosphate, and potassium and also for the improvement of detergents and other products of great value for humans. The bat guano hosts various classes of microorganisms (viruses, bacteria, algae, fungi, and protists), which are adapted to the cave environment. Since guano is highly acidic, these microorganisms can be considered as extremophiles. They produce functional organic compounds in extreme conditions that could be of interest not only in the drug industry but also in different biotechnological areas. Here, we review already available information on the ecological and economic effects of bats and their guano. We report their food preferences, foraging behaviors, and environmental impacts. Information on these aspects may be useful in finding a solution about protection and preservation of bat populations.

An Alternative Molecular View of Evolution: How DNA was Altered over Geological Time

Four natural phenomena are cited for their defiance of conventional neo-Darwinian analysis: human intelligence; cat domesticity; the Cambrian explosion; and convergent evolution. 1. Humans are now far more intelligent than needed in their hunting–gathering days >10,000 years ago. 2. Domestic cats evolved from wildcats via major genetic and physical changes, all occurring in less than 12,000 years. 3. The Cambrian explosion refers to the remarkable expansion of species that mystifies evolutionists, as there is a total lack of fossil evidence for precursors of this abundant new life. 4. Convergent evolution often involves formation of complex, multigene traits in two or more species that have no common ancestor. These four evolutionary riddles are discussed in terms of a proposed “preassembly” mechanism in which genes and gene precursors are collected silently and randomly over extensive time periods within huge non-coding sections of DNA. This is followed by epigenetic release of the genes, when the environment so allows, and by natural selection. In neo-Darwinism, macroevolution of complex traits involves multiple mutation/selections, with each of the resulting intermediates being more favorable to the species than the previous one. Preassembly, in contrast, invokes natural selection only after a partially or fully formed trait is already in place. Preassembly does not supplant neo-Darwinism but, instead, supplements neo-Darwinism in those important instances where the classical theory is wanting.

Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera

The revision of the sub-order Microchiroptera is one of the most intriguing outcomes in recent mammalian molecular phylogeny. The unexpected sister–taxon relationship between rhinolophoid microbats and megabats, with the exclusion of other microbats, suggests that megabats arose in a relatively short period of time from a microbat-like ancestor. In order to understand the genetic mechanism underlying adaptive evolution in megabats, we determined the whole-genome sequences of two rousette megabats, Leschenault’s rousette (Rousettus leschenaultia) and the Egyptian fruit bat (R. aegyptiacus). The sequences were compared with those of 22 other mammals, including nine bats, available in the database. We identified that megabat genomes are distinct in that they have extremely low activity of SINE retrotranspositions, expansion of two chemosensory gene families, including the trace amine receptor (TAAR) and olfactory receptor (OR), and elevation of the dN/dS ratio in genes for immunity and protein catabolism. The adaptive signatures discovered in the genomes of megabats may provide crucial insight into their distinct evolution, including key processes such as virus resistance, loss of echolocation, and frugivorous feeding.

Phylogenetic relationships in the genus Cheracebus (Callicebinae, Pitheciidae)

Cheracebus is a new genus of New World primate of the family Pitheciidae, subfamily Callicebinae. Until recently, Cheracebus was classified as the torquatus species group of the genus Callicebus. The genus Cheracebus has six species: C. lucifer, C. lugens, C. regulus, C. medemi, C. torquatus, and C. purinus, which are all endemic to the Amazon biome. Before the present study, there had been no conclusive interpretation of the phylogenetic relationships among most of the Cheracebus species. The present study tests the monophyly of the genus and investigates the relationships among the different Cheracebus species, based on DNA sequencing of 16 mitochondrial and nuclear markers. The phylogenetic analyses were based on Maximum Likelihood, Bayesian Inference, and multispecies coalescent approaches. The divergence times and genetic distances between the Cheracebus taxa were also estimated. The analyses confirmed the monophyly of the genus and a well-supported topology, with the following arrangement: ((C. torquatus, C. lugens), (C. lucifer (C. purinus, C. regulus))). A well-differentiated clade was also identified within part of the geographic range of C. lugens, which warrants further investigation to confirm its taxonomic status.

Neural oscillations in the fronto-striatal network predict vocal output in bats

The ability to vocalize is ubiquitous in vertebrates, but neural networks underlying vocal control remain poorly understood. Here, we performed simultaneous neuronal recordings in the frontal cortex and dorsal striatum (caudate nucleus, CN) during the production of echolocation pulses and communication calls in bats. This approach allowed us to assess the general aspects underlying vocal production in mammals and the unique evolutionary adaptations of bat echolocation. Our data indicate that before vocalization, a distinctive change in high-gamma and beta oscillations (50–80 Hz and 12–30 Hz, respectively) takes place in the bat frontal cortex and dorsal striatum. Such precise fine-tuning of neural oscillations could allow animals to selectively activate motor programs required for the production of either echolocation or communication vocalizations. Moreover, the functional coupling between frontal and striatal areas, occurring in the theta oscillatory band (4–8 Hz), differs markedly at the millisecond level, depending on whether the animals are in a navigational mode (that is, emitting echolocation pulses) or in a social communication mode (emitting communication calls). Overall, this study indicates that fronto-striatal oscillations could provide a neural correlate for vocal control in bats.

In bats, rhythmic activity in frontal and striatal areas of the brain provide a neural correlate for vocal control, which can be used to predict whether the ensuing vocalizations are for echolocation or social communication.

Commensalism outweighs phylogeographical structure in its effect on phenotype of a Sudanian savanna rodent

The murid rodent Praomys daltoni is widespread in Sudanian savanna and woodlands of West Africa, and previous study of mitochondrial DNA variability suggested that it encompasses the phenotypically (small, grey-bellied) and ecologically (commensal) distinct form, Praomys derooi. Here, we comprehensively examined the genetic and morphological diversity within the complex. Six mitochondrial lineages showed a fine-scale phylogeographical pattern, whereas delimitation based on nuclear loci pooled four of them into a single widespread unit. A newly discovered lineage from southern Mauritania stands apart from the rest of the complex and might represent an unrecognized species. At the same time, the internal position of P. derooi (C2 mitochondrial lineage) was confirmed by the multilocus analysis. The magnitude of genetic distances between major phylogeographical lineages was typical for interspecific divergence in other clades of Praomys, despite the little differences among them in morphology (skull and upper molar row shapes). The most pronounced morphological shift was associated with a transition to commensalism, especially in P. derooi, but also in other lineages. This makes the whole complex a suitable model for the study of phenotypic novelty, the evolution of commensalism and conditions for ecological speciation.

Serological Evidence of Thailand Orthohantavirus or Antigenically Related Virus Infection Among Rodents in a Chronic Kidney Disease of Unknown Etiology Endemic Area, Girandurukotte, Sri Lanka

We have reported high seroprevalence to Thailand orthohantavirus (THAIV) or THAIV-related orthohantavirus (TRHV) among patients with chronic kidney disease of unknown etiology in Girandurukotte, Sri Lanka. THAIV or TRHV infection is considered to be transmitted by rodent hosts in this area, but its reservoir rodents have not yet been identified. Hence, 116 rodents were captured, and seroprevalences were examined by indirect immunofluorescent antibody assay (immunofluorescence assay [IFA]) using antigens of THAIV strain Thai749-infected Vero E6 cells and recombinant nucleocapsid protein of THAIV expressed in Vero E6 cell. Molecular biological species identification of rodents was carried out by sequencing rag1, irbp, and mitochondrial cytb genes. The majority (112/116) of the captured rodents were lineage Ib of black rats (Rattus rattus). Among them, 19.6% (22/112) of the rats possessed antibodies against THAIV. Also, a lesser bandicoot rat (Bandicota bengalensis), which belongs to the Sri Lankan endemic genetic lineage, was seropositive (1/1). Two Mus booduga and one Murinae sp. were seronegative. Rodent sera showed less cross-reactivities to antigens of Vero E6 cells infected with Hantaan orthohantavirus (HTNV), Seoul orthohantavirus (SEOV), and Puumala orthohantavirus (PUUV) in IFA. These results suggest that the hantavirus present in rodents in Sri Lanka is related to THAIV or TRHV rather than to SEOV, HTNV, or PUUV. However, it might be serologically distinct from the prototype THAIV strain, Thai749, used in this study. This study revealed that black rats and lesser bandicoot rats belonging to Sri Lankan endemic lineages are possible reservoirs for THAIV or TRHV in Girandurukotte. Further multiple geographical studies are needed to confirm the THAIV or TRHV reservoir status of black and lesser bandicoot rats in Sri Lanka.

De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats

High-throughput RNA sequencing is a powerful tool that allows us to perform gene prediction and analyze tissue-specific overexpression of genes, but also at species level comparisons can be performed, although in a more restricted manner. In the present study complete liver transcriptomes of five tropical bat species were De novo assembled and annotated. Highly expressed genes in the five species were involved in glycolysis and lipid metabolism pathways. Cross-species differential expression analysis was conducted using single copy orthologues shared across the five species. Between 22 and 29 orthologs were upregulated for each species. We detected upregulated expression in Artibeus jamaicensis genes related to fructose metabolism pathway. Such findings can be correlated with A. jamaicensis dietary habits, as it was the unique frugivorous species included. This is the first report of transcriptome assembly by RNA-seq in these species, except for A. jamaicensis and as far as our knowledge is the first cross-species comparisons of transcriptomes and gene expression in tropical bats.

Postcranial heterochrony, modularity, integration and disparity in the prenatal ossification in bats (Chiroptera)

BACKGROUND

Self-powered flight is one of the most energy-intensive types of locomotion found in vertebrates. It is also associated with a range of extreme morpho-physiological adaptations that evolved independently in three different vertebrate groups. Considering that development acts as a bridge between the genotype and phenotype on which selection acts, studying the ossification of the postcranium can potentially illuminate our understanding of bat flight evolution. However, the ontogenetic basis of vertebrate flight remains largely understudied. Advances in quantitative analysis of sequence heterochrony and morphogenetic growth have created novel approaches to study the developmental basis of diversification and the evolvability of skeletal morphogenesis. Assessing the presence of ontogenetic disparity, integration and modularity from an evolutionary approach allows assessing whether flight may have resulted in evolutionary differences in the magnitude and mode of development in bats.

RESULTS

We quantitatively compared the prenatal ossification of the postcranium (24 bones) between bats (14 species), non-volant mammals (11 species) and birds (14 species), combining for the first time prenatal sequence heterochrony and developmental growth data. Sequence heterochrony was found across groups, showing that bat postcranial development shares patterns found in other flying vertebrates but also those in non-volant mammals. In bats, modularity was found as an axial-appendicular partition, resembling a mammalian pattern of developmental modularity and suggesting flight did not repattern prenatal postcranial covariance in bats.

CONCLUSIONS

Combining prenatal data from 14 bat species, this study represents the most comprehensive quantitative analysis of chiropteran ossification to date. Heterochrony between the wing and leg in bats could reflect functional needs of the newborn, rather than ecological aspects of the adult. Bats share similarities with birds in the development of structures involved in flight (i.e. handwing and sternum), suggesting that flight altriciality and early ossification of pedal phalanges and sternum are common across flying vertebrates. These results indicate that the developmental modularity found in bats facilitates intramodular phenotypic diversification of the skeleton. Integration and disparity increased across developmental time in bats. We also found a delay in the ossification of highly adaptable and evolvable regions (e.g. handwing and sternum) that are directly associated with flight performance.

Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny

Background

Spiny mice of the genus Acomys are distributed mainly in dry open habitats in Africa and the Middle East, and they are widely used as model taxa for various biological disciplines (e.g. ecology, physiology and evolutionary biology). Despite their importance, large distribution and abundance in local communities, the phylogeny and the species limits in the genus are poorly resolved, and this is especially true for sub-Saharan taxa. The main aims of this study are (1) to reconstruct phylogenetic relationships of Acomys based on the largest available multilocus dataset (700 genotyped individuals from 282 localities), (2) to identify the main biogeographical divides in the distribution of Acomys diversity in dry open habitats in Afro-Arabia, (3) to reconstruct the historical biogeography of the genus, and finally (4) to estimate the species richness of the genus by application of the phylogenetic species concept.

Results

The multilocus phylogeny based on four genetic markers shows presence of five major groups of Acomys called here subspinosus, spinosissimus, russatus, wilsoni and cahirinus groups. Three of these major groups (spinosissimus, wilsoni and cahirinus) are further sub-structured to phylogenetic lineages with predominantly parapatric distributions. Combination of alternative species delimitation methods suggests the existence of 26 molecular operational taxonomic units (MOTUs), potentially corresponding to separate species. The highest genetic diversity was found in Eastern Africa. The origin of the genus Acomys is dated to late Miocene (ca. 8.7 Ma), when the first split occurred between spiny mice of eastern (Somali-Masai) and south-eastern (Zambezian) savannas. Further diversification, mostly in Plio-Pleistocene, and the current distribution of Acomys were influenced by the interplay of global climatic factors (e.g., Messinian salinity crisis, intensification of Northern Hemisphere glaciation) with local geomorphology (mountain chains, aridity belts, water bodies). Combination of divergence dating, species distribution modelling and historical biogeography analysis suggests repeated “out-of-East-Africa” dispersal events into western Africa, the Mediterranean region and Arabia.

Conclusions

The genus Acomys is very suitable model for historical phylogeographic and biogeographic reconstructions of dry non-forested environments in Afro-Arabia. We provide the most thorough phylogenetic reconstruction of the genus and identify major factors that influenced its evolutionary history since the late Miocene. We also highlight the urgent need of integrative taxonomic revision of east African taxa.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1380-9) contains supplementary material, which is available to authorized users.

As Blind as a Bat? Opsin Phylogenetics Illuminates the Evolution of Color Vision in Bats

Through their unique use of sophisticated laryngeal echolocation bats are considered sensory specialists amongst mammals and represent an excellent model in which to explore sensory perception. Although several studies have shown that the evolution of vision is linked to ecological niche adaptation in other mammalian lineages, this has not yet been fully explored in bats. Recent molecular analysis of the opsin genes, which encode the photosensitive pigments underpinning color vision, have implicated high-duty cycle (HDC) echolocation and the adoption of cave roosting habits in the degeneration of color vision in bats. However, insufficient sampling of relevant taxa has hindered definitive testing of these hypotheses. To address this, novel sequence data was generated for the SWS1 and MWS/LWS opsin genes and combined with existing data to comprehensively sample species representing diverse echolocation types and niches (SWS1 n = 115; MWS/LWS n = 45). A combination of phylogenetic analysis, ancestral state reconstruction, and selective pressure analyses were used to reconstruct the evolution of these visual pigments in bats and revealed that although both genes are evolving under purifying selection in bats, MWS/LWS is highly conserved but SWS1 is highly variable. Spectral tuning analyses revealed that MWS/LWS opsin is tuned to a long wavelength, 555-560 nm in the bat ancestor and the majority of extant taxa. The presence of UV vision in bats is supported by our spectral tuning analysis, but phylogenetic analyses demonstrated that the SWS1 opsin gene has undergone pseudogenization in several lineages. We do not find support for a link between the evolution of HDC echolocation and the pseudogenization of the SWS1 gene in bats, instead we show the SWS1 opsin is functional in the HDC echolocator, Pteronotus parnellii. Pseudogenization of the SWS1 is correlated with cave roosting habits in the majority of pteropodid species. Together these results demonstrate that the loss of UV vision in bats is more widespread than was previously considered and further elucidate the role of ecological niche specialization in the evolution of vision in bats.

Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion

Murid rodents of the genus Aethomys are one of the most common rodents in drier habitats in sub-Saharan Africa. Among them, the red veld rat Aethomys chrysophilus is the most widespread species with the core distribution located in the Zambezian bioregion. In this study, we describe phylogeographic structure of the species and estimate its age from a time-calibrated phylogeny of the genus. Seven parapatric clades were identified in the mitochondrial cytochrome b phylogeny, where some of the distributions of these clades have been separated by previously described biogeographical divides (Zambezi-Kafue river system, Rukwa Rift and the Eastern Arc Mountains). One internal clade corresponded to populations previously described as a distinct species, Aethomys ineptus. The whole A. chrysophilus complex was estimated to be 1.3 (0.5–2.4) Mya old, with A. ineptus originating 0.7 (0.1–1.4) Mya before present. The internal position of A. ineptus was also recovered in phylogenetic reconstruction based on two nuclear genes and thus it is not a consequence of mitochondrial introgression. In addition, we analyzed skull form variation across the species’ distributional range and found no significant difference between A. ineptus and the rest of A. chrysophilus complex.

Fossils know it best: Using a new set of fossil calibrations to improve the temporal phylogenetic framework of murid rodents (Rodentia: Muridae)

Murid rodents (Rodentia: Muridae) represent the most diverse and abundant mammalian family. In this study, we provide a refined set of fossil calibrations which is used to reconstruct a dated phylogeny of the family using a multilocus dataset (six nuclear and nine mitochondrial gene fragments) encompassing 161 species representing 82 murid genera from four extant subfamilies (Deomyinae, Gerbillinae, Lophiomyinae and Murinae). In comparison with previous studies on murid or muroid rodents, our work stands out for the implementation of nine robust fossil constraints within the Muridae thanks to a thorough review of the fossil record. Before being assigned to specific nodes of the phylogeny, all potential fossil constraints were carefully assessed; they were also subjected to several cross-validation analyses. The resulting phylogeny is consistent with previous phylogenetic studies on murids, and recovers the monophyly of all sampled murid subfamilies and tribes. Based on nine controlled fossil calibrations, our inferred temporal timeframe indicates that the murid family likely originated in the course of the Early Miocene, 22.0-17.0 million years ago (Ma), and that most major lineages (i.e. tribes) started diversifying ca. 10 Ma. Historical biogeography analyses support the tropical origin for the family, with an initial internal split (vicariance event) between Afrotropical and Oriental (Indomalaya and Philippines) lineages. During the course of their diversification, the biogeographic pattern of murids is marked by several dispersal events toward the Australasian and the Palearctic regions. The Afrotropical region was also secondarily colonized at least three times from the Indomalaya, indicating that the latter region has acted as a major centre of diversification for the family.

Unmasking the complexity of species identification in Australasian flying-foxes

Pteropus (flying-foxes) are a speciose group of non-echolocating large bats, with five extant Australian species and 24 additional species distributed amongst the Pacific Islands. In 2015, an injured flying-fox with unusual facial markings was found in Sydney, Australia, following severe and widespread storms. Based on an initial assessment, the individual belonged to Pteropus but could not be readily identified to species. As a consequence, four hypotheses for its identification/origin were posited: the specimen represented (1) an undescribed Australian species; or (2) a morphological variant of a recognised Australian species; or (3) a hybrid individual; or (4) a vagrant from the nearby Southwest Pacific Islands. We used a combination of morphological and both mitochondrial- and nuclear DNA-based identification methods to assess these hypotheses. Based on the results, we propose that this morphologically unique Pteropus most likely represents an unusual P. alecto (black flying-fox) potentially resulting from introgression from another Pteropus species. Unexpectedly, this individual, and the addition of reference sequence data from newly vouchered specimens, revealed a previously unreported P. alecto mitochondrial DNA lineage. This lineage was distinct from currently available haplotypes. It also suggests long-term hybridisation commonly occurs between P. alecto and P. conspicillatus (spectacled flying-fox). This highlights the importance of extensive reference data, and the inclusion of multiple vouchered specimens for each species to encompass both intraspecific and interspecific variation to provide accurate and robust species identification. Moreover, our additional reference data further demonstrates the complexity of Pteropus species relationships, including hybridisation, and potential intraspecific biogeographical structure that may impact on their management and conservation.

Mammalia: Chiroptera: Immunology of Bats

Bats are a large and diverse group comprising approximately 20% of all living mammalian species. They are the only mammals capable of powered flight and have many unique characteristics, including long lifespans, echolocation, and hibernation, and play key roles in insect control, pollination, and seed dispersal. The role of bats as natural reservoirs of a variety of high-profile viruses that are highly pathogenic in other susceptible species yet cause no clinical disease in bats has led to a resurgence of interest in their immune systems. Equally compelling is the urgency to understand the immune mechanisms responsible for the susceptibility of bats to the fungus responsible for white syndrome, which threatens to wipe out a number of species of North American bats. In this chapter we review the current knowledge in the field of bat immunology, focusing on recent highlights and the need for further investigations in this area.

Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades

Mitochondrial uncoupling protein 1 (UCP1) is essential for nonshivering thermogenesis in brown adipose tissue and is widely accepted to have played a key thermoregulatory role in small-bodied and neonatal placental mammals that enabled the exploitation of cold environments. We map ucp1 sequences from 133 mammals onto a species tree constructed from a ~51-kb sequence alignment and show that inactivating mutations have occurred in at least 8 of the 18 traditional placental orders, thereby challenging the physiological importance of UCP1 across Placentalia. Selection and timetree analyses further reveal that ucp1 inactivations temporally correspond with strong secondary reductions in metabolic intensity in xenarthrans and pangolins, or in six other lineages coincided with a ~30 million-year episode of global cooling in the Paleogene that promoted sharp increases in body mass and cladogenesis evident in the fossil record. Our findings also demonstrate that members of various lineages (for example, cetaceans, horses, woolly mammoths, Steller's sea cows) evolved extreme cold hardiness in the absence of UCP1-mediated thermogenesis. Finally, we identify ucp1 inactivation as a historical contingency that is linked to the current low species diversity of clades lacking functional UCP1, thus providing the first evidence for species selection related to the presence or absence of a single gene product.

Analytical Biases Associated with GC-Content in Molecular Evolution

Molecular evolution is being revolutionized by high-throughput sequencing allowing an increased amount of genome-wide data available for multiple species. While base composition summarized by GC-content is one of the first metrics measured in genomes, its genomic distribution is a frequently neglected feature in downstream analyses based on DNA sequence comparisons. Here, we show how base composition heterogeneity among loci and taxa can bias common molecular evolution analyses such as phylogenetic tree reconstruction, detection of natural selection and estimation of codon usage. We then discuss the biological, technical and methodological causes of these GC-associated biases and suggest approaches to overcome them.

Brain Computation Is Organized via Power-of-Two-Based Permutation Logic

There is considerable scientific interest in understanding how cell assemblies—the long-presumed computational motif—are organized so that the brain can generate intelligent cognition and flexible behavior. The Theory of Connectivity proposes that the origin of intelligence is rooted in a power-of-two-based permutation logic (N = 2ⁱ–1), producing specific-to-general cell-assembly architecture capable of generating specific perceptions and memories, as well as generalized knowledge and flexible actions. We show that this power-of-two-based permutation logic is widely used in cortical and subcortical circuits across animal species and is conserved for the processing of a variety of cognitive modalities including appetitive, emotional and social information. However, modulatory neurons, such as dopaminergic (DA) neurons, use a simpler logic despite their distinct subtypes. Interestingly, this specific-to-general permutation logic remained largely intact although NMDA receptors—the synaptic switch for learning and memory—were deleted throughout adulthood, suggesting that the logic is developmentally pre-configured. Moreover, this computational logic is implemented in the cortex via combining a random-connectivity strategy in superficial layers 2/3 with nonrandom organizations in deep layers 5/6. This randomness of layers 2/3 cliques—which preferentially encode specific and low-combinatorial features and project inter-cortically—is ideal for maximizing cross-modality novel pattern-extraction, pattern-discrimination and pattern-categorization using sparse code, consequently explaining why it requires hippocampal offline-consolidation. In contrast, the nonrandomness in layers 5/6—which consists of few specific cliques but a higher portion of more general cliques projecting mostly to subcortical systems—is ideal for feedback-control of motivation, emotion, consciousness and behaviors. These observations suggest that the brain’s basic computational algorithm is indeed organized by the power-of-two-based permutation logic. This simple mathematical logic can account for brain computation across the entire evolutionary spectrum, ranging from the simplest neural networks to the most complex.