Distinct Genes with Similar Functions Underlie Convergent Evolution in Myotis Bat Ecomorphs.

Convergence offers an opportunity to explore to what extent evolution can be predictable when genomic compositions and environmental triggers are similar. Here we present an emergent model system to study convergent evolution in nature in a mammalian group, the bat genus Myotis. Three foraging strategies - gleaning, trawling, and aerial hawking, each characterized by different sets of phenotypic features - have evolved independently multiple times in different biogeographic regions in isolation for millions of years. To investigate the genomic basis of convergence and explore the functional genomic changes linked to ecomorphological convergence, we sequenced and annotated 17 new genomes and screened 16,426 genes for positive selection and associations between relative evolutionary rates and foraging strategies across 30 bat species representing all Myotis ecomorphs across geographic regions as well as among sister groups. We identify genomic changes that describe both phylogenetic and ecomorphological trends. We infer that colonization of new environments may have first required changes in genes linked to hearing sensory perception, followed by changes linked to fecundity and development, metabolism of carbohydrates, and heme degradation. These changes may be linked to prey acquisition and digestion and match phylogenetic trends. Our findings also suggest that the repeated evolution of ecomorphs does not always involve changes in the same genes but rather in genes with the same molecular functions such as developmental and cellular processes.

Food for everyone: Differential feeding habits of cryptic bat species inferred from DNA metabarcoding.

Ecological theory postulates that niches of co-occurring species must differ along some ecological dimensions in order to allow their stable coexistence. Yet, many biological systems challenge this competitive exclusion principle. Insectivorous bats from the Northern Hemisphere typically form local assemblages of multiple species sharing highly similar functional traits and pertaining to identical feeding guilds. Although their trophic niche can be accessed with unprecedented details using genetic identification of prey, the underlying mechanisms of resource partitioning remain vastly unexplored. Here, we studied the differential diet of three closely-related bat species of the genus Plecotus in sympatry and throughout their entire breeding season using DNA metabarcoding. Even at such a small geographic scale, we identified strong seasonal and spatial variation of their diet composition at both intra- and interspecific levels. Indeed, while the different bats fed on a distinct array of prey during spring, they showed higher trophic niche overlap during summer and fall, when all three species switched their hunting behaviour to feed on few temporarily abundant moths. By recovering 19 ecological traits for over 600 prey species, we further inferred that each bat species used different feeding grounds and hunting techniques, suggesting that niche partitioning was primarily habitat-driven. The two most-closely related bat species exhibited very distinct foraging habitat preferences, while the third, more distantly-related species was more generalist. These results highlight the need of temporally comprehensive samples to fully understand species coexistence, and that valuable information can be derived from the taxonomic identity of prey obtained by metabarcoding approaches.

Evolution of immune chemoreceptors into sensors of the outside world.

Changes in gene expression patterns represent an essential source of evolutionary innovation. A striking case of neofunctionalization is the acquisition of neuronal specificity by immune formyl peptide receptors (Fprs). In mammals, Fprs are expressed by immune cells, where they detect pathogenic and inflammatory chemical cues. In rodents, these receptors are also expressed by sensory neurons of the vomeronasal organ, an olfactory structure mediating innate avoidance behaviors. Here we show that two gene shuffling events led to two independent acquisitions of neuronal specificity by Fprs. The first event targeted the promoter of a V1R receptor gene. This was followed some 30 million years later by a second genomic accident targeting the promoter of a V2R gene. Finally, we show that expression of a vomeronasal Fpr can reverse back to the immune system under inflammatory conditions via the production of an intergenic transcript linking neuronal and immune Fpr genes. Thus, three hijackings of regulatory elements are sufficient to explain all aspects of the complex expression patterns acquired by a receptor family that switched from sensing pathogens inside the organism to sensing the outside world through the nose.

The genome sequence of Daubenton's bat, Myotis daubentonii (Kuhl, 1817).

We present a genome assembly from an individual male Myotis daubentonii (Daubenton's bat; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence is 2,127.8 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.34 kilobases in length.

Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation.

The emergence of COVID-19 and severe acute respiratory syndrome (SARS) has prioritized understanding bats' viral tolerance. Myotis bats are exceptionally species rich and have evolved viral tolerance. They also exhibit swarming, a cryptic behavior where large, multi-species assemblages gather for mating, which has been hypothesized to promote interspecific hybridization. To resolve the coevolution of genome architecture and their unusual antiviral tolerance, we undertook a phylogenomic analysis of 60 Old World Myotis genomes. We demonstrate an extensive history of introgressive hybridization that has replaced the species phylogeny across 17%-93% of the genome except for pericentromeric regions of macrochromosomes. Introgression tracts were enriched on microchromosome regions containing key antiviral pathway genes overexpressed during viral challenge experiments. Together, these results suggest that the unusual Myotis karyotype may have evolved to selectively position immune-related genes in high recombining genomic regions prone to introgression of divergent alleles, including a diversity of interleukin loci responsible for the release of pro-inflammatory cytokines.

Molecular phylogenetic reconstructions identify East Asia as the cradle for the evolution of the cosmopolitan genus Myotis (Mammalia, Chiroptera).

Sequences of the mitochondrial cytochrome b (1140 bp) and nuclear Rag 2 (1148 bp) genes were used to assess the evolutionary history of the cosmopolitan bat genus Myotis, based on a worldwide sampling of over 88 named species plus 7 species with uncertain nomenclature. Phylogenetic reconstructions of this comprehensive taxon sampling show that most radiation of species occurred independently within each biogeographic region. Our molecular study supports an early divergence of species from the New World, where all Nearctic and Neotropical species plus a lineage from the Palaearctic constitute a monophyletic clade, sister to the remaining Old World taxa. The major Old World clade includes all remaining Eurasian taxa, most Oriental species, one Oceanian, and all Ethiopian species. Another lineage, including M. latirostris from Taiwan, appears at the base of these two major biogeographic clades and, because it bears nyctalodont molars, could be considered as a distinct genus. However, this molar configuration is also found in crown-group species, indicating that these dental characters are variable in the genus Myotis and may confound interpretation of the fossil record. Molecular datings suggest an origin of all recent Myotis in the early Miocene (about 21MYA with 95% highest posterior density interval 23-20MYA). This period was characterized by a global climatic cooling that reduced the availability of tropical habitats and favoured the development of more temperate vegetation. This sharp climatic change might have triggered the evolution of Myotis in the Northern continents, because Myotis ancestors seem to have been well adapted and successful in such temperate habitats. Ancestral area reconstructions based on the molecular phylogeny suggest that the eastern portion of the Asian continent was an important center of origin for the early diversification of all Myotis lineages, and involved relatively few subsequent transcontinental range expansions.

The genome sequence of the Soprano Pipistrelle, Pipistrellus pygmaeus (Leach, 1825).

We present a genome assembly from an individual male Pipistrellus pygmaeus (the Soprano Pipistrelle; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence is 1,895.1 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.18 kilobases in length.

Biogeography of Old World emballonurine bats (Chiroptera: Emballonuridae) inferred with mitochondrial and nuclear DNA.

Extant bats of the genus Emballonura have a trans-Indian Ocean distribution, with two endemic species restricted to Madagascar, and eight species occurring in mainland southeast Asia and islands in the western Pacific Ocean. Ancestral Emballonura may have been more widespread on continental areas, but no fossil identified to this genus is known from the Old World. Emballonura belongs to the subfamily Emballonurinae, which occurs in the New and Old World. Relationships of all Old World genera of this subfamily, including Emballonura and members of the genera Coleura from Africa and western Indian Ocean islands and Mosia nigrescens from the western Pacific region, are previously unresolved. Using 1833 bp of nuclear and mitochondrial genes, we reconstructed the phylogenetic history of Old World emballonurine bats. We estimated that these lineages diverged around 30 million years ago into two monophyletic sister groups, one represented by the two taxa of Malagasy Emballonura, Coleura and possibly Mosia, and the other by a radiation of Indo-Pacific Emballonura, hence, rendering the genus Emballonura paraphyletic. The fossil record combined with these phylogenetic relationships suggest at least one long-distance dispersal event across the Indian Ocean, presumably of African origin, giving rise to all Indo-Pacific Emballonura species (and possibly Mosia). Cladogenesis of the extant Malagasy taxa took place during the Quaternary giving rise to two vicariant species, E. atrata in the humid east and E. tiavato in the dry west.

Out of Southeast Asia: A new species of thick-thumbed bat (Chiroptera: Vespertilionidae: Glischropus) from Meghalaya, north-eastern India.

Thick-thumbed bats of the genus Glischropus are currently composed of four recognized species from Southeast Asia, two of which were described in recent times. Among these species, G. aquilus is endemic to Sumatra, G. javanus is restricted to western Java, whereas G. bucephalus is widely distributed north to the Isthmus of Kra and G. tylopus is widespread south to this zoogeographic boundary. Two recently collected Glischropus specimens from Meghalaya state in north-eastern India extend the known distribution range of the genus westward into South Asia by ca. 1000 km. Morphological examination of these specimens and comparison with all known species in this genus revealed marked differences in colouration, dental characters and bacular traits. We therefore describe the Meghalaya specimens as a new species. The discovery of the new species from a forest patch adjacent to Nongkhyllem Wildlife Sanctuary from where another specialized bamboo-dwelling species (Eudiscopus denticulus) was reported recently also underscore the importance of the area from a conservation point of view.

Citizen science and online data: Opportunities and challenges for snake ecology and action against snakebite.

The secretive behavior and life history of snakes makes studying their biology, distribution, and the epidemiology of venomous snakebite challenging. One of the most useful, most versatile, and easiest to collect types of biological data are photographs, particularly those that are connected with geographic location and date-time metadata. Photos verify occurrence records, provide data on phenotypes and ecology, and are often used to illustrate new species descriptions, field guides and identification keys, as well as in training humans and computer vision algorithms to identify snakes. We scoured eleven online and two offline sources of snake photos in an attempt to collect as many photos of as many snake species as possible, and attempt to explain some of the inter-species variation in photograph quantity among global regions and taxonomic groups, and with regard to medical importance, human population density, and range size. We collected a total of 725,565 photos-between 1 and 48,696 photos of 3098 of the world's 3879 snake species (79.9%), leaving 781 "most wanted" species with no photos (20.1% of all currently-described species as of the December 2020 release of The Reptile Database). We provide a list of most wanted species sortable by family, continent, authority, and medical importance, and encourage snake photographers worldwide to submit photos and associated metadata, particularly of "missing" species, to the most permanent and useful online archives: The Reptile Database, iNaturalist, and HerpMapper.

Philippine bats of the genus Kerivoula (Chiroptera: Vespertilionidae): Overview and assessment of variation in K. pellucida and K. whiteheadi.

Bats of the genus Kerivoula (Mammalia, Chiroptera) are widespread in the Philippines with four reported species, but have been poorly known due to a paucity of specimens. We provide the first molecular phylogeny for Philippine Kerivoula, which supports the existence of four distinct clades that we treat as species (K. hardwickii, K. papillosa, K. pellucida, and K. whiteheadi); these four overlap broadly geographically. Each of these may be recognized on the basis of cytochrome b sequences and external and craniodental morphology. Detailed examination of K. pellucida shows little geographic differentiation within the Philippines, but they differ subtly from those on the Sunda Shelf. We consider K. whiteheadi to be composed of four recognizable clades, each restricted to a geographic region within the Philippines. We consider K. bicolor, from peninsular Thailand, and K. pusilla, from Borneo, to be distinct from K. whiteheadi. Our data indicate the presence of two species within the Philippines currently lumped as K. hardwickii; further study of these is needed. A calibrated phylogeny suggests that Kerivoula began arriving in the Philippines about 10 MYA, with each of the four current lineages arriving independently.

Molecular cophylogenetic relationships between European bats and their ectoparasitic mites (Acari, Spinturnicidae).

Cospeciation between host-parasite species is generally thought to result in mirror-image congruent phylogenies. Incongruence can be explained by mechanisms such as host switching, duplication, failure to speciate and sorting events. To investigate the level of association in the host-parasite relationship between Spinturnicid mites and their bat hosts, we constructed the phylogenetic tree of the genus Spinturnix (Acari, Mesostigmata) and compared it to the host phylogeny. We sequenced 938bp of the mitochondrial 16S rDNA and Cytochrome Oxydase subunit I (COI) genes among eleven morphospecies of Spinturnix collected on 20 European Vespertilionid and Rhinolophid bat species. Phylogenetic reconstruction of hosts and parasites showed statistical evidence for cospeciation and suggested that their evolutionary history involved also failure to speciate events and host switches. The latter seem to be mainly promoted by similar roosting habits of the host. As currently understood, host associations of Spinturnicid mites likely results from a complex interaction between the phylogenetic history of the host and the behaviour and the ecology of both parasite and host.

Diversification rates have no effect on the convergent evolution of foraging strategies in the most speciose genus of bats, Myotis.

Adaptive radiations are defined as rapid diversification with phenotypic innovation led by colonization to new environments. Notably, adaptive radiations can occur in parallel when habitats with similar selective pressures are accessible promoting convergent adaptions. Although convergent evolution appears to be a common process, it is unclear what are the main drivers leading the reappearance of morphologies or ecological roles. We explore this question in Myotis bats, the only Chiropteran genus with a worldwide distribution. Three foraging strategies-gleaning, trawling, and aerial netting-repeatedly evolved in several regions of the world, each linked to characteristic morphologies recognized as ecomorphs. Phylogenomic, morphometric, and comparative approaches were adopted to investigate convergence of such foraging strategies and skull morphology as well as factors that explain diversification rates. Genomic and morphometric data were analyzed from ∼80% extant taxa. Results confirm that the ecomorphs evolved multiple times, with trawling evolving more often and foliage gleaning most recently. Skull morphology does not reflect common ancestry and evolves convergently with foraging strategy. Although diversification rates have been roughly constant across the genus, speciation rates are area-dependent and higher in taxa with temperate distributions. Results suggest that in this species-rich group of bats, first, stochastic processes have led divergence into multiple lineages. Then, natural selection in similar niches has promoted repeated adaptation of phenotypes and foraging strategies. Myotis bats are thus a remarkable case of ecomorphological convergence and an emerging model system for investigating the genomic basis of parallel adaptive radiation.

The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus.

Metabarcoding of feces has revolutionized the knowledge of animal diets by providing unprecedented resolution of consumed resources. However, it is still unclear how different methodological approaches influence the ecological conclusions that can be drawn from such data. Here, we propose a critical evaluation of several data treatments on the inferred diet of the bat Plecotus auritus using guano regularly collected from various colonies throughout the entire active season. First and unlike previous claims, our data indicates that DNA extracted from large amounts of fecal material issued from guano accumulates yield broader taxonomic diversity of prey than smaller numbers of pellets would do, provided that extraction buffer volumes are adapted to such increased amounts of material. Second, trophic niche analyses based on prey occurrence data uncover strong seasonality in the bat's diet and major differences among neighboring maternity colonies. Third, while the removal of rare prey items is not always warranted as it introduces biases affecting particularly samples with greater prey species richness. Fourth, examination of distinct taxonomic depths in diet analyses highlights different aspects of food consumption providing a better understanding of the consumer's diet. Finally, the biologically meaningful patterns recovered with presence-absence approaches are virtually lost when attempting to quantify prey consumed using relative read abundances. Even in an ideal situation where reference barcodes are available for most potential prey species, inferring realistic patterns of prey consumption remains relatively challenging. Although best practice in metabarcoding analyses will depend on the aims of the study, several previous methodological recommendations seem unwarranted for studying such diverse diets as that of brown long-eared bats.

The hidden side of invasions: massive introgression by local genes.

Despite hundreds of reports involving both plants and animals, the mechanisms underlying introgression remain obscure, even if some form of selection is frequently invoked. Introgression has repeatedly been reported in species that have recently colonized a new habitat, suggesting that demographic processes should be given more attention for understanding the mechanisms of introgression. Here we show by spatially explicit simulations that massive introgression of neutral genes takes place during the invasion of an occupied territory if interbreeding is not severely prevented between the invading and the local species. We also demonstrate that introgression occurs almost exclusively from the local to the invading species, especially for populations located far away from the source of the invasion, and this irrespective of the relative densities of the two species. This pattern is strongest at markers experiencing reduced gene flow, in keeping with the observation that organelle genes are often preferentially introgressed across species boundaries. A survey of the literature shows that a majority of published empirical studies of introgression during range expansions, in animals and in plants, follow the predictions of our model. Our results imply that speciation genes can be identified by comparing genomes of interfertile native and invading species pairs.

The biogeography of Miniopterus bats (Chiroptera: Miniopteridae) from the Comoro Archipelago inferred from mitochondrial DNA.

The endemic fauna of the Comoro Archipelago is composed of a mixture of taxa originating from Africa and Madagascar. Bats are the only native land dwelling mammals on this archipelago, but the biogeographical origins for the vast majority of species within this group are ambiguous. We report here genetic analyses based on two mitochondrial DNA markers to infer the origin of Comorian bats belonging to a reputed species complex of Miniopterus that is further distributed across Africa and Madagascar. Phylogenetic reconstructions show that east African M. minor are not closely related to the insular Miniopterus of Madagascar and the Comoros (Grande Comore and Anjouan). The latter cluster into two distinct, monophyletic clades (Clade 1 and Clade 2). Representatives of these clades occur sympatrically both on the Comoros and on Madagascar, and are distinguished by a large genetic distance (K2P: 9.9% for cytochrome b). No haplotypes are shared between any islands, suggesting the absence of contemporary gene flow. Populations of the widespread Clade 1 are furthermore characterized by a significant inter-island structure (Phi(CT) = 0.249), and by high haplotype and nucleotide diversities (h = 0.90-0.98, pi = 0.04-0.06). Demographic analyses of Clade 1 suggest secondary contact between two distinct phylogroups (Subclade 1 A and 1B) that reached Grande Comore and Anjouan, and a large, stable population with a long evolutionary history on Madagascar. These results and the current distribution of related lineages suggest that the Comoros were colonized independently at least two or three times by ancestors from Madagascar.

Italy as a major Ice Age refuge area for the bat Myotis myotis (Chiroptera: Vespertilionidae) in Europe.

The distribution of biota from the temperate regions changed considerably during the climatic fluctuations of the Quaternary. This is especially true for many bat species that depend on warm roosts to install their nursery colonies. Surveys of genetic variation among European bats have shown that the southern peninsulas (Iberia and the Balkans) harbour endemic diversity, but to date, no such surveys have been conducted in the third potential glacial refuge area, the Apennine peninsula. We report here the phylogeographical analysis of 115 greater mouse-eared bats (Myotis myotis) sampled throughout Italy, and show that 15 of the 18 different haplotypes found in the mitochondrial control region of these bats were unique to the Apennine peninsula. Colonies within this region also showed substantial genetic structure at both mitochondrial (Phi(ST) = 0.47, P < 0.001) and nuclear markers (F(ST) = 0.039, P < 0.001). Based on a comprehensive survey of 575 bats from Europe, these genetic markers further indicate that central Italian populations of M. myotis are more closely related to Greek samples from across the Adriatic Sea, than to other Italian bats. Mouse-eared bat populations from the Apennine peninsula thus represent a complex mixture of several endemic lineages, which evolved in situ, with others that colonized this region more recently along an Adriatic route. Our broad survey also confirms that the Alps represent a relatively impermeable barrier to gene flow for Apennine lineages, even for vagile animals such as bats. These results underline the conservation value of bats from this region and the need to include the Apennine peninsula in phylogeographical surveys in order to provide a more accurate view of the evolution of bats in Europe.

Biogeographic origin and radiation of the Old World crocidurine shrews (Mammalia: Soricidae) inferred from mitochondrial and nuclear genes.

The crocidurine shrews include the most speciose genus of mammals, Crocidura. The origin and evolution of their radiation is, however, poorly understood because of very scant fossil records and a rather conservative external morphology between species. Here, we use an alignment of 3560 base pairs of mitochondrial and nuclear DNA to generate a phylogenetic hypothesis for the evolution of Old World shrews of the subfamily Crocidurinae. These molecular data confirm the monophyly of the speciose African and Eurasian Crocidura, which also includes the fossorial, monotypic genus Diplomesodon. The phylogenetic reconstructions give further credit to a paraphyletic position of Suncus shrews, which are placed into at least two independent clades (one in Africa and sister to Sylvisorex and one in Eurasia), at the base of the Crocidura radiation. Therefore, we recommend restricting the genus Suncus to the Palaearctic and Oriental taxa, and to consider all the African Suncus as Sylvisorex. Using molecular dating and biogeographic reconstruction analyses, we suggest a Palaearctic-Oriental origin for Crocidura dating back to the Upper Miocene (6.8 million years ago) and several subsequent colonisations of the Afrotropical region by independent lineages of Crocidura.

Porous barriers? Assessment of gene flow within and among sympatric long-eared bat species.

Species are the basic units for measuring biodiversity and for comprehending biological interactions. Yet, their delineation is often contentious, especially in groups that are both diverse and phenotypically conservative. Three cryptic species of long-eared bats, Plecotus auritus, P. austriacus, and P. macrobullaris, co-occur over extensive areas of Western Europe. The latter is a fairly recent discovery, questioning the overall diversity of the entire Plecotus complex. Yet, high morphological and acoustic similarities compromise the reliable identification of long-eared bats in the field. We postulate that such extensive phenotypic overlap, along with the recurrent observation of morphologically intermediate individuals, may hide rampant interspecific hybridization. Based on a geographic sampling centered on areas of sympatry in the Alps and Corsica, we assessed the level of reproductive isolation of these three Plecotus species with mitochondrial and nuclear markers, looking at both inter- and intraspecific genetic population structuring. No sign of hybridization was detected between these three species that appear well separated biologically. Genetic structuring of populations, however, reflected different species-specific responses to environmental connectivity, that is, to the presence of orographic or sea barriers. While the Alpine range and the Ligurian Sea coincided with sharp genetic discontinuities in P. macrobullaris and P. austriacus, the more ubiquitous P. auritus showed no significant population structuration. There were clear phylogeographic discrepancies between microsatellite and mitochondrial markers at the intraspecific level, however, which challenges the reliance on simple barcoding approaches for the delineation of sound conservation units.

The taxonomic status of Myotis aelleni Baud, 1979 (Chiroptera, Vespertilionidae).

Myotis aelleni Baud, 1979 was described based on a large series from Chubut, Argentina, and is known only from the type locality and Río Negro, also in Argentina. According to the original description, M. aelleni is closest morphologically to M. chiloensis (Waterhouse, 1840), but can be distinguished based on the tricolored dorsal hairs and skull size and shape. The taxonomic status of M. aelleni has been questioned but the species is still treated as valid. Based on qualitative and quantitative analyses of the type series of M. aelleni, and series of M. chiloensis, including the neotype, we recognize M. aelleni as a junior synonym of M. chiloensis. M. aelleni and M. chiloensis have bicolor dorsal hairs and cannot be distinguished on the basis of the skull size and shape. After synonymy, M. chiloensis occur from Central Chile and western Argentina to central Patagonia and Tierra del Fuego archipelago. Twenty-one species of Myotis occur in South America, including Trinidad and Tobago.