Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations

A genomic hotspot of diversifying selection and structural change in the hoary bat (Lasiurus cinereus)

Background

Previous work found that numerous genes positively selected within the hoary bat (Lasiurus cinereus) lineage are physically clustered in regions of conserved synteny. Here I further validate and expand on those finding utilizing an updated L. cinereus genome assembly and additional bat species as well as other tetrapod outgroups.

Methods

A chromosome-level assembly was generated by chromatin-contact mapping and made available by DNAZoo (www.dnazoo.org). The genomic organization of orthologous genes was extracted from annotation data for multiple additional bat species as well as other tetrapod clades for which chromosome-level assemblies were available from the National Center for Biotechnology Information (NCBI). Tests of branch-specific positive selection were performed for L. cinereus using PAML as well as with the HyPhy package for comparison.

Results

Twelve genes exhibiting significant diversifying selection in the L. cinereus lineage were clustered within a 12-Mb genomic window; one of these (Trpc4) also exhibited diversifying selection in bats generally. Ten of the 12 genes are landmarks of two distinct blocks of ancient synteny that are not linked in other tetrapod clades. Bats are further distinguished by frequent structural rearrangements within these synteny blocks, which are rarely observed in other Tetrapoda. Patterns of gene order and orientation among bat taxa are incompatible with phylogeny as presently understood, implying parallel evolution or subsequent reversals. Inferences of positive selection were found to be robust to alternative phylogenetic topologies as well as a strong shift in background nucleotide composition in some taxa.

Discussion

This study confirms and further localizes a genomic hotspot of protein-coding divergence in the hoary bat, one that also exhibits an increased tempo of structural change in bats compared with other mammals. Most genes in the two synteny blocks have elevated expression in brain tissue in humans and model organisms, and genetic studies implicate the selected genes in cranial and neurological development, among other functions.

Multi-scale assessment of roost selection by 'ōpe'ape'a, the Hawaiian hoary bat (Lasiurus semotus)

The Hawaiian hoary bat (Lasiurus semotus; Chiroptera: Vespertilionidae), commonly and locally known as 'ōpe'ape'a, is a solitary, insectivorous, and foliage-roosting species distributed across a wide range of habitats in lowland and montane environments. The species, as with many others in the Hawaiian archipelago, are facing a suite of challenges due to habitat loss and degradation, introduced predators and pests, and climate change. An understanding of the roost requirements of foliage-roosting tree bats is critical to their conservation as these habitats provide several important benefits to survival and reproduction. Because little is known about 'ōpe'ape'a roost ecology and considerable effort is needed to capture and track bats to roost locations, we examined resource selection at multiple spatial scales-perch location within a roost tree, roost tree, and forest stand. We used a discrete choice modeling approach to investigate day-roost selection and describe attributes of roost trees including those used as maternity roosts. 'Ōpe'ape'a were found roosting in 19 tree species and in an assortment of landcover types including native and non-native habitats. Our results are largely consistent with findings of other studies of foliage-roosting, insectivorous tree bats where bats selected roost locations that may offer protection and thermoregulatory benefits.

A population in perpetual motion: Highly dynamic roosting behavior of a tropical island endemic bat

Although island endemic bats are a source of considerable conservation concerns, their biology remains poorly known. Here, we studied the phenology and roosting behavior of a tropical island endemic species: the Reunion free-tailed bat (Mormopterus francoismoutoui). This widespread and abundant species occupies various natural and anthropogenic environments such as caves and buildings. We set up fine-scale monitoring of 19 roosts over 27 months in Reunion Island and analyzed roost size and composition, sexual and age-associated segregation of individuals, as well as the reproductive phenology and body condition of individuals. Based on extensive data collected from 6721 individuals, we revealed a highly dynamic roosting behavior, with marked seasonal sex-ratio variation, linked to distinct patterns of sexual aggregation among roosts. Despite the widespread presence of pregnant females all over the island, parturition was localized in a few roosts, and flying juveniles dispersed rapidly toward all studied roosts. Our data also suggested a 7-month delay between mating and pregnancy, highlighting a likely long interruption of the reproductive cycle in this tropical bat. Altogether, our results suggest a complex social organization in the Reunion free-tailed bat, with important sex-specific seasonal and spatial movements, including the possibility of altitudinal migration. Bat tracking and genetic studies would provide additional insights into the behavioral strategies that shape the biology of this enigmatic bat species. The fine-scale spatiotemporal data revealed by our study will serve to the delineation of effective conservation plans, especially in the context of growing urbanization and agriculture expansion in Reunion Island.

Genetic diversity, structure, and effective population size of an endangered, endemic hoary bat, 'ōpe'ape'a, across the Hawaiian Islands

Island bat species are disproportionately at risk of extinction, and Hawai'i's only native terrestrial land mammal, the Hawaiian hoary bat (Lasiurus semotus) locally known as 'ōpe'ape'a, is no exception. To effectively manage this bat species with an archipelago-wide distribution, it is important to determine the population size on each island and connectivity between islands. We used 18 nuclear microsatellite loci and one mitochondrial gene from 339 individuals collected from 1988-2020 to evaluate genetic diversity, population structure and estimate effective population size on the Islands of Hawai'i, Maui, O'ahu, and Kaua'i. Genetic differentiation occurred between Hawai'i and Maui, both of which were differentiated from O'ahu and Kaua'i. The population on Maui presents the greatest per-island genetic diversity, consistent with their hypothesized status as the original founding population. A signature of isolation by distance was detected between islands, with contemporary migration analyses indicating limited gene flow in recent generations, and male-biased sex dispersal within Maui. Historical and long-term estimates of genetic effective population sizes were generally larger than contemporary estimates, although estimates of contemporary genetic effective population size lacked upper bounds in confidence intervals for Hawai'i and Kaua'i. Contemporary genetic effective population sizes were smaller on O'ahu and Maui. We also detected evidence of past bottlenecks on all islands with the exception of Hawai'i. Our study provides population-level estimates for the genetic diversity and geographic structure of 'ōpe'ape'a, that could be used by agencies tasked with wildlife conservation in Hawai'i.

High genetic connectivity among large populations of Pteronotus gymnonotus in bat caves in Brazil and its implications for conservation

Bat caves in the Neotropical region harbor exceptional bat populations (> 100,000 individuals). These populations play a wider role in ecological interactions, are vulnerable due to their restriction to caves, and have a disproportionate conservation value. Current knowledge of bat caves in Brazil is still small. However, systematic monitoring of some bat caves in northeastern Brazil shows that they experience strong population fluctuations over short periods of time, suggesting large-scale movements between roosts and a much broader use of the landscape than previously considered. Spatio-temporal reproductive connectivity between distant populations would change our understanding of the use of roosts among bat species in Brazil, and important gaps in knowledge of long-distance bat movements in the country would be filled. Here, we used ddRADseq data to analyze the genetic structure of Pteronotus gymnonotus across nine bat caves over 700 km. Our results indicate the lack of a clear geographic structure with gene flow among all the caves analyzed, suggesting that P. gymnonotus uses a network of bat caves geographically segregated hundreds of kilometers apart. Facing strong anthropogenic impacts and an underrepresentation of caves in conservation action plans worldwide, the genetic connectivity demonstrated here confirms that bat caves are priority sites for bat and speleological conservation in Brazil and elsewhere. Moreover, our results demonstrate a warning call: the applied aspects of the environmental licensing process of the mining sector and its impact must be reviewed, not only in Brazil, but wherever this licensing process affects caves having exceptional bat populations.

Positively selected genes in the hoary bat (Lasiurus cinereus) lineage: prominence of thymus expression, immune and metabolic function, and regions of ancient synteny

Background

Bats of the genus Lasiurus occur throughout the Americas and have diversified into at least 20 species among three subgenera. The hoary bat (Lasiurus cinereus) is highly migratory and ranges farther across North America than any other wild mammal. Despite the ecological importance of this species as a major insect predator, and the particular susceptibility of lasiurine bats to wind turbine strikes, our understanding of hoary bat ecology, physiology, and behavior remains poor.

Methods

To better understand adaptive evolution in this lineage, we used whole-genome sequencing to identify protein-coding sequence and explore signatures of positive selection. Gene models were predicted with Maker and compared to seven well-annotated and phylogenetically representative species. Evolutionary rate analysis was performed with PAML.

Results

Of 9,447 single-copy orthologous groups that met evaluation criteria, 150 genes had a significant excess of nonsynonymous substitutions along the L. cinereus branch (P < 0.001 after manual review of alignments). Selected genes as a group had biased expression, most strongly in thymus tissue. We identified 23 selected genes with reported immune functions as well as a divergent paralog of Steep1 within suborder Yangochiroptera. Seventeen genes had roles in lipid and glucose metabolic pathways, partially overlapping with 15 mitochondrion-associated genes; these adaptations may reflect the metabolic challenges of hibernation, long-distance migration, and seasonal variation in prey abundance. The genomic distribution of positively selected genes differed significantly from background expectation by discrete Kolmogorov-Smirnov test (P < 0.001). Remarkably, the top three physical clusters all coincided with islands of conserved synteny predating Mammalia, the largest of which shares synteny with the human cat-eye critical region (CECR) on 22q11. This observation coupled with the expansion of a novel Tbx1-like gene family may indicate evolutionary innovation during pharyngeal arch development: both the CECR and Tbx1 cause dosage-dependent congenital abnormalities in thymus, heart, and head, and craniodysmorphy is associated with human orthologs of other positively selected genes as well.

Influencing Activity of Bats by Dimly Lighting Wind Turbine Surfaces with Ultraviolet Light

Simple Summary

Bats often fly near wind turbines. The fatalities associated with this behavior continue to be an issue for wind energy development and wildlife conservation. We tested an experimental method intended to reduce bat fatalities at the wind turbines. We assumed that bats navigate over long distances at night by dim-light vision and might be dissuaded from approaching artificially lit structures. For over a year, we experimentally lit wind turbines at night with dim, flickering ultraviolet (UV) light while measuring the presence and activity of bats, birds, and insects with thermal-imaging cameras. We detected no statistical differences in the activity of the bats, insects, or birds at a test turbine when lit with UV light compared with that of unlit nights. Additional experiments to test this or other possible bat-deterrence methods may benefit from considering subtle measures of animal response that can provide useful information on the possible behavioral effects of fatality-reduction experiments.

Abstract

Wind energy producers need deployable devices for wind turbines that prevent bat fatalities. Based on the speculation that bats approach turbines after visually mistaking them for trees, we tested a potential light-based deterrence method. It is likely that the affected bats see ultraviolet (UV) light at low intensities. Here, we present the results of a multi-month experiment to cast dim, flickering UV light across wind turbine surfaces at night. Our objectives were to refine and test a practical system for dimly UV-illuminating turbines while testing whether the experimental UV treatment influenced the activity of bats, birds, and insects. We mounted upward-facing UV light arrays on turbines and used thermal-imaging cameras to quantify the presence and activity of night-flying animals. The results demonstrated that the turbines can be lit to the highest reaches of the blades with “invisible” UV light, and the animal responses to such experimental treatment can be concurrently monitored. The UV treatment did not significantly change nighttime bat, insect, or bird activity at the wind turbine. Our findings show how observing flying animals with thermal cameras at night can help test emerging technologies intended to variably affect their behaviors around wind turbines.

Oceanic records of North American bats and implications for offshore wind energy development in the United States

Offshore wind energy is a growing industry in the United States, and renewable energy from offshore wind is estimated to double the country's total electricity generation. There is growing concern that land-based wind development in North America is negatively impacting bat populations, primarily long-distance migrating bats, but the impacts to bats from offshore wind energy are unknown. Bats are associated with the terrestrial environment, but have been observed over the ocean. In this review, we synthesize historic and contemporary accounts of bats observed and acoustically recorded in the North American marine environment to ascertain the spatial and temporal distribution of bats flying offshore. We incorporate studies of offshore bats in Europe and of bat behavior at land-based wind energy studies to examine how offshore wind development could impact North American bat populations. We find that most offshore bat records are of long-distance migrating bats and records occur during autumn migration, the period of highest fatality rates for long-distance migrating bats at land-based wind facilities in North America. We summarize evidence that bats may be attracted to offshore turbines, potentially increasing their exposure to risk of collision. However, higher wind speeds offshore can potentially reduce the amount of time that bats are exposed to risk. We identify knowledge gaps and hypothesize that a combination of operational minimization strategies may be the most effective approach for reducing impacts to bats and maximizing offshore energy production.