Social organization and genetic structure: insights from codistributed bat populations

Fine scale genetics reveals the subtle negative effects of roads on an endangered bat

The effective management of species with small and fragmented populations requires an in-depth understanding of how the effects of human-induced habitat disturbance shape the structure and gene flow at fine spatial scales. Identification of putative environmental barriers that affect individual exchange among subpopulations is imperative to prevent extinction risks. Here, we investigated how landscape affects the gene flow and relatedness structure of a population of the endangered lesser horseshoe bat (Rhinolophus hipposideros). We also assessed the effects of sexbiased dispersal on genetic relatedness. We genotyped 287 bat samples collected across southern Portugal and developed resistance surfaces for landscape variables hypothesized to affect gene flow. Then, we used spatially explicit models to fit relatedness distance through the resistance surfaces. We found genetic evidence of sex-biased dispersal and identified a significant fine scale structuring in the relatedness regarding females, the philopatric sex. Males displayed uniform levels of relatedness throughout the landscape. The results indicated less relatedness between the female´ from roosts located on proximity of roads than in roosts away from roads. Also, when analysing the sexes together the relatedness on roosts separated by highway were subtly less related in comparison to those occurring on the same side. Roads seem to be major shapers of the contemporary population structure of females, regardless of being relatively recent structures in the landscape. Furthermore, the relatedness patterns detected suggested that high tree density among roosts and continuity of forest patches in broader surrounding areas, promotes the relatedness among individuals. Landscape heterogeneity among roosts slightly decreases genetic relatedness. Nevertheless, those relationships are still weak, suggesting that population structuring driven by those factors is slowly ongoing. Thus, effective management measures should focus on issues for promoting safe road passages and suitable habitat corridors, allowing for the exchange of individuals and gene flow among lesser horseshoe bat roosts.

How do genetic relatedness and spatial proximity shape African swine fever infections in wild boar?

The importance of social and spatial structuring of wildlife populations for disease spread, though widely recognized, is still poorly understood in many host-pathogen systems. In particular, system specific kin relationships among hosts can create contact heterogeneities and differential disease transmission rates. Here, we investigate how distance-dependent infection risk is influenced by genetic relatedness in a novel host-pathogen system: wild boar (Sus scrofa) and African swine fever (ASF). We hypothesized that infection risk would correlate positively with proximity and relatedness to ASF-infected individuals but expected those relationships to weaken with distance between individuals due to decay in contact rates and genetic similarity. We genotyped 323 wild boar samples (243 ASF-negative and 80 ASF-positive) collected in north-eastern Poland in 2014-2016 and modeled the effects of geographic distance, genetic relatedness, and ASF virus transmission mode (direct or carcass-based) on the probability of ASF infection. Infection risk was positively associated with spatial proximity and genetic relatedness to infected individuals with generally stronger effect of distance. In the high-contact zone (0-2 km), infection risk was shaped by the presence of infected individuals rather than by relatedness to them. In the medium-contact zone (2-5 km), infection risk decreased but was still associated with relatedness and paired infections were more frequent among relatives. At farther distances, infection risk further declined with relatedness and proximity to positive individuals, and was 60% lower among unrelated individuals in the no-contact zone (33% in10-20 km) compared with among relatives in the high-contact zone (93% in 0-2 km). Transmission mode influenced the relationship between proximity or relatedness and infection risk. Our results indicate that the presence of nearby infected individuals is most important for shaping ASF infection rates through carcass-based transmission, while relatedness plays an important role in shaping transmission rates between live animals. This article is protected by copyright. All rights reserved.

Mobility and infectiousness in the spatial spread of an emerging fungal pathogen

Emerging infectious diseases can have devastating effects on host communities, causing population collapse and species extinctions. The timing of novel pathogen arrival into naïve species communities can have consequential effects that shape the trajectory of epidemics through populations. Pathogen introductions are often presumed to occur when hosts are highly mobile. However, spread patterns can be influenced by a multitude of other factors including host body condition and infectiousness. White-nose syndrome (WNS) is a seasonal emerging infectious disease of bats, which is caused by the fungal pathogen Pseudogymnoascus destructans. Within-site transmission of P. destructans primarily occurs over winter; however, the influence of bat mobility and infectiousness on the seasonal timing of pathogen spread to new populations is unknown. We combined data on host population dynamics and pathogen transmission from 22 bat communities to investigate the timing of pathogen arrival and the consequences of varying pathogen arrival times on disease impacts. We found that midwinter arrival of the fungus predominated spread patterns, suggesting that bats were most likely to spread P. destructans when they are highly infectious, but have reduced mobility. In communities where P. destructans was detected in early winter, one species suffered higher fungal burdens and experienced more severe declines than at sites where the pathogen was detected later in the winter, suggesting that the timing of pathogen introduction had consequential effects for some bat communities. We also found evidence of source-sink population dynamics over winter, suggesting some movement among sites occurs during hibernation, even though bats at northern latitudes were thought to be fairly immobile during this period. Winter emergence behaviour symptomatic of white-nose syndrome may further exacerbate these winter bat movements to uninfected areas. Our results suggest that low infectiousness during host migration may have reduced the rate of expansion of this deadly pathogen, and that elevated infectiousness during winter plays a key role in seasonal transmission. Furthermore, our results highlight the importance of both accurate estimation of the timing of pathogen spread and the consequences of varying arrival times to prevent and mitigate the effects of infectious diseases.

Fragmentation does not affect gene flow in forest populations of the dusky pipistrelle bat on the eastern seaboard of South Africa

The Eastern Cape Province harbors almost half of the indigenous forest in South Africa, but these forests are threatened by large-scale agricultural and urban development planned for the coming decade. Additional anthropogenic development is likely to cause further fragmentation and degradation of forests inhabited by the dusky pipistrelle bat (Pipistrellus hesperidus). We used eight microsatellite markers to study the genetic diversity, population structure, and migration, of P. hesperidus (n = 120) across 14 sites in the Eastern Cape and KwaZulu-Natal provinces of South Africa. We examined the effect of contemporary land cover types on genetic differentiation to assess whether current levels of urbanization and agricultural development affect gene flow. High gene flow and low population structure were evident across sampled sites, apart from genetic discontinuities at the northern (Oribi Gorge Nature Reserve) and southern (Alexandria Forest) ends of the seaboard. Genetic discontinuity at Oribi Gorge may relate to anthropogenic modification of two rivers surrounding the forest, while the Alexandria-linked barrier is a climatic break known as the Bedford gap. Migration rates generally were low between sites except for one Scarp forest, Manubi State Forest, from which individuals dispersed to other sites. The Amatole Mistbelt forests supported high genetic diversity, and likely served as a refugium for P. hesperidus during the Last Glacial Maximum. The composition of land cover classes between sites was a poor predictor of genetic differentiation, although it seems likely that P. hesperidus uses riparian habitats and wetlands for dispersal. Lastly, urban and agricultural development did not have a significant effect on genetic differentiation, which may reflect the wide niche breadth and intermediate distribution range of the species. This study provides insights into genetic diversity and gene flow of P. hesperidus across the study region prior to agricultural intensification and large-scale urbanization.

Dispersal ability predicts spatial genetic structure in native mammals persisting across an urbanization gradient

As the rate of urbanization continues to increase globally, a growing body of research is emerging that investigates how urbanization shapes the movement-and consequent gene flow-of species in cities. Of particular interest are native species that persist in cities, either as small relict populations or as larger populations of synanthropic species that thrive alongside humans in new urban environments. In this study, we used genomic sequence data (SNPs) and spatially explicit individual-based analyses to directly compare the genetic structure and patterns of gene flow in two small mammals with different dispersal abilities that occupy the same urbanized landscape to evaluate how mobility impacts genetic connectivity. We collected 215 white-footed mice (Peromyscus leucopus) and 380 big brown bats (Eptesicus fuscus) across an urban-to-rural gradient within the Providence, Rhode Island (U.S.A.) metropolitan area (population =1,600,000 people). We found that mice and bats exhibit clear differences in their spatial genetic structure that are consistent with their dispersal abilities, with urbanization having a stronger effect on Peromyscus mice. There were sharp breaks in the genetic structure of mice within the Providence urban core, as well as reduced rates of migration and an increase in inbreeding with more urbanization. In contrast, bats showed very weak genetic structuring across the entire study area, suggesting a near-panmictic gene pool likely due to the ability to disperse by flight. Genetic diversity remained stable for both species across the study region. Mice also exhibited a stronger reduction in gene flow between island and mainland populations than bats. This study represents one of the first to directly compare multiple species within the same urban-to-rural landscape gradient, an important gap to fill for urban ecology and evolution. Moreover, here we document the impacts of dispersal capacity on connectivity for native species that have persisted as the urban landscape matrix expands.

Social structure and relatedness in the fringe-lipped bat (Trachops cirrhosus)

General insights into the causes and effects of social structure can be gained from comparative analyses across socially and ecologically diverse taxa, such as bats, but long-term data are lacking for most species. In the neotropical fringe-lipped bat, Trachops cirrhosus, social transmission of foraging behaviour is clearly demonstrated in captivity, yet its social structure in the wild remains unclear. Here, we used microsatellite-based estimates of relatedness and records of 157 individually marked adults from 106 roost captures over 6 years, to infer whether male and female T. cirrhosus have preferred co-roosting associations and whether such associations were influenced by relatedness. Using a null model that controlled for year and roosting location, we found that both male and female T. cirrhosus have preferred roosting partners, but that only females demonstrate kin-biased association. Most roosting groups (67%) contained multiple females with one or two reproductive males. Relatedness patterns and recapture records corroborate genetic evidence for female philopatry and male dispersal. Our study adds to growing evidence that many bats demonstrate preferred roosting associations, which has the potential to influence social information transfer.

Combining noninvasive genetics and a new mammalian sex-linked marker provides new tools to investigate population size, structure and individual behaviour: An application to bats

Monitoring wild populations is crucial for their effective management. Noninvasive genetic methods provide robust data from individual free-ranging animals, which can be used in capture-mark-recapture (CMR) models to estimate demographic parameters without capturing or disturbing them. However, sex- and status-specific behaviour, which may lead to differences in detection probabilities, is rarely considered in monitoring. Here, we investigated population size, sex ratio, sex- and status-related behaviour in 19 Rhinolophus hipposideros maternity colonies (Northern France) with a noninvasive genetic CMR approach (using faeces) combined with parentage assignments. The use of the DDX3X/Y-Mam sexual marker designed in this study, which shows inter- and intrachromosomal length polymorphism across placental mammals, together with eight polymorphic microsatellite markers, produced high-quality genetic data with limited genotyping errors and allowed us to reliably distinguish different categories of individuals (males, reproductive and nonreproductive females) and to estimate population sizes. We showed that visual counts represent well-adult female numbers and that population composition in maternity colonies changes dynamically during the summer. Before parturition, colonies mainly harbour pregnant and nonpregnant females with a few visiting males, whereas after parturition, colonies are mainly composed of mothers and their offspring with a few visiting nonmothers and males. Our approach gives deeper insight into sex- and status-specific behaviour, a prerequisite for understanding population dynamics and developing effective monitoring and management strategies. Provided sufficient samples can be obtained, this approach can be readily applied to a wide range of species.

How do rivers, geographic distance, and dispersal behavior influence genetic structure in two sympatric New World monkeys?

Dispersal, one of the major factors affecting the gene flow between populations, shapes the spatial distribution of genetic diversity within species. Alouatta macconnelli and Saguinus midas are two Neotropical monkey species that sympatrically inhabit the Guiana shield in northern Amazonia and are likely to differ in their dispersal behavior and vagility. We took advantage of their sympatry to investigate, over a fine geographical scale (∼50 km long), the relationship between spatial genetic structure, on the one hand, and geographical features and the species' dispersal behavior on the other. A total of 84 A. macconnelli individuals from 25 social units and 76 S. midas individuals from 19 social units were genotyped for nine microsatellite markers. Both species displayed high genetic diversity and allelic richness. However, patterns of genetic structure differed between the two species. In A. macconnelli, no genetic substructuring was observed, while in S. midas we detected significant structuring, but this structuring was not correlated with geographical features, such as the location of individuals relative to the river and/or the distance between them. Instead, the geographical distribution of genetic variation observed for each species is predominantly explained by each species' dispersal pattern. We identified bisexual dispersal for both species, but with significant differences, either in the distance or in the rate of dispersal, between species and sexes. Genetic relatedness within social units was higher in S. midas than in A. macconnelli: gene flow between social units seems limited in S. midas, especially for females, while high dispersal characterizes A. macconnelli, where females seem to disperse at lower rate but at a longer distance than males.

Research priorities for the Pilbara leaf-nosed bat (Rhinonicteris aurantia Pilbara form)

Significant biodiversity offset funds have been allocated towards conservation research on threatened species as part of the environmental approvals process for resource development in the Pilbara region of Western Australia. One of these species is the Pilbara leaf-nosed bat (Rhinonicteris aurantia Pilbara form), which is entirely reliant on roosting in a limited number of caves and disused mines, many of which exist in the mineral-bearing strata that are the focus of mining activity. A research agenda for the Pilbara leaf-nosed bat was developed during a workshop attended by scientists, environmental consultants and mining industry representatives. Five research priorities were identified: (1) collate existing data contained within unpublished environmental surveys; (2) clarify and better characterise the number and distribution of day roosts; (3) better understand habitat requirements, particularly foraging habitat, and the movement of bats between roosts; (4) provide more robust estimates of total population and colony size, and improve understanding of social behaviour; and (5) investigate appropriate buffers in a range of mining contexts and protocols for artificial roost construction. Meta-analysis of current data, confirmation of potential day roosts, and long-term monitoring of activity patterns would rapidly increase our knowledge of the Pilbara leaf-nosed bat to enable effective conservation actions.

Responses of Tropical Bats to Habitat Fragmentation, Logging, and Deforestation

Land-use change is a key driver of the global biodiversity crisis and a particularly serious threat to tropical biodiversity. Throughout the tropics, the staggering pace of deforestation, logging, and conversion of forested habitat to other land uses has created highly fragmented landscapes that are increasingly dominated by human-modified habitats and degraded forests. In this chapter, we review the responses of tropical bats to a range of land-use change scenarios, focusing on the effects of habitat fragmentation, logging, and conversion of tropical forest to various forms of agricultural production. Recent landscape-scale studies have considerably advanced our understanding of how tropical bats respond to habitat fragmentation and disturbance at the population, ensemble, and assemblage level. This research emphasizes that responses of bats are often species and ensemble specific, sensitive to spatial scale, and strongly molded by the characteristics of the prevailing landscape matrix. Nonetheless, substantial knowledge gaps exist concerning other types of response by bats. Few studies have assessed responses at the genetic, behavioral, or physiological level, with regard to disease prevalence, or the extent to which human disturbance erodes the capacity of tropical bats to provide key ecosystem services. A strong geographic bias, with Asia and, most notably, Africa, being strongly understudied, precludes a comprehensive understanding of the effects of fragmentation and disturbance on tropical bats. We strongly encourage increased research in the Paleotropics and emphasize the need for long-term studies, approaches designed to integrate multiple scales, and answering questions that are key to conserving tropical bats in an era of environmental change and dominance of modified habitats (i.e., the Anthropocene).

Genetic connectivity among swarming sites in the wide ranging and recently declining little brown bat (Myotis lucifugus)

Characterizing movement dynamics and spatial aspects of gene flow within a species permits inference on population structuring. As patterns of structuring are products of historical and current demographics and gene flow, assessment of structure through time can yield an understanding of evolutionary dynamics acting on populations that are necessary to inform management. Recent dramatic population declines in hibernating bats in eastern North America from white-nose syndrome have prompted the need for information on movement dynamics for multiple bat species. We characterized population genetic structure of the little brown bat, Myotis lucifugus, at swarming sites in southeastern Canada using 9 nuclear microsatellites and a 292-bp region of the mitochondrial genome. Analyses of F ST, ΦST, and Bayesian clustering (STRUCTURE) found weak levels of genetic structure among swarming sites for the nuclear and mitochondrial genome (Global F ST = 0.001, P < 0.05, Global ΦST = 0.045, P < 0.01, STRUCTURE K = 1) suggesting high contemporary gene flow. Hierarchical AMOVA also suggests little structuring at a regional (provincial) level. Metrics of nuclear genetic structure were not found to differ between males and females suggesting weak asymmetries in gene flow between the sexes. However, a greater degree of mitochondrial structuring does support male-biased dispersal long term. Demographic analyses were consistent with past population growth and suggest a population expansion occurred from approximately 1250 to 12,500 BP, following Pleistocene deglaciation in the region. Our study suggests high gene flow and thus a high degree of connectivity among bats that visit swarming sites whereby mainland areas of the region may be best considered as one large gene pool for management and conservation.

Fine-scale genetic structure and cryptic associations reveal evidence of kin-based sociality in the African forest elephant

Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau K_r tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana) and Asian (Elephas maximus) species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau K_r tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0–5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and based on matrilines, with some individuals having more associates than observed from group sizes alone.

Fragmentation of Atlantic forest has not affected gene flow of a widespread seed-dispersing bat

Habitat loss and resultant fragmentation are major threats to biodiversity, particularly in tropical and subtropical ecosystems. It is increasingly urgent to understand fragmentation effects, which are often complex and vary across taxa, time and space. We determined whether recent fragmentation of Atlantic forest is causing population subdivision in a widespread and important Neotropical seed disperser: Artibeus lituratus (Chiroptera: Phyllostomidae). Genetic structure within highly fragmented forest in Paraguay was compared to that in mostly contiguous forest in neighbouring Misiones, Argentina. Further, observed genetic structure across the fragmented landscape was compared with expected levels of structure for similar time spans in realistic simulated landscapes under different degrees of reduction in gene flow. If fragmentation significantly reduced successful dispersal, greater population differentiation and stronger isolation by distance would be expected in the fragmented than in the continuous landscape, and genetic structure in the fragmented landscape should be similar to structure for simulated landscapes where dispersal had been substantially reduced. Instead, little genetic differentiation was observed, and no significant correlation was found between genetic and geographic distance in fragmented or continuous landscapes. Furthermore, comparison of empirical and simulated landscapes indicated empirical results were consistent with regular long-distance dispersal and high migration rates. Our results suggest maintenance of high gene flow for this relatively mobile and generalist species, which could be preventing or significantly delaying reduction in population connectivity in fragmented habitat. Our conclusions apply to A. lituratus in Interior Atlantic Forest, and do not contradict broad evidence that habitat fragmentation is contributing to extinction of populations and species, and poses a threat to biodiversity worldwide.

Dispersal, mating events and fine-scale genetic structure in the lesser flat-headed bats

Population genetic structure has important consequences in evolutionary processes and conservation genetics in animals. Fine-scale population genetic structure depends on the pattern of landscape, the permanent movement of individuals, and the dispersal of their genes during temporary mating events. The lesser flat-headed bat (Tylonycteris pachypus) is a nonmigratory Asian bat species that roosts in small groups within the internodes of bamboo stems and the habitats are fragmented. Our previous parentage analyses revealed considerable extra-group mating in this species. To assess the spatial limits and sex-biased nature of gene flow in the same population, we used 20 microsatellite loci and mtDNA sequencing of the ND2 gene to quantify genetic structure among 54 groups of adult flat-headed bats, at nine localities in South China. AMOVA and F(ST) estimates revealed significant genetic differentiation among localities. Alternatively, the pairwise F(ST) values among roosting groups appeared to be related to the incidence of associated extra-group breeding, suggesting the impact of mating events on fine-scale genetic structure. Global spatial autocorrelation analyses showed positive genetic correlation for up to 3 km, indicating the role of fragmented habitat and the specialized social organization as a barrier in the movement of individuals among bamboo forests. The male-biased dispersal pattern resulted in weaker spatial genetic structure between localities among males than among females, and fine-scale analyses supported that relatedness levels within internodes were higher among females than among males. Finally, only females were more related to their same sex roost mates than to individuals from neighbouring roosts, suggestive of natal philopatry in females.

Environmental margin and island evolution in Middle Eastern populations of the Egyptian fruit bat

Here, we present a study of the population genetic architecture and microevolution of the Egyptian fruit bat (Rousettus aegyptiacus) at the environmental margins in the Middle East using mitochondrial sequences and nuclear microsatellites. In contrast to the rather homogenous population structure typical of cave-dwelling bats in climax tropical ecosystems, a relatively pronounced isolation by distance and population diversification was observed. The evolution of this pattern could be ascribed to the complicated demographic history at higher latitudes related to the range margin fragmentation and complex geomorphology of the studied area. Lineages from East Africa and Arabia show divergent positions. Within the northwestern unit, the most marked pattern of the microsatellite data set is connected with insularity, as demonstrated by the separate status of populations from Saharan oases and Cyprus. These demes also exhibit a reduction in genetic variability, which is presumably connected with founder effects, drift and other potential factors related to island evolution as site-specific selection. Genetic clustering indicates a semipermeability of the desert barriers in the Sahara and Arabian Peninsula and a corridor role of the Nile Valley. The results emphasize the role of the island environment in restricting the gene flow in megabats, which is also corroborated by biogeographic patterns within the family, and suggests the possibility of nascent island speciation on Cyprus. Demographic analyses suggest that the colonization of the region was connected to the spread of agricultural plants; therefore, the peripatric processes described above might be because of or strengthened by anthropogenic changes in the environment.