Genetic approaches to the conservation of migratory bats: a study of the eastern red bat (Lasiurus borealis)

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.

Acoustic and Genetic Data Can Reduce Uncertainty Regarding Populations of Migratory Tree-Roosting Bats Impacted by Wind Energy

Wind turbine-related mortality may pose a population-level threat for migratory tree-roosting bats, such as the hoary bat (Lasiurus cinereus) in North America. These species are dispersed within their range, making it impractical to estimate census populations size using traditional survey methods. Nonetheless, understanding population size and trends is essential for evaluating and mitigating risk from wind turbine mortality. Using various sampling techniques, including systematic acoustic sampling and genetic analyses, we argue that building a weight of evidence regarding bat population status and trends is possible to (1) assess the sustainability of mortality associated with wind turbines; (2) determine the level of mitigation required; and (3) evaluate the effectiveness of mitigation measures to ensure population viability for these species. Long-term, systematic data collection remains the most viable option for reducing uncertainty regarding population trends for migratory tree-roosting bats. We recommend collecting acoustic data using the statistically robust North American Bat Monitoring Program (NABat) protocols and that genetic diversity is monitored at repeated time intervals to show species trends. There are no short-term actions to resolve these population-level questions; however, we discuss opportunities for relatively short-term investments that will lead to long-term success in reducing uncertainty.

Discordance in maternal and paternal genetic markers in lesser long-nosed bat Leptonycteris yerbabuenae, a migratory bat: recent expansion to the North and male phylopatry

Leptonycteris yerbabuenae, the lesser long-nosed bat is an abundant migratory nectar-feeding bat found in most of Mexico, and in some areas of northern Central America and small sections of southwestern USA. We analyzed the distribution of the maternal and paternal lineages of this species with phylogeographic methods based on two mitochondrial markers, Cyt-b and D-loop, and a marker located in the Y chromosome, DBY. We obtained tissue samples from 220 individuals from 23 localities. Levels of genetic diversity (haplotype diversity, Hd ) were high (Cyt-b = 0.757; D-loop = 0.8082; DBY = 0.9137). No clear patterns of population genetic structure were found for mitochondrial markers, while male genetic differentiation suggested the presence of two lineages: one from Mexican Pacific coast states and another from central-southern Mexico; in accordance to strong male philopatry and higher female migration. We used genealogical reconstructions based on Bayesian tools to calculate divergence times, and to test coalescent models to explain changes in L. yerbabuenae historical demography. Our results show that recent demographic changes were consistent with global climatic changes (∼130,000 kyr ago for Cyt-b and ∼160,000 kyr for D-loop) and divergence times dated from molecular genealogies exhibited older divergence times, Cyt-b (4.03 mya), D-loop (10.26 mya) and DBY (12.23 mya). Accordingly, the female lineage underwent demographic expansion associated to Pleistocene climate change, whereas the male lineage remained constant.

Genetic diversity, population structure, and effective population size in two yellow bat species in south Texas

There are increasing concerns regarding bat mortality at wind energy facilities, especially as installed capacity continues to grow. In North America, wind energy development has recently expanded into the Lower Rio Grande Valley in south Texas where bat species had not previously been exposed to wind turbines. Our study sought to characterize genetic diversity, population structure, and effective population size in Dasypterus ega and D. intermedius, two tree-roosting yellow bats native to this region and for which little is known about their population biology and seasonal movements. There was no evidence of population substructure in either species. Genetic diversity at mitochondrial and microsatellite loci was lower in these yellow bat taxa than in previously studied migratory tree bat species in North America, which may be due to the non-migratory nature of these species at our study site, the fact that our study site is located at a geographic range end for both taxa, and possibly weak ascertainment bias at microsatellite loci. Historical effective population size (NEF) was large for both species, while current estimates of Ne had upper 95% confidence limits that encompassed infinity. We found evidence of strong mitochondrial differentiation between the two putative subspecies of D. intermedius (D. i. floridanus and D. i. intermedius) which are sympatric in this region of Texas, yet little differentiation using microsatellite loci. We suggest this pattern is due to secondary contact and hybridization and possibly incomplete lineage sorting at microsatellite loci. We also found evidence of some hybridization between D. ega and D. intermedius in this region of Texas. We recommend that our data serve as a starting point for the long-term genetic monitoring of these species in order to better understand the impacts of wind-related mortality on these populations over time.

Using trace elements to identify the geographic origin of migratory bats

The expansion of the wind energy industry has had benefits in terms of increased renewable energy production but has also led to increased mortality of migratory bats due to interactions with wind turbines. A key question that could guide bat-related management activities is identifying the geographic origin of bats killed at wind-energy facilities. Generating this information requires developing new methods for identifying the geographic sources of individual bats. Here we explore the viability of assigning geographic origin using trace element analyses of fur to infer the summer molting location of eastern red bats (Lasiurus borealis). Our approach is based on the idea that the concentration of trace elements in bat fur is related through the food chain to the amount of trace elements present in the soil, which varies across large geographic scales. Specifically, we used inductively coupled plasma–mass spectrometry to determine the concentration of fourteen trace elements in fur of 126 known-origin eastern red bats to generate a basemap for assignment throughout the range of this species in eastern North America. We then compared this map to publicly available soil trace element concentrations for the U.S. and Canada, used a probabilistic framework to generate likelihood-of-origin maps for each bat, and assessed how well trace element profiles predicted the origins of these individuals. Overall, our results suggest that trace elements allow successful assignment of individual bats 80% of the time while reducing probable locations in half. Our study supports the use of trace elements to identify the geographic origin of eastern red and perhaps other migratory bats, particularly when combined with data from other biomarkers such as genetic and stable isotope data.

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

We examine the genetic history and population status of Hawaiian hoary bats (Lasiurus semotus), the most isolated bats on Earth, and their relationship to northern hoary bats (Lasiurus cinereus), through whole-genome analysis of single-nucleotide polymorphisms mapped to a de novo-assembled reference genome. Profiles of genomic diversity and divergence indicate that Hawaiian hoary bats are distinct from northern hoary bats, and form a monophyletic group, indicating a single ancestral colonization event 1.34 Ma, followed by substantial divergence between islands beginning 0.51 Ma. Phylogenetic analysis indicates Maui is central to the radiation across the archipelago, with the southward expansion to Hawai'i and westward to O'ahu and Kaua'i. Because this endangered species is of conservation concern, a clearer understanding of the population genetic structure of this bat in the Hawaiian Islands is of timely importance.

High Frequency of Multiple Paternity in Eastern Red Bats, Lasiurus borealis, Based on Microsatellite Analysis

Most species of bats give birth to only 1 pup each year, although Eastern red bats (Lasiurus borealis) can produce up to 5 pups per litter. Offspring in a single litter have been documented to be at different stages of development, suggesting that multiple paternity occurs. We tested the null hypothesis of genetic monogamy in red bats using 6 autosomal microsatellites and 1 X-linked microsatellite from 31 parent/offspring groups for a total of 128 bats. We sampled both pregnant females and mothers with pups that were obtained from bats submitted to departments of health in Oklahoma and Texas for rabies testing. Multiple paternity was assessed using a maximum-likelihood approach, hypothesis testing, and X-linked locus exclusion. The mean polymorphic information content of our markers was high (0.8819) and combined non-exclusion probability was low (0.00027). Results from the maximum-likelihood approach showed that 22 out of 31 (71%) parent/offspring groups consisted of half siblings, hypothesis testing rejected full sibship in 61% of parent/offspring groups, and X-linked locus exclusion suggested multiple paternity in at least 12 parent/offspring groups, rejecting our hypothesis of genetic monogamy. This frequency of multiple paternity is the highest reported thus far for any bat species. High levels of multiple paternity have the potential to impact interpretations of genetic estimates of effective population size in this species. Further, multiple paternity might be an adaptive strategy to allow for increased genetic variation and large litter size, which would be beneficial to a species threatened by population declines from wind turbines.

Geographic origins and population genetics of bats killed at wind-energy facilities

An unanticipated impact of wind-energy development has been large-scale mortality of insectivorous bats. In eastern North America, where mortality rates are among the highest in the world, the hoary bat (Lasiurus cinereus) and the eastern red bat (L. borealis) comprise the majority of turbine-associated bat mortality. Both species are migratory tree bats with widespread distributions; however, little is known regarding the geographic origins of bats killed at wind-energy facilities or the diversity and population structure of affected species. We addressed these unknowns by measuring stable hydrogen isotope ratios (δ² H) and conducting population genetic analyses of bats killed at wind-energy facilities in the central Appalachian Mountains (USA) to determine the summering origins, effective size, structure, and temporal stability of populations. Our results indicate that ~1% of hoary bat mortalities and ~57% of red bat mortalities derive from non-local sources, with no relationship between the proportion of non-local bats and sex, location of mortality, or month of mortality. Additionally, our data indicate that hoary bats in our sample consist of an unstructured population with a small effective size (N_e ) and either a stable or declining history. Red bats also showed no evidence of population genetic structure, but in contrast to hoary bats, the diversity contained in our red bat samples is consistent with a much larger N_e that reflects a demographic expansion after a bottleneck. These results suggest that the impacts of mortality associated with intensive wind-energy development may affect bat species dissimilarly, with red bats potentially better able to absorb sustained mortality than hoary bats because of their larger N_e . Our results provide important baseline data and also illustrate the utility of stable isotopes and population genetics for monitoring bat populations affected by wind-energy development.

Genetic diversity in migratory bats: Results from RADseq data for three tree bat species at an Ohio windfarm

Genetic analyses can identify the scale at which wildlife species are impacted by human activities, and provide demographic information useful for management. Here, we use thousands of nuclear DNA genetic loci to assess whether genetic structure occurs within Lasiurus cinereus (Hoary Bat), L. borealis (Red Bat), and Lasionycteris noctivagans (Silver-Haired Bat) bats found at a wind turbine site in Ohio, and to also estimate demographic parameters in each of these three groups. Our specific goals are to: 1) demonstrate the feasibility of isolating RADseq loci from these tree bat species, 2) test for genetic structure within each species, including any structure that may be associated with time (migration period), and 3) use coalescent-based modeling approaches to estimate genetically-effective population sizes and patterns of population size changes over evolutionary timescales. Thousands of loci were successfully genotyped for each species, demonstrating the value of RADseq for generating polymorphic loci for population genetic analyses in these bats. There was no evidence for genetic differentiation between groups of samples collected at different times throughout spring and fall migration, suggesting that individuals from each species found at the wind facility are from single panmictic populations. Estimates of present-day effective population sizes varied across species, but were consistently large, on the order of 10⁵–10⁶. All populations show evidence of expansions that date to the Pleistocene. These results, along with recent work also suggesting limited genetic structure in bats across North America, argue that additional biomarker systems such as stable-isotopes or trace elements should be investigated as alternative and/or complementary approaches to genetics for sourcing individuals collected at single wind farm sites.