First molecular phylogenetic insights into the evolution of free-tailed bats in the subfamily Molossinae (Molossidae, Chiroptera)

Heterogeneity in the preferential diet of neotropical bats impacts the pancreatic islet mass and α and β cell distribution

Whether there is a relationship between bats' dietary patterns and evolutionary endocrine pancreas adaptation is not clearly understood. Aiming to contribute to this topic, we evaluated some metabolic and structural parameters in the following adult bats: the frugivorous Artibeus lituratus, the nectarivorous Anoura caudifer, the hematophagous Desmodus rotundus, and the insectivorous Molossus molossus. A. lituratus and A. caudifer diets consist of high amounts of simple carbohydrates, while D. rotundus and M. molossus diets consist of high amounts of proteins or protein and fat, respectively. In our results, A. lituratus and A. caudifer bats exhibited the highest values of relative islet mass (%), islet density (number of islets per pancreas area), and the lowest values of intestinal length among the four species. When adjusted by the body mass (mg/g of body mass), both D. rotundus and A. caudifer bats exhibited the highest islet mass values among the groups. Blood glucose was similar between A. lituratus, D. rotundus, and M. molossus, with the lowest values for the A. caudifer bats. M. molossus bats had the highest plasma cholesterol values among the studied species but exhibited similar plasma triacylglycerol with D. rotundus and A. caudifer bats. β- and α-cell distribution within A. lituratus, A. caudifer, and M. molossus islets achieved an approximate average value of ∼ 66% and ∼ 28%, respectively, a pattern inverted in D. rotundus islets (53% of α cells and 40% of β cells). A. caudifer and D. rotundus exhibited the highest and the lowest β/α-cells ratio per islet, respectively. We conclude that the macronutrient predominance in each bat-eating niche correlates with the morphophysiological pancreas features being the nectarivorous A. caudifer the species with the highest islet mass per body mass and β/α-cells ratio, while the hematophagous D. rotundus showed the highest α-cells apparatus.

The genome sequence of Tadarida brasiliensis I. Geoffroy Saint-Hilaire, 1824 [Molossidae; Tadarida]

We present a genome assembly from an individual male Tadarida brasiliensis (The Brazilian free-tailed bat; Chordata; Mammalia; Chiroptera; Molossidae). The genome sequence is 2.28 Gb in span. The majority of the assembly is scaffolded into 25 chromosomal pseudomolecules, with the X and Y sex chromosomes assembled.

The coevolutionary mosaic of bat betacoronavirus emergence risk

Pathogen evolution is one of the least predictable components of disease emergence, particularly in nature. Here, building on principles established by the geographic mosaic theory of coevolution, we develop a quantitative, spatially explicit framework for mapping the evolutionary risk of viral emergence. Driven by interest in diseases like Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and Coronavirus disease 2019 (COVID-19), we examine the global biogeography of bat-origin betacoronaviruses, and find that coevolutionary principles suggest geographies of risk that are distinct from the hotspots and coldspots of host richness. Further, our framework helps explain patterns like a unique pool of merbecoviruses in the Neotropics, a recently discovered lineage of divergent nobecoviruses in Madagascar, and-most importantly-hotspots of diversification in southeast Asia, sub-Saharan Africa, and the Middle East that correspond to the site of previous zoonotic emergence events. Our framework may help identify hotspots of future risk that have also been previously overlooked, like West Africa and the Indian subcontinent, and may more broadly help researchers understand how host ecology shapes the evolution and diversity of pandemic threats.

Revising the diversity within the Dwarf Dog-faced Bat, Molossopstemminckii (Chiroptera, Molossidae), with the revalidation of the endangered Molossopsgriseiventer

The genus Molossops includes two monotypic species of insectivore bats distributed in South America: Molossopsneglectus and Molossopstemminckii. Both can be differentiated, based on sizes, M.temminckii being smaller (forearm less than 33 mm). Despite being monotypic, at least two additional subspecies have been described for M.temminckii, of which M.temminckiigriseiventer from the inter-Andean Valley of the Magdalena River in Colombia might represent a valid taxon. To test the taxonomic status of M.t.griseiventer, we reviewed specimens of M.temminckii from cis- and trans-Andean localities in Colombia. We used Cytochrome-b and Cytochrome Oxidase I comparisons to test the phylogenetic position of cis- and trans-Andean samples and compared qualitative morphology, morphometric and bioacoustics. Our results show that M.t.griseiventer is differentiated from cis-Andean specimens, providing further evidence of its validity at the species level. Furthermore, M.temminckii (sensu stricto) is also distributed in Colombia, but both M.griseiventer and M.temminckii are allopatric, with the Andes acting as a barrier. The specific identity of the specimens from the Caribbean Region of Colombia needs a new evaluation, but our results clearly show that the diversity of Molossops is underestimated.

Paraphyly of the Pipistrelles (Pipistrellus; Vespertilionidae) is Confirmed by the Analysis of the Nuclear Gene Markers

There are evidences that the genus Pipistrellus (true pipistrelles) in its current understanding may be paraphyletic. We have studied for the first time the phylogenetic relationships between the majority of supraspecific taxa of the subtribe Pipistrellina based on the analysis of the sequences of three nuclear genes (RAG2, APOB, and DMP1). Our data support the monophyly of the subtribe itself, but definitely show that the genus Pipistrellus in the modern sense is paraphyletic with respect to noctules, Nyctalus, and thick thumb pipistrelles, Glischropus (which both are morphologically distinct taxa). Moreover, noctules are extremely close to the "western" clade of Pipistrellus. The latter genus should probably be divided into two or more separate genera, or Nyctalus and Glischropus should be treated as its subgenera.

Polyctenidae (Hemiptera: Cimicoidea) species in the Afrotropical region: Distribution, host specificity, and first insights to their molecular phylogeny

Polyctenidae bugs are rarely studied, hematophagous, and highly specialized ectoparasites of bats. There are only 32 described species worldwide, including six species in the Afrotropical region. Knowledge on these parasites is limited, and most studies are restricted to the New World polyctenid species. Here we report additional records of Adroctenes horvathi from Kenya and South Africa, as well as Hypoctenes faini from Rwanda. We present an updated list of published polyctenid records in the Afrotropical region indicating their host specificity and their geographical distribution. We report global infection patterns and sex ratio of polyctenids based on previously published data, including Old and New World species. Lastly, we demonstrate the first molecular phylogeny of Polyctenidae, showing their phylogenetic relationship with the closely related family Cimicidae.

A new species of Molossus (Chiroptera: Molossidae) from Argentina

Fourteen species of bats in the genus Molossus currently are recognized in the Neotropical region; only three are known from Argentina. Here, we describe a new species based on specimens collected in the province of Santa Fe, Argentina, in the Pampa ecoregion. The new species can be distinguished from its congeners by its general strong orange coloration, forearm length > 41 mm, dorsal hairs bicolor and long (~5 mm), infraorbital foramen laterally oriented, and long and forward-projected (pincer-like) upper incisors. The external and cranial morphology of the new species are described and comparisons made with other species of similar size and with those present in its distributional area. Wilcoxon tests and multivariate analyses (nonmetric multidimensional scaling ordination and PERMANOVA) were carried out to determine the morphometric differences between the new species and other seven species of Molossus. The species tree, estimated by *BEAST from the concatenation of mitochondrial and nuclear genes, suggests that Molossus sp. nov. is basal within the clade formed by {{M. aztecus, M. rufus}, {{M. currentium, M. pretiosus}, M. sinaloae}} with a posterior probability of 0.82.

Does evolution of echolocation calls and morphology in Molossus result from convergence or stasis?

Although many processes of diversification have been described to explain variation of morphological traits within clades that have obvious differentiation among taxa, not much is known about these patterns in complexes of cryptic species. Molossus is a genus of bats that is mainly Neotropical, occurring from the southeastern United States to southern Argentina, including the Caribbean islands. Molossus comprises some groups of species that are morphologically similar but phylogenetically divergent, and other groups of species that are genetically similar but morphologically distinct. This contrast allows investigation of unequal trait diversification and the evolution of morphological and behavioural characters. In this study, we assessed the role of phylogenetic history in a genus of bat with three cryptic species complexes, and evaluated if morphology and behavior are evolving concertedly. The Genotype by Sequence genomic approach was used to build a species-level phylogenetic tree for Molossus and to estimate the ancestral states of morphological and echolocation call characters. We measured the correlation of phylogenetic distances to morphological and echolocation distances, and tested the relationship between morphology and behavior when the effect of phylogeny is removed. Morphology evolved via a mosaic of convergence and stasis, whereas call design was influenced exclusively through local adaptation and convergent evolution. Furthermore, the frequency of echolocation calls is negatively correlated with the size of the bat, but other characters do not seem to be evolving in concert. We hypothesize that slight variation in both morphology and behaviour among species of the genus might result from niche specialization, and that traits evolve to avoid competition for resources in similar environments.

Optimization of Genotype by Sequencing data for phylogenetic purposes

• Herein we propose a framework for assembling and analyzing Genotype by Sequencing (GBS) data to better understand evolutionary relationships within a group of closely related species using the mastiff bats (Molossus) as our model system. Many species within this genus have low-levels of genetic variation within and between morphologically distinct species, and the relationships among them remain unresolved using traditional Sanger sequencing methods. Given that both de novo and reference genome pipelines can be used to assemble next generation sequences, and that several tree inference methodologies have been proposed for single nucleotide polymorphism (SNP) data, we test whether different alignments and phylogenetic approaches produce similar results. We also examined how the process of SNP identification and mapping can affect the consistency of the analyses. Different alignments and phylogenetic inferences produced consistent results, supporting the GBS approach for answering evolutionary questions on a macroevolutionary scale when the genetic distance among phenotypically identifiable clades is low. We highlight the importance of exploring the relationships among groups using different assembly assumptions and also distinct phylogenetic inference methods, particularly when addressing phylogenetic questions in genetic and morphologically conservative taxa. • The method uses the comparison of several filter settings, alignments, and tree inference approaches on Genotype by Sequencing data. • Consistent results were found among several approaches. • The methodology successfully recovered well supported species boundaries and phylogenetic relationships among species of mastiff bats not hypothesized by previous methods.

Next generation sequencing data in the phylogenetic relationships of the genus Molossus (Chiroptera, Molossidae)

The mastiff bat Molossus is a broadly distributed genus within the family Molossidae. Molossus includes groups of species that are either morphologically or genetically very similar, rendering the taxonomy of this genus confusing and unstable. In this paper, we provide inferred phylogenetic relationships of Molossus based on the genotype by sequencing approach from 189 specimens of three species of New World mastiff bats (Molossus, Promops, and Eumops). We also present data on divergent tree topologies produced by alignments using de novo and reference genome approaches and distinct phylogenetic methods (maximum likelihood and coalescent approaches). These data provide the first highly resolved phylogenetic tree for Molossus, not recovered by previous studies using Sanger sequencing. Our dataset brings new insights on relationships among species and show how different approaches might affect phylogenetic resolution and topologies.

High Duty Cycle Echolocation May Constrain the Evolution of Diversity within Horseshoe Bats (Family: Rhinolophidae)

The phenotype of organisms is the net result of various evolutionary forces acting upon their lineages over time. When an innovative trait arises that confers a substantial advantage in terms of survival and reproduction, the evolution of adaptive complexes between such an innovation and other traits may constrain diversification of that lineage. The specialized echolocation system of the Rhinolophidae may represent such an innovation which affects other parts of the phenotype. We investigated a potential constraint on the diversity of phenotypes of several species of horseshoe bats within a phylogenetic framework. If phenotypic convergence stems from stasis as a result of the specialized echolocation system, phenotypes should converge not only among members of the same species and between sexes but also among species. We analyzed the phenotypic diversity of >800 individuals of 13–16 species. The phenotypes in the horseshoe bats did indeed converge. There was no sexual size dimorphism in mass, forearm length and wingspan within species and there was marked interspecific similarity in both wing and echolocation variables but marked variability in body mass. Furthermore, correlations of wing and echolocation variables with mass suggest that variability within horseshoe bats was largely the result of selection on body size with allometric responses in wing and echolocation parameters, a potential consequence of constraints imposed by their specialized echolocation.

Molecular data on the CO1 and beta fibrinogen gene in the evolutionary relationships of the mastiff bat (Chiroptera, Molossidae, Molossus)

Molossus is one of the most diverse genera of free-tailed bats in the pantropical family Molossidae and occurs though all the Neotropics. Nevertheless, the taxonomy and phylogeny of this group is poorly understood. Here, we present the data on evolutionary relationships of Molossus based on DNA barcodes of COI gene from 346 specimens of Molossus and its sister genus Promops and another New World molossid Eumops. Of these specimens, 50 are new sequences and 296 were obtained from GenBank. In addition, the nuclear gene beta fibrinogen was sequenced from a subset of 35 specimens. These data provide the basis for further exploration and understanding of the phylogenetic relationships of the genus Molossus (Loureiro et al., 2018) [1].

First complete mitochondrial genomes of molossid bats (Chiroptera: Molossidae)

Bats represent around one-fourth of the world's mammals and their taxonomy is still controversial. Molossids are one of the most diverse bat families with a wide knowledge gap. In this study, we report the first complete mitochondrial genomes of three molossid bats: the European free-tailed bat Tadarida teniotis, the La Touche's free-tailed bat Tadarida latouchei, and the Wrinkle-lipped free-tailed bat Chaerephon plicatus. The mitogenomes are 16,869 and 16,784 bp long for T. teniotis and T. latouchei, respectively, while in C. plicatus it is at least 16,216 bp although the control region was not fully recovered due to its higher divergence from T. teniotis. The genomes show conserved synteny with other mammalian mitogenomes, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region (d-loop). All protein-coding genes start with the ATG start codon, except for ND2, ND3, and ND5 which begin with ATA or ATT. Eleven protein-coding genes terminated in a canonical stop codon, TAA or TAG, two contain incomplete stop codons, T or TA. Cytochrome b terminates in the mitochondria-specific stop codon AGA. These mitogenomes provide a valuable resource for future studies of Molossidae and other bat and mammal species.

The Value of Molecular vs. Morphometric and Acoustic Information for Species Identification Using Sympatric Molossid Bats

A fundamental condition for any work with free-ranging animals is correct species identification. However, in case of bats, information on local species assemblies is frequently limited especially in regions with high biodiversity such as the Neotropics. The bat genus Molossus is a typical example of this, with morphologically similar species often occurring in sympatry. We used a multi-method approach based on molecular, morphometric and acoustic information collected from 962 individuals of Molossus bondae, M. coibensis, and M. molossus captured in Panama. We distinguished M. bondae based on size and pelage coloration. We identified two robust species clusters composed of M. molossus and M. coibensis based on 18 microsatellite markers but also on a more stringently determined set of four markers. Phylogenetic reconstructions using the mitochondrial gene co1 (DNA barcode) were used to diagnose these microsatellite clusters as M. molossus and M. coibensis. To differentiate species, morphological information was only reliable when forearm length and body mass were combined in a linear discriminant function (95.9% correctly identified individuals). When looking in more detail at M. molossus and M. coibensis, only four out of 13 wing parameters were informative for species differentiation, with M. coibensis showing lower values for hand wing area and hand wing length and higher values for wing loading. Acoustic recordings after release required categorization of calls into types, yielding only two informative subsets: approach calls and two-toned search calls. Our data emphasizes the importance of combining morphological traits and independent genetic data to inform the best choice and combination of discriminatory information used in the field. Because parameters can vary geographically, the multi-method approach may need to be adjusted to local species assemblies and populations to be entirely informative.

Phylogeny of Molossidae Gervais (Mammalia: Chiroptera) inferred by morphological data

Molossidae is a large (roughly 100 species) pantropically distributed clade of swift aerially insectivorous bats for which the phylogeny remains relatively unknown and little studied compared with other speciose groups of bats. We investigated phylogenetic relationships among 62 species, representing all extant molossid genera and most of the subgenera, using 102 morphological characters from the skull, dentition, postcrania, external morphology, tongue, and penis, based on direct observation and literature reports. Both parsimony and Bayesian analyses were used in phylogenetic reconstruction. Our analysis supports two main clades of molossids, both of which mingle Old World and New World taxa. One clade is comprised of Mormopterus,Platymops, Sauromys, Neoplatymops, Molossops, Cynomops, Cheiromeles, Molossus, and Promops. The other clade includes Tadarida, Otomops, Nyctinomops, Eumops, Chaerephon, and Mops. The position of Myopterus with respect to these two groups is unclear. As in other recent analyses, we find that several genera do not appear to be monophyletic (e.g. Tadarida, Chaerephon, and Molossops sensu lato). We recommend that the subgenera of Molossops sensu lato and Austronomus be recognized at the generic level. We conclude that much more data are needed to investigate lower level problems (generic monophyly and relationships within genera) and to resolve the higher-level branching pattern of the family.

Driving factors for the evolution of species-specific echolocation call design in new world free-tailed bats (molossidae)

Phylogeny, ecology, and sensorial constraints are thought to be the most important factors influencing echolocation call design in bats. The Molossidae is a diverse bat family with a majority of species restricted to tropical and subtropical regions. Most molossids are specialized to forage for insects in open space, and thus share similar navigational challenges. We use an unprecedented dataset on the echolocation calls of 8 genera and 18 species of New World molossids to explore how habitat, phylogenetic relatedness, body mass, and prey perception contribute to echolocation call design. Our results confirm that, with the exception of the genus Molossops, echolocation calls of these bats show a typical design for open space foraging. Two lines of evidence point to echolocation call structure of molossids reflecting phylogenetic relatedness. First, such structure is significantly more similar within than among genera. Second, except for allometric scaling, such structure is nearly the same in congeneric species. Despite contrasting body masses, 12 of 18 species call within a relatively narrow frequency range of 20 to 35 kHz, a finding that we explain by using a modeling approach whose results suggest this frequency range to be an adaptation optimizing prey perception in open space. To conclude, we argue that the high variability in echolocation call design of molossids is an advanced evolutionary trait allowing the flexible adjustment of echolocation systems to various sensorial challenges, while conserving sender identity for social communication. Unraveling evolutionary drivers for echolocation call design in bats has so far been hampered by the lack of adequate model organisms sharing a phylogenetic origin and facing similar sensorial challenges. We thus believe that knowledge of the echolocation call diversity of New World molossid bats may prove to be landmark to understand the evolution and functionality of species-specific signal design in bats.

A molecular and morphological investigation of species boundaries and phylogenetic relationships in Australian free-tailed bats Mormopterus (Chiroptera : Molossidae)

The taxonomic uncertainty surrounding several prominent genera of Australian microbat has been a long-standing impediment to research and conservation efforts on these groups. The free-tail bat genus Mormopterus is perhaps the most significant example, with a long history of acknowledged species-level confusion. This study uses a combined molecular and morphological approach to conduct a comprehensive assessment of species and subgeneric boundaries, between-species phylogenetic affinities and within-species phylogeographic structure in Australian members of Mormopterus. Phylogenetic analyses based on 759 base pairs of the NADH Dehydrogenase subunit 2 mitochondrial gene were concordant with species boundaries delineated using an expanded allozyme dataset and by phallic morphology, and also revealed strong phylogeographic structure within two species. The levels of divergence evident in the molecular and morphological analyses led us to recognise three subgenera within Australia: Micronomus, Setirostris subgen. nov. and Ozimops subgen. nov. Within Ozimops we recognise seven Australian species, three of which are new, and none are conspecific with Indo-Papuan species. The family Molossidae now comprises eleven species across three subgenera in Australia, making it the continent’s second most speciose family of bats.

Evolutionary origins of ultrasonic hearing and laryngeal echolocation in bats inferred from morphological analyses of the inner ear

Introduction

Many mammals have evolved highly adapted hearing associated with ecological specialisation. Of these, bats possess the widest frequency range of vocalisations and associated hearing sensitivities, with frequencies of above 200 kHz in some lineages that use laryngeal echolocation. High frequency hearing in bats appears to have evolved via structural modifications of the inner ear, however, studying these minute features presents considerable challenges and hitherto few such attempts have been made. To understand these adaptations more fully, as well as gain insights into the evolutionary origins of ultrasonic hearing and echolocation in bats, we undertook micro-computed tomography (μCT) scans of the cochleae of representative bat species from 16 families, encompassing their broad range of ecological diversity. To characterise cochlear gross morphology, we measured the relative basilar membrane length and number of turns, and compared these values between echolocating and non-echolocating bats, as well as other mammals.

Results

We found that hearing and echolocation call frequencies in bats correlated with both measures of cochlear morphology. In particular, relative basilar membrane length was typically longer in echolocating species, and also correlated positively with the number of cochlear turns. Ancestral reconstructions of these parameters suggested that the common ancestor of all extant bats was probably capable of ultrasonic hearing; however, we also found evidence of a significant decrease in the rate of morphological evolution of the basilar membrane in multiple ancestral branches within the Yangochiroptera suborder. Within the echolocating Yinpterochiroptera, there was some evidence of an increase in the rate of basilar membrane evolution in some tips of the tree, possibly associated with reported shifts in call frequency associated with recent speciation events.

Conclusions

The two main groups of echolocating bat were found to display highly variable inner ear morphologies. Ancestral reconstructions and rate shift analyses of ear morphology point to a complex evolutionary history, with the former supporting ultrasonic hearing in the common bat ancestor but the latter suggesting that morphological changes associated with echolocation might have occurred later. These findings are consistent with theories that sophisticated laryngeal echolocation, as seen in modern lineages, evolved following the divergence of the two main suborders.

White-striped freetail bat in Tasmania – resident, vagrant or climate change migrant?

The white-striped freetail bat (Austronomus australis) is distributed throughout mainland Australia, but historically has not been known from the island of Tasmania, off south-eastern mainland Australia. Between 2009 and 2012, echolocation calls identified as those of A. australis were recorded in Tasmania during bat call surveys. There are three hypotheses that could explain the discovery of this species in Tasmania: that A. australis is a previously undetected resident; it is a vagrant; or it is undergoing a southwards range expansion or shift. Based on the limited evidence available, including this species’ long-range flight capabilities (including over open water out to sea), I suggest that this species is a periodic vagrant to Tasmania and that monitoring is necessary to identify whether this species is undergoing a southwards range extension into Tasmania.