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

Southern Africa's Great Escarpment as an amphitheater of climate-driven diversification and a buffer against future climate change in bats

Hosting 1460 plant and 126 vertebrate endemic species, the Great Escarpment (hereafter, Escarpment) forms a semi-circular "amphitheater" of mountains girdling southern Africa from arid west to temperate east. Since arid and temperate biota are usually studied separately, earlier studies overlooked the biogeographical importance of the Escarpment as a whole. Bats disperse more widely than other mammalian taxa, with related species and intraspecific lineages occupying both arid and temperate highlands of the Escarpment, providing an excellent model to address this knowledge gap. We investigated patterns of speciation and micro-endemism from modeled past, present, and future distributions in six clades of southern African bats from three families (Rhinolophidae, Cistugidae, and Vespertilionidae) having different crown ages (Pleistocene to Miocene) and biome affiliations (temperate to arid). We estimated mtDNA relaxed clock dates of key divergence events across the six clades in relation both to biogeographical features and patterns of phenotypic variation in crania, bacula and echolocation calls. In horseshoe bats (Rhinolophidae), both the western and eastern "arms" of the Escarpment have facilitated dispersals from the Afrotropics into southern Africa. Pleistocene and pre-Pleistocene "species pumps" and temperate refugia explained observed patterns of speciation, intraspecific divergence and, in two cases, mtDNA introgression. The Maloti-Drakensberg is a center of micro-endemism for bats, housing three newly described or undescribed species. Vicariance across biogeographic barriers gave rise to 29 micro-endemic species and intraspecific lineages whose distributions were congruent with those identified in other phytogeographic and zoogeographic studies. Although Köppen-Geiger climate models predict a widespread replacement of current temperate ecosystems in southern Africa by tropical or arid ecosystems by 2070-2100, future climate Maxent models for 13 bat species (all but one of those analyzed above) showed minimal range changes in temperate species from the eastern Escarpment by 2070, possibly due to the buffering effect of mountains to climate change.

Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri)

Studying hybrid zones that form between morphologically cryptic taxa offers valuable insights into the mechanisms of cryptic speciation and the evolution of reproductive barriers. Although hybrid zones have long been the focus of evolutionary studies, the awareness of cryptic hybrid zones increased recently due to rapidly growing evidence of biological diversity lacking obvious phenotypic differentiation. The characterization of cryptic hybrid zones with genome-wide analysis is in its early stages and offers new perspectives for studying population admixture and thus the impact of gene flow. In this study, we investigate the population genomics of the Myotis nattereri complex in one of its secondary contact zones, where a putative hybrid zone is formed between two of its cryptic lineages. By utilizing a whole-genome shotgun sequencing approach, we aim to characterize this cryptic hybrid zone in detail. Demographic analysis suggests that the cryptic lineages diverged during the Pliocene, c. 3.6 million years ago. Despite this ancient separation, the populations in the contact zone exhibit mitochondrial introgression and a considerable amount of mixing in nuclear genomes. The genomic structure of the populations corresponds to geographic locations and the genomic admixture changes along a geographic gradient. These findings suggest that there is no effective hybridization barrier between both lineages, nevertheless, their population structure is shaped by dispersal barriers. Our findings highlight how such deeply diverged cryptic lineages can still readily hybridize in secondary contact.

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.

Calibrated microphone array recordings reveal that a gleaning bat emits low-intensity echolocation calls even in open-space habitat

Echolocating bats use ultrasound for orientation and prey capture in darkness. Ultrasound is strongly attenuated in air. Consequently, aerial-hawking bats generally emit very intense echolocation calls to maximize detection range. However, call levels vary more than tenfold (>20 dB) between species and are tightly linked to the foraging strategy. The brown long-eared bat (Plecotus auritus) is a primarily gleaning, low-amplitude species that may occasionally hawk airborne prey. We used state-of-the-art calibrated acoustic 3D-localization and automated call analysis to measure P. auritus' source levels. Plecotus auritus emits echolocation calls of low amplitude (92 dB rmsSPL re. 20 µPa at 10 cm) even while flying in open-space. While P. auritus thus probably benefits from delayed evasive manoeuvres of eared insects, we propose that low-amplitude echolocation did not evolve as an adaptive countermeasure, but is limited by morphological constraints.

Increasing species richness along elevational gradients is associated with niche packing in bat assemblages

The change in species richness along elevational gradients is a well-known pattern in nature. Niche theory predicts that increasing species richness in assemblages can either lead to denser packing of niche space ('niche packing') or an expansion into its novel regions ('niche expansion'). Traditionally, these scenarios have been studied using functional traits but stable isotopes provide advantages such as identifying the degree of resource specialisation, or niche partitioning among functionally similar species. In this study, we evaluate the relevance of niche packing versus niche expansion by investigating stable carbon and nitrogen isotopic niche width and overlap among 23 bat species from six functional groups across a 1500 m elevational gradient in the Himalaya. Our results suggest that an increase in species richness in the low elevation is accompanied by small niche width with high overlap, whereas the high elevation assemblage shows large niche width with low overlap among functional group members. At the functional group level, edge-space foraging, trawling, and active gleaning bats have the highest niche width while passive gleaning bats that are only found in high elevations are isotopic specialists showing low overlap with other groups. Edge and open-space foraging bats showed idiosyncratic changes in niche width across elevations. We also find that the niches of rhinolophid bats overlap with edge-space and open-space foraging bats despite their unique functional traits. These results support the idea that at low elevations high species richness is associated with niche packing while at high elevations strong niche partitioning prevails in dynamic and resource-poor environments. We conclude that although high elevation animal assemblages are often 'functionally underdispersed', that is show homogenous functional traits, our approach based on stable isotopes demonstrates niche partitioning among such functionally similar species.

Systematics of the New World bats Eptesicus and Histiotus suggest trans-marine dispersal followed by Neotropical cryptic diversification

Biodiversity can be boosted by colonization of new habitats such as remote islands and separated continents. Molecular studies have suggested that recently evolved organisms probably colonized already separated continents by dispersal, either via land bridge connections or crossing the ocean. Here we test the on-land and trans-marine dispersal hypotheses by evaluating possibilities of colonization routes over the Bering land bridge and across the Atlantic Ocean in the cosmopolitan bat genus Eptesicus (Chiroptera, Vespertilionidae). Previous molecular studies have found New World Eptesicus more closely related to Histiotus, a Neotropical endemic lineage with enlarged ears, than to Old World Eptesicus. However, phylogenetic relationships within the New World group remained unresolved and their evolutionary history was unclear. Here we studied the systematics of New World Eptesicus and Histiotus using extensive taxonomic and geographic sampling, and genomic data from thousands of ultra-conserved elements (UCEs). We estimated phylogenetic trees using concatenation and multispecies coalescent. All analyses supported four major New World clades and a novel topology where E. fuscus and Histiotus are sister clades that together diverged from two sister clades of Neotropical Eptesicus. Intra-clade divergence suggested cryptic diversity that has been concealed by morphological features, especially in the Neotropics where taxonomic re-evaluations are warranted. Molecular dating estimated that Old World and New World clades diverged around 17 million years ago followed by radiation of major New World clades in the mid-Miocene, when climatic changes might have facilitated global dispersal and radiation events. Biogeographic ancestral reconstruction supported the Neotropical origin of the New World clades, suggesting a trans-Atlantic colonization route from North Africa to the northern Neotropics. We highlight that trans-marine dispersal may be more prevalent than currently acknowledged and may be an important first step to global biodiversification.

Do the evolutionary interactions between moths and bats promote niche partitioning between bats and birds?

Ecological theory suggests that the coexistence of species is promoted by the partitioning of available resources, as in dietary niche partitioning where predators partition prey. Yet, the mechanisms underlying dietary niche partitioning are not always clear. We used fecal DNA metabarcoding to investigate the diets of seven nocturnal insectivorous bird and bat species. Low diet overlap (2%-22%) supported resource partitioning among all species. Differences in diet corresponded with species identity, prey detection method, and foraging behavior of predators. Insects with ultrasonic hearing capabilities were consumed significantly more often by birds than bats, consistent with an evolved avoidance of echolocating strategies. In turn, bats consumed a greater proportion of noneared insects such as spruce budworms. Overall, our results suggest that evolutionary interactions among bats and moths translate to dietary niche partitioning and coexistence among bats and nocturnal birds.

Inter- and intraspecific variation in the Artibeus species complex demonstrates size and shape partitioning among species

Neotropical leaf-nosed bats (family Phyllostomidae) are one of the most diverse mammalian families and Artibeus spp. is one of the most speciose phyllostomid genera. In spite of their species diversity, previous work on Artibeus crania using linear morphometrics has uncovered limited interspecific variation. This dearth of shape variation suggests that differences in cranial morphology are not contributing to niche partitioning across species, many of which are often found in sympatry. Using two-dimensional geometric morphometric methods on crania from eleven species from the Artibeus species complex, the current study demonstrates substantial cranial interspecific variation, sexual size and shape dimorphism, and intraspecific geographic variation. The majority of species were shown to have a unique size and shape, which suggests that each species may be taking advantage of slightly different ecological resources. Further, both sexual size and shape dimorphism were significant in the Artibeus species complex. Male and female Artibeus are known to have sex specific foraging strategies, with males eating near their roosts and females feeding further from their roosts. The presence of cranial sexual dimorphism in the Artibeus species complex, combined with previous work showing that different fruit size and hardness is correlated with different cranial shapes in phyllostomids, indicates that the males and females may be utilizing different food resources, leading to divergent cranial morphotypes. Additional field studies will be required to confirm this emergent hypothesis. Finally, significant geographical shape variation was found in a large intraspecific sample of Artibeus lituratus crania. However, this variation was not correlated with latitude and instead may be linked to local environmental factors. Additional work on ecology and behavior in the Artibeus species complex underlying the morphological variation uncovered in this study will allow for a better understanding of how the group has reached its present diversity.

Comment on “Population genetics reveal Myotis keenii (Keen’s myotis) and Myotis evotis (long-eared myotis) to be a single species”

Genetic exchange and hybridization appear common among the western long-eared bats from North America. Multiple sources of evidence indicate that lineages within this group are evolving independently, despite genetic exchange. However, evidence of gene flow raises questions about the species-level status of some lineages. C.L. Lausen et al. (2019. Can. J. Zool. 97(3): 267–279) proposed that Myotis evotis (H. Allen, 1864) (long-eared myotis) and Myotis keenii (Merriam, 1895) (Keen’s myotis) are one species, not two. This conclusion is based on analyses of cytochrome b and microsatellite data suggesting gene flow between these taxa. Microsatellites are not reliable markers for identifying species because homoplasy can be a major confounding factor, which appears to be true in this case. We reanalyzed the dataset of C.L. Lausen et al. (2019) and show that it is not reliable to distinguish between gene flow or homoplasy, and that these data do not support the conclusion that M. evotis and M. keenii represent a single species. Previous morphological and genomic studies indicate that these are separate species despite previous genetic exchange between them. Failing to recognize that gene flow can occur between independently evolving lineages is counterproductive for conservation because it can lead to neglect of important independent lineages, and likewise failing to use proper tools to delimit species is counterproductive to efforts to quantify biodiversity and design conservation strategies.

Phylogenetics of mud snakes (Squamata: Serpentes: Homalopsidae): A paradox of both undescribed diversity and taxonomic inflation

Mud snakes (Serpentes: Homalopsidae) are a family of 55 described, mainly aquatic, species primarily distributed throughout mainland Southeast Asia and the Indo-Australian Archipelago. Although they have been the focus of prior research, the basic relationships amongst genera and species remain poorly known. We used a combined mitochondrial and nuclear gene dataset to infer their phylogenetic relationships, using the highest levels of taxon and geographic sampling for any homalopsid phylogeny to date (62% generic and 62% species coverage; 140 individuals). Our results recover two reciprocally monophyletic groups: the fangless Brachyorrhos and its sister clade comprised of all rear-fanged homalopsids. Most genera and interspecific relationships were monophyletic and strongly supported, but intergeneric relationships and intraspecific population structure lack support. We find evidence of both undescribed diversity as well as cases of taxonomic inflation within several species. Tree-based species delimitation approaches (mPTP) support potential new candidate species as distinct from their conspecifics and also suggest that many named taxa may not be distinct species. Divergence date estimation and lineage-through-time analyses indicate lower levels of speciation in the Eocene, with a subsequent burst in diversification in the Miocene. Homalopsids may have diversified most rapidly during the Pliocene and Pleistocene, possibly in relation to tectonic shifts and sea-level fluctuations that took place in Sundaland and the Sahul Shelf. Our analyses provide new insights on homalopsid taxonomy, a baseline phylogeny for the family, and further biogeographic implications demonstrating how dynamic tectonics and Quaternary sea level changes may have shaped a widespread, diverse family of snakes.

Molecular and morphological revision of small Myotinae from the Himalayas shed new light on the poorly known genus Submyotodon (Chiroptera: Vespertilionidae)

The systematics status of the constituent species of the M. mystacinus morphogroup in the Himalayan region has long been marred by uncertainty. Lack of integrative studies combining morphological and genetic data from specimens recently collected in this region has hampered our understanding of cryptic variations in this complex taxonomic group. To address this issue, new material from the Himalayan region of India and Nepal was obtained and vouchered specimens in the holdings of various museums were also re-examined. As comparative material, a large series of relevant specimens from South and Southeast Asia were also included in this revision. Using a combination of multivariate analysis of craniodental characters and molecular reconstructions, we critically evaluated the systematic position of the small Myotinae in the Himalayas. We establish that M. nipalensis forms a very distinct lineage (which also includes the recently described M. annatessae) and refute previous taxonomic suggestions that it is related to M. davidii. Our study also conclusively proved the common occurrence of the poorly known genus Submyotodon in the Himalayan region (Afghanistan, Pakistan, India, Nepal and China) and evidenced species-level divergences within that genus. Submyotodon species share nyctalodont or semi-nyctalodont lower molar configuration with few other small and unrelated Myotinae from Asia suggesting that these unusual dental characters are homoplasious in this subfamily. We also noticed a very confused taxonomic situation associated with many DNA sequences of Asian Myotis deposited in public repositories and call for possibilities of better data curation.

Phylogeny and foraging behaviour shape modular morphological variation in bat humeri

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

Heterogeneous relationships between rates of speciation and body size evolution across vertebrate clades

Several theories predict that rates of phenotypic evolution should be related to the rate at which new lineages arise. However, drawing general conclusions regarding the coupling between these fundamental evolutionary rates has been difficult due to the inconsistent nature of previous results combined with uncertainty over the most appropriate methodology with which to investigate such relationships. Here we propose and compare the performance of several different approaches for testing associations between lineage-specific rates of speciation and phenotypic evolution using phylogenetic data. We then use the best-performing method to test relationships between rates of speciation and body size evolution in five major vertebrate clades (amphibians, birds, mammals, ray-finned fish and squamate reptiles) at two phylogenetic scales. Our results provide support for the long-standing view that rates of speciation and morphological evolution are generally positively related at broad macroevolutionary scales, but they also reveal a substantial degree of heterogeneity in the strength and direction of these associations at finer scales across the vertebrate tree of life.

Patterns of mtDNA introgression suggest population replacement in Palaearctic whiskered bat species

Secondary contacts can play a major role in the evolutionary histories of species. Various taxa diverge in allopatry and later on come into secondary contact during range expansions. When they meet, their interactions and the extent of gene flow depend on the level of their ecological differentiation and the strength of their reproductive isolation. In this study, we present the multilocus phylogeography of two cryptic whiskered bat species, Myotis mystacinus and M. davidii, with a particular focus on their putative sympatric zone. Our findings suggest that M. mystacinus and M. davidii evolved in allopatry and came into secondary contact during range expansions. Individuals in the area of secondary contact, in Anatolia and the Balkans, have discordant population assignments based on the mitochondrial and the nuclear datasets. These observed patterns suggest that the local M. mystacinus populations hybridized with expanding M. davidii populations, which resulted in mitochondrial introgression from the former. In the introgression area, M. mystacinus individuals with concordant nuclear and mitochondrial genotypes were identified in relatively few locations, suggesting that the indigenous populations might have been largely replaced by invading M. davidii. Changing environmental conditions coupled with ecological competition is the likely reason for this replacement. Our study presents one possible example of a historical population replacement that was captured in phylogeographic patterns.