Parallel declines in species and genetic diversity in tropical forest fragments

Land use to agriculture and planted forests strongly affect the genetic diversity of Baccharis crispa Spreng., a native herb of South America

Human population growth constantly requires an increase in the production of food and products from the timber industry. To meet this demand, agriculture and planted forests are advancing over natural areas. In view of this, it is necessary to know the effects of land use for different purposes (grain production, pastures, planted forests, fruit production and among other uses) on the genetic diversity of populations of native species. This knowledge can assist in land use planning as well as in the development of conservation strategies for native species. In this study, we evaluated the effect of land use for agriculture (mainly for cereal production) and planted forests on the genetic diversity of Baccharis crispa Spreng., a herb native to South America. To achieve our goals, we compared population genetic data obtained with three molecular markers (microsatellites, inter-simple sequence repeat and isoenzymes) with data on land use for agriculture and planted forests from 15 different locations. Our results showed that regardless of the molecular marker used, the greater the use of land for agriculture and planted forests, the lower was the genetic diversity of B. crispa populations. Baccharis crispa is a semi-perennial species that needs at least one year to reach its reproductive period, which is prevented in agricultural areas due to the land being turned over or dissected with herbicides every 6 months. In the studied regions, the planted forests are of eucalypt and/or pine, which besides being species with a high production of allelopathic substances, produce strong shading and B. crispa is a species that inhabits open grassland that needs a high incidence of sunlight for development. The data obtained in our study can assist in the decision-making to use land in order to reconcile the production of supplies for humanity and for the conservation of nature.

Species and genetic diversity relationships in benthic macroinvertebrate communities along a salinity gradient

BACKGROUND

Species- and genetic diversity can change in parallel, resulting in a species-genetic diversity correlation (SGDC) and raising the question if the same drivers influence both biological levels of diversity. The SGDC can be either positive or negative, depending on whether the species diversity and the genetic diversity of the measured species respond in the same or opposite way to drivers. Using a traditional species diversity approach together with ultra-conserved elements and high throughput sequencing, we evaluated the SGDCs in benthic macrofauna communities in the Baltic Sea, a geologically young brackish water sea characterised by its steep salinity gradient and low species richness. Assessing SGDCs from six focal marine invertebrate species from different taxonomic groups and with differing life histories and ecological functions on both a spatial and temporal scale gives a more comprehensive insight into the community dynamics of this young ecosystem and the extrinsic factors that might drive the SGDCs.

RESULTS

No significant correlations between species diversity and genetic diversity were found for any of the focal species. However, both negative and positive trends of SGDCs for the individual focal species were observed. When examining the environmental drivers, no common trends between the species were found, even when restricting the analysis to specific taxonomic classes. Additionally, there were no common environmental factors driving the diversity relationships for species sharing the same SGDC trend (positive or negative). Local population dynamics, together with the invasion history of the individual species and their unique adaptation to the distinctive environment of the Baltic Sea, are expected to be of major influence on the outcome of the SGDCs.

CONCLUSIONS

The present results highlight the importance of assessing SGDCs using multiple species, not just a single indicator species. This emphasises a need to pay attention to the ecology and life history of the focal species. This study also provides insight into the large differences in both patterns and drivers of genetic diversity, which is important when including genetic biodiversity in conservation plans. We conclude that the effects of environmental and biological factors and processes that affects diversity patterns at both the community and genetic levels are likely species dependent, even in an environment such as the Baltic Sea with strong environmental gradients.

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.

Stretching the Habitat Envelope: Insectivorous Bat Guilds Can Use Rubber Plantations, but Need Understorey Vegetation and Forest Buffers

Effects of land-cover change on insectivorous bat activity can be negative, neutral or positive, depending on foraging strategies of bats. In tropical agroforestry systems with high bat diversity, these effects can be complex to assess. We investigated foraging habitat use by three insectivorous bat guilds in forests and rubber plantations in the southern Western Ghats of India. Specifically, we monitored acoustic activity of bats in relation to (1) land-cover types and vegetation structure, and (2) plantation management practices. We hypothesized that activity of open-space aerial (OSA) and edge-space aerial (ESA) bat guilds would not differ; but narrow-space, flutter-detecting (NSFD) bat guild activity would be higher, in structurally heterogeneous forest habitats than monoculture rubber plantations. We found that bat activity of all guilds was highest in areas with high forest cover and lowest in rubber plantations. Higher bat activity was associated with understorey vegetation in forests and plantations, which was expected for NSFD bats, but was a surprise finding for OSA and ESA bats. Within land-cover types, open areas and edge-habitats had higher OSA and ESA activity respectively, while NSFD bats completely avoided open habitats. In terms of management practices, intensively managed rubber plantations with regular removal of understorey vegetation had the lowest bat activity for all guilds. Intensive management can undermine potential ecosystem services of insectivorous bats (e.g., insect pest-control in rubber plantations and surrounding agro-ecosystems), and magnify threats to bats from human disturbances. Low-intensity management and maintenance of forest buffers around plantations can enable persistence of insectivorous bats in tropical forest-plantation landscapes.

A Meta-Analysis Indicates Positive Correlation between Genetic Diversity and Species Diversity

Simple Summary

Understanding species and genetic correlations (SGDCs) is essential to establish community composition. In this study, 295 observations from 39 studies explored the SGDCs and the underlying drivers through conducting a global meta-analysis. A positive correlation was found, suggesting that parallel processes (environmental heterogeneity, area, and connectivity etc.) have effects on two diversities. As current biodiversity hotspots have mainly been identified based on high species diversity and high endemism of taxon, the understanding of SGDC will substantially help us to determine whether and how genetic diversity can be used in identifying biodiversity hotspots, as well as in developing conservation practices and policies for biodiversity.

Abstract

Species diversity (SD) and genetic diversity (GD) are the two basic levels of biodiversity. In general, according to the consensus view, the parallel effects of environmental heterogeneity, area, and connectivity on two levels, can drive a positive correlation between GD and SD. Conversely, a negative correlation or no correlation would be expected if these effects are not parallel. Our understanding of the relationships between SD and GD among different ecosystems, sampling methods, species, and under climate change remains incomplete. In the present study, we conducted a hierarchical meta-analysis based on 295 observations from 39 studies and found a positive correlation between genetic diversity and species diversity (95% confidence interval, 7.6–22.64%). However, significant relationships were not found in some ecosystems when we conducted species–genetic diversity correlation analysis based on a single ecosystem. Moreover, the magnitudes of the correlations generally decreased with the number of sampling units and the annual average the temperature of sampling units. Our results highlight the positive correlation between GD and SD, thereby indicating that protecting SD involves protecting GD in conservation practice. Furthermore, our results also suggest that global increases in temperature during the 21st century will have significant impacts on global biodiversity.

Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible

Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.

Gene Flow in Volant Vertebrates: Species Biology, Ecology and Climate Change

Gene flow, the exchange of genetic material between populations is an important biological process, which shapes and maintains biodiversity. The successful movement of individuals between populations depends on multiple factors determined by species biology and the environment. One of the most important factors regulating gene flow is the ability to move, and flight allows individuals to easily move across geographical barriers. Volant vertebrates are found on some of the remotest islands and contribute significantly to the biodiversity and ecosystem. The availability of next-generation sequencing data for non-model animals has substantially improved our understanding of gene flow and its consequences, allowing us to look at fine-scale patterns. However, most of our understanding regarding gene flow comes from the temperate regions and the Neotropics. The lack of studies from species-rich Asia is striking. In this review, we outline the importance of gene flow and the factors affecting gene flow, especially for volant vertebrates. We especially discuss research studies from tropical biomes of South and Southeast Asia, highlight the lacuna in literature and provide an outline for future studies in this species-rich region.

The impact of anthropogenic disturbances on the genetic diversity of terrestrial species: A global meta-analysis

Human activities are primarily responsible for habitat loss and changes in natural environments around the world. It has been suggested that populations inhabiting human-modified landscapes experience reduced gene flow, inbreeding depression, and loss of alleles due to genetic drift. However, empirical evidence shows the contrasting effects of anthropogenic disturbances on the genetic diversity of species. We performed a meta-analysis of 61 studies that compared the genetic diversity of plant and/or animal populations in disturbed and more preserved areas (316 paired comparisons) to investigate the genetic responses to different disturbance types. There is a negative effect (effect size: -0.45; 95% confidence interval: -0.61, -0.29) of disturbances on genetic diversity, in which the most detrimental effects are caused by the loss of connectivity and forest cover. The methodological approach can explain part of the heterogeneity among the genetic responses detected by primary studies: (a) studies using the number of effective alleles did not detect genetic erosion, while all other indices revealed negative responses to disturbances; and (b) only studies performed with transferred or a combination of transferred and specific microsatellites detected negative responses. The effects on animal populations are more detrimental than in plant populations. Only plant species with a shrub life form, self-incompatible reproductive systems, and biotic pollination and seed dispersal showed negative responses to disturbances. Despite heterogeneity among studies, there is an overall negative effect of disturbances on genetic diversity, which indicates that remaining populations inhabiting human-modified landscapes have reduced evolutionary potential and are prone to local extinction.

Genetic population structure of endangered ring-tailed lemurs (Lemur catta) from nine sites in southern Madagascar

Madagascar's ring-tailed lemurs (Lemur catta) are experiencing rapid population declines due to ongoing habitat loss and fragmentation, as well as increasing exploitation for bushmeat and the illegal pet trade. Despite being the focus of extensive and ongoing behavioral studies, there is comparatively little known about the genetic population structuring of the species. Here, we present the most comprehensive population genetic analysis of ring-tailed lemurs to date from across their likely remaining geographic range. We assessed levels of genetic diversity and population genetic structure using multilocus genotypes for 106 adult individuals from nine geographically representative localities. Population structure and F ST analyses revealed moderate genetic differentiation with localities being geographically partitioned into northern, southern, western and also potentially central clusters. Overall genetic diversity, in terms of allelic richness and observed heterozygosity, was high in the species (AR = 4.74, H O = 0.811). In fact, it is the highest among all published lemur estimates to date. While these results are encouraging, ring-tailed lemurs are currently affected by ongoing habitat fragmentation and occur at lower densities in poorer quality habitats. The effects of continued isolation and fragmentation, coupled with climate-driven environmental instability, will therefore likely impede the long-term viability of the species.

Founder effects and species introductions: A host versus parasite perspective

Species colonizations (both natural and anthropogenic) can be associated with genetic founder effects, where founding populations demonstrate significant genetic bottlenecks compared to native populations. Yet, many successfully established free-living species exhibit little reduction in genetic diversity-possibly due to multiple founding events and/or high propagule pressure during introductions. Less clear, however, is whether parasites may show differential signatures to their free-living  hosts. Parasites with indirect life cycles may particularly be more prone to founder effects (i.e., more genetically depauperate) because of inherently smaller founding populations and complex life cycles. We investigated this question in native (east coast) and introduced (west coast) North American populations of a host snail Tritia obsoleta (formerly Ilyanassa obsoleta, the eastern mudsnail) and four trematode parasite species that obligately infect it. We examined genetic diversity, gene flow, and population structure using two molecular markers (mitochondrial and nuclear) for the host and the parasites. In the host snail, we found little to no evidence of genetic founder effects, while the trematode parasites showed significantly lower genetic diversity in the introduced versus native ranges. Moreover, the parasite's final host influenced infection prevalence and genetic diversity: Trematode species that utilized fish as final hosts demonstrated lower parasite diversity and heightened founder effects in the introduced range than those trematodes using birds as final hosts. In addition, inter-regional gene flow was strongest for comparisons that included the putative historical source region (mid-Atlantic populations of the US east coast). Overall, our results broaden understanding of the role that colonization events (including recent anthropogenic introductions) have on genetic diversity in non-native organisms by also evaluating less studied groups like parasites.

Effects of habitat fragmentation on the bats of Kakamega Forest, western Kenya

Habitat loss and fragmentation are major threats to biodiversity worldwide, and little is known about their effects on bats in Africa. We investigated effects of forest fragmentation on bat assemblages at Kakamega Forest, western Kenya, examining captures at edge and interior locations in three forest fragments (Buyangu, 3950 ha; Kisere, 400 ha; and Malava, 100 ha) varying in forest area and human-use regimes. Basal area, canopy cover, tree density and intensity of human use were used as predictors of bat abundance and species richness. A total of 3456 mist-net hours and 3168 harp-trap hours resulted in the capture of 4983 bats representing 26 species, eight families and four foraging ensembles (frugivores, forest-interior insectivores, forest-edge insectivores and open-space insectivores). Frugivores were frequently captured at the edges of the larger, better-protected forests, but also in the interior of the smaller, more open fragment. Forest-interior insectivores and narrow-space foragers predominated in the interiors of larger fragments but avoided the smallest one. Forest specialists showed positive associations with forest variables (canopy cover, basal area and tree density), whereas frugivores responded positively to the human-use indicators. On these bases, specialist species appear to be especially vulnerable to forest fragmentation.

Species and genetic diversity are not congruent in fragmented dry grasslands

Biological diversity comprises both species diversity (SD) and genetic diversity (GD), and it has been postulated that both levels of diversity depend on similar mechanisms. Species-genetic diversity correlations (SGDC) are therefore supposed to be generally positive. However, in contrast to theory, empirical data are contradictory. Furthermore, there is a pronounced lack of multispecies studies including also the ecological factors potentially driving species and genetic diversity. We analyzed the relationship between the species diversity of dry grasslands and the genetic diversity of several dry grassland plant species, therefore, in the context of habitat fragmentation and habitat conditions. Our study revealed a lack of correlation between species and genetic diversity. We demonstrated previously that SD mainly depends on habitat conditions (vegetation height and cover of litter), whereas GD is significantly affected by habitat fragmentation (distance to the nearest dry grassland in 1830 and connectivity in 2013). This seems to be the main reason why SD and GD are not congruent in fragmented grasslands. Our results support, hence, the observation that positive SGDCs can mainly be found in natural, island-like study systems in equilibrium and at similar levels of heterogeneity. In fragmented dry grassland ecosystems, which differ in heterogeneity, this state of equilibrium may not have been reached mitigating the positive relationship between SD and GD. From our study, it can be concluded that in fragmented dry grasslands, the protection of SD does not necessarily ensure the conservation of GD.

Partitioning genetic and species diversity refines our understanding of species-genetic diversity relationships

Disentangling the origin of species-genetic diversity correlations (SGDCs) is a challenging task that provides insight into the way that neutral and adaptive processes influence diversity at multiple levels. Genetic and species diversity are comprised by components that respond differently to the same ecological processes. Thus, it can be useful to partition species and genetic diversity into their different components to infer the mechanisms behind SGDCs. In this study, we applied such an approach using a high-elevation Andean wetland system, where previous evidence identified neutral processes as major determinants of the strong and positive covariation between plant species richness and AFLP genetic diversity of the common sedge Carex gayana. To tease apart putative neutral and non-neutral genetic variation of C. gayana, we identified loci putatively under selection from a dataset of 1,709 SNPs produced using restriction site-associated DNA sequencing (RAD-seq). Significant and positive relationships between local estimates of genetic and species diversities (α-SGDCs) were only found with the putatively neutral loci datasets and with species richness, confirming that neutral processes were primarily driving the correlations and that the involved processes differentially influenced local species diversity components (i.e., richness and evenness). In contrast, SGDCs based on genetic and community dissimilarities (β-SGDCs) were only significant with the putative non-neutral datasets. This suggests that selective processes influencing C. gayana genetic diversity were involved in the detected correlations. Together, our results demonstrate that analyzing distinct components of genetic and species diversity simultaneously is useful to determine the mechanisms behind species-genetic diversity relationships.

A synthesis of ecological and evolutionary determinants of bat diversity across spatial scales

Background

Diversity patterns result from ecological to evolutionary processes operating at different spatial and temporal scales. Species trait variation determine the spatial scales at which organisms perceive the environment. Despite this knowledge, the coupling of all these factors to understand how diversity is structured is still deficient. Here, we review the role of ecological and evolutionary processes operating across different hierarchically spatial scales to shape diversity patterns of bats—the second largest mammal order and the only mammals with real flight capability.

Main body

We observed that flight development and its provision of increased dispersal ability influenced the diversification, life history, geographic distribution, and local interspecific interactions of bats, differently across multiple spatial scales. Niche packing combined with different flight, foraging and echolocation strategies and differential use of air space allowed the coexistence among bats as well as for an increased diversity supported by the environment. Considering distinct bat species distributions across space due to their functional characteristics, we assert that understanding such characteristics in Chiroptera improves the knowledge on ecological processes at different scales. We also point two main knowledge gaps that limit progress on the knowledge on scale-dependence of ecological and evolutionary processes in bats: a geographical bias, showing that research on bats is mainly done in the New World; and the lack of studies addressing the mesoscale (i.e. landscape and metacommunity scales).

Conclusions

We propose that it is essential to couple spatial scales and different zoogeographical regions along with their functional traits, to address bat diversity patterns and understand how they are distributed across the environment. Understanding how bats perceive space is a complex task: all bats can fly, but their perception of space varies with their biological traits.

Electronic supplementary material

The online version of this article (10.1186/s12898-018-0174-z) contains supplementary material, which is available to authorized users.

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.

Riverine fish diversity varies according to geographical isolation and land use modification

Understanding the environmental factors driving species-genetic diversity correlations (SGDCs) is critical for designing appropriate conservation and management strategies to protect biodiversity. Yet, few studies have explored the impact of changing land use patterns on SGDCs specifically in aquatic communities. This study examined patterns of genetic diversity in roach (Rutilus rutilus L.) together with fish species composition across 19 locations in a large river catchment, spanning a gradient in land use. Our findings show significant correlations between some, but not all, species and genetic diversity end points. For example, genetic and species differentiation showed a weak but significant linear relationship across the Thames catchment, but additional diversity measures such as allelic richness and fish population abundance did not. Further examination of patterns in species and genetic diversity indicated that land use intensification has a modest effect on fish diversity compared to the combined influence of geographical isolation and land use intensification. These results indicate that environmental changes in riparian habitats have the potential to amplify shifts in the composition of stream fish communities in poorly connected river stretches. Conservation and management strategies for fish populations should, therefore, focus on enhancing connectivity between river stretches and limit conversion of nearby land to arable or urban use to maintain current levels of biodiversity.

Comparative landscape genetics of two frugivorous bats in a biological corridor undergoing agricultural intensification

Agricultural intensification in tropical landscapes poses a new threat to the ability of biological corridors to maintain functional connectivity for native species. We use a landscape genetics approach to evaluate impacts of expanding pineapple plantations on two widespread and abundant frugivorous bats in a biological corridor in Costa Rica. We hypothesize that the larger, more mobile Artibeus jamaicensis will be less impacted by pineapple than the smaller Carollia castanea. In 2012 and 2013, we sampled 735 bats in 26 remnant forest patches surrounded by different proportions of forest, pasture, crops and pineapple. We used 10 microsatellite loci for A. jamaicensis and 16 microsatellite loci for C. castanea to estimate genetic diversity and gene flow. Canonical correspondence analyses indicate that land cover type surrounding patches has no impact on genetic diversity of A. jamaicensis. However, for C. castanea, both percentage forest and pineapple surrounding patches explained a significant proportion of the variation in genetic diversity. Least-cost transect analyses (LCTA) and pairwise G″st suggest that for A. jamaicensis, pineapple is more permeable to gene flow than expected, while as expected, forest is the most permeable land cover for gene flow of C. castanea. For both species, LCTA indicate that development may play a role in inhibiting gene flow. The current study answers the call for landscape genetic research focused on tropical and agricultural landscapes, highlights the value of comparative landscape genetics in biological corridor design and management and is one of the few studies of biological corridors in any ecosystem to implement a genetic approach to test corridor efficacy.

Seasonal Fluctuations of Astrovirus, But Not Coronavirus Shedding in Bats Inhabiting Human-Modified Tropical Forests

Emerging infectious diseases (EIDs) are considered a major threat to global health. Most EIDs appear to result from increased contact between wildlife and humans, especially when humans encroach into formerly pristine habitats. Habitat deterioration may also negatively affect the physiology and health of wildlife species, which may eventually lead to a higher susceptibility to infectious agents and/or increased shedding of the pathogens causing EIDs. Bats are known to host viruses closely related to important EIDs. Here, we tested in a paleotropical forest with ongoing logging and fragmentation, whether habitat disturbance influences the occurrence of astro- and coronaviruses in eight bat species. In contrast to our hypothesis, anthropogenic habitat disturbance was not associated with corona- and astrovirus detection rates in fecal samples. However, we found that bats infected with either astro- or coronaviruses were likely to be coinfected with the respective other virus. Additionally, we identified two more risk factors influencing astrovirus shedding. First, the detection rate of astroviruses was higher at the beginning of the rainy compared to the dry season. Second, there was a trend that individuals with a poor body condition had a higher probability of shedding astroviruses in their feces. The identification of risk factors for increased viral shedding that may potentially result in increased interspecies transmission is important to prevent viral spillovers from bats to other animals, including humans.

The relationship between least-cost and resistance distance

Least-cost modelling and circuit theory are common analogs used in ecology and evolution to model gene flow or animal movement across landscapes. Least-cost modelling estimates the least-cost distance, whereas circuit theory estimates resistance distance. The bias added in choosing one method over the other has not been well documented. We designed an experiment to test whether both methods were linearly related. We also tested the sensitivity of these metrics to variation in Euclidean distance, spatial autocorrelation, the number of pixels representing the landscape, and data aggregation. We found that least-cost and resistance distance were not linearly related unless a transformation was applied. Resistance distance was less sensitive to the number of pixels representing a landscape and was also less sensitive than least-cost distance to the Euclidean distance between nodes. Spatial autocorrelation did not affect either method or the relationship between methods. Resistance distance was more sensitive to aggregation in any form compared to least-cost distance. Therefore, the metric used to infer movement or gene flow and the manipulations applied to the data used to calculate these metrics may govern findings.

Habitat disturbance results in chronic stress and impaired health status in forest-dwelling paleotropical bats

Anthropogenic habitat disturbance is a major threat to biodiversity worldwide. Yet, before population declines are detectable, individuals may suffer from chronic stress and impaired immunity in disturbed habitats, making them more susceptible to pathogens and adverse weather conditions. Here, we tested in a paleotropical forest with ongoing logging and fragmentation, whether habitat disturbance influences the body mass and immunity of bats. We measured and compared body mass, chronic stress (indicated by neutrophil to lymphocyte ratios) and the number of circulating immune cells between several bat species with different roost types living in recovering areas, actively logged forests, and fragmented forests in Sabah, Malaysia. In a cave-roosting species, chronic stress levels were higher in individuals from fragmented habitats compared with conspecifics from actively logged areas. Foliage-roosting species showed a reduced body mass and decrease in total white blood cell counts in actively logged areas and fragmented forests compared with conspecifics living in recovering habitats. Our study highlights that habitat disturbance may have species-specific effects on chronic stress and immunity in bats that are potentially related to the roost type. We identified foliage-roosting species as particularly sensitive to forest habitat deterioration. These species may face a heightened extinction risk in the near future if anthropogenic habitat alterations continue.

Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat

Positive species-genetic diversity correlations (SGDCs) are often thought to result from the parallel influence of neutral processes on genetic and species diversity. Yet, confounding effects of non-neutral mechanisms have not been explored. Here, we investigate the impact of non-neutral genetic diversity on SGDCs in high Andean wetlands. We compare correlations between plant species diversity and genetic diversity (GD) calculated with and without loci potentially under selection (outlier loci). The study system includes 2188 specimens from five species (three common aquatic macroinvertebrate and two dominant plant species) that were genotyped for 396 amplified fragment length polymorphism loci. We also appraise the importance of neutral processes on SGDCs by investigating the influence of habitat fragmentation features. Significant positive SGDCs were detected for all five species (mean SGDC = 0.52 ± 0.05). While only a few outlier loci were detected in each species, they resulted in significant decreases in GD and in SGDCs. This supports the hypothesis that neutral processes drive species-genetic diversity relationships in high Andean wetlands. Unexpectedly, the effects on genetic diversity GD of the habitat fragmentation characteristics in this study increased with the presence of outlier loci in two species. Overall, our results reveal pitfalls in using habitat features to infer processes driving SGDCs and show that a few loci potentially under selection are enough to cause a significant downward bias in SGDC. Investigating confounding effects of outlier loci thus represents a useful approach to evidence the contribution of neutral processes on species-genetic diversity relationships.

A review of the ecosystem functions in oil palm plantations, using forests as a reference system

Oil palm plantations have expanded rapidly in recent decades. This large-scale land-use change has had great ecological, economic, and social impacts on both the areas converted to oil palm and their surroundings. However, research on the impacts of oil palm cultivation is scattered and patchy, and no clear overview exists. We address this gap through a systematic and comprehensive literature review of all ecosystem functions in oil palm plantations, including several (genetic, medicinal and ornamental resources, information functions) not included in previous systematic reviews. We compare ecosystem functions in oil palm plantations to those in forests, as the conversion of forest to oil palm is prevalent in the tropics. We find that oil palm plantations generally have reduced ecosystem functioning compared to forests: 11 out of 14 ecosystem functions show a net decrease in level of function. Some functions show decreases with potentially irreversible global impacts (e.g. reductions in gas and climate regulation, habitat and nursery functions, genetic resources, medicinal resources, and information functions). The most serious impacts occur when forest is cleared to establish new plantations, and immediately afterwards, especially on peat soils. To variable degrees, specific plantation management measures can prevent or reduce losses of some ecosystem functions (e.g. avoid illegal land clearing via fire, avoid draining of peat, use of integrated pest management, use of cover crops, mulch, and compost) and we highlight synergistic mitigation measures that can improve multiple ecosystem functions simultaneously. The only ecosystem function which increases in oil palm plantations is, unsurprisingly, the production of marketable goods. Our review highlights numerous research gaps. In particular, there are significant gaps with respect to socio-cultural information functions. Further, there is a need for more empirical data on the importance of spatial and temporal scales, such as differences among plantations in different environments, of different sizes, and of different ages, as our review has identified examples where ecosystem functions vary spatially and temporally. Finally, more research is needed on developing management practices that can offset the losses of ecosystem functions. Our findings should stimulate research to address the identified gaps, and provide a foundation for more systematic research and discussion on ways to minimize the negative impacts and maximize the positive impacts of oil palm cultivation.

Conservation of the Ethiopian church forests: Threats, opportunities and implications for their management

In the central and northern highlands of Ethiopia, native forest and forest biodiversity is almost confined to sacred groves associated with churches. Local communities rely on these 'church forests' for essential ecosystem services including shade and fresh water but little is known about their region-wide distribution and conservation value. We (1) performed the first large-scale spatially-explicit assessment of church forests, combining remote-sensing and field data, to assess the number of forests, their size, shape, isolation and woody plant species composition, (2) determined their plant communities and related these to environmental variables and potential natural vegetation, (3) identified the main challenges to biodiversity conservation in view of plant population dynamics and anthropogenic disturbances, and (4) present guidelines for management and policy. The 394 forests identified in satellite images were on average ~2ha in size and generally separated by ~2km from the nearest neighboring forest. Shape complexity, not size, decreased from the northern to the central highlands. Overall, 148 indigenous tree, shrub and liana species were recorded across the 78 surveyed forests. Patch α-diversity increased with mean annual precipitation, but typically only 25 woody species occurred per patch. The combined results showed that >50% of tree species present in tropical northeast Africa were still present in the 78 studied church forests, even though individual forests were small and relatively species-poor. Tree species composition of church forests varied with elevation and precipitation, and resembled the potential natural vegetation. With a wide distribution over the landscape, these church forests have high conservation value. However, long-term conservation of biodiversity of individual patches and evolutionary potential of species may be threatened by isolation, small sizes of tree species populations and disturbance, especially when considering climate change. Forest management interventions are essential and should be supported by environmental education and other forms of public engagement.

Soil properties drive a negative correlation between species diversity and genetic diversity in a tropical seasonal rainforest

A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community.

Parallel declines in species and genetic diversity driven by anthropogenic disturbance: a multispecies approach in a French Atlantic dune system

Numerous studies assess the correlation between genetic and species diversities, but the processes underlying the observed patterns have only received limited attention. For instance, varying levels of habitat disturbance across a region may locally reduce both diversities due to extinctions, and increased genetic drift during population bottlenecks and founder events. We investigated the regional distribution of genetic and species diversities of a coastal sand dune plant community along 240 kilometers of coastline with the aim to test for a correlation between the two diversity levels. We further quantify and tease apart the respective contributions of natural and anthropogenic disturbance factors to the observed patterns. We detected significant positive correlation between both variables. We further revealed a negative impact of urbanization: Sites with a high amount of recreational infrastructure within 10 km coastline had significantly lowered genetic and species diversities. On the other hand, a measure of natural habitat disturbance had no effect. This study shows that parallel variation of genetic and species diversities across a region can be traced back to human landscape alteration, provides arguments for a more resolute dune protection, and may help to design priority conservation areas.

Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data

Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and Murina recondita are both endemic to Taiwan and are putative sister species. To test for nonallopatric divergence and gene flow in these taxa, we generated sequences using Sanger and next-generation sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita; however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species Murina eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *beast and isolation-with-migration and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.

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).

Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers

The demographic history of Rhinolophus hipposideros (lesser horseshoe bat) was reconstructed across its European, North African and Middle-Eastern distribution prior to, during and following the most recent glaciations by generating and analysing a multimarker data set. This data set consisted of an X-linked nuclear intron (Bgn; 543 bp), mitochondrial DNA (cytb-tRNA-control region; 1630 bp) and eight variable microsatellite loci for up to 373 individuals from 86 localities. Using this data set of diverse markers, it was possible to determine the species' demography at three temporal stages. Nuclear intron data revealed early colonization into Europe from the east, which pre-dates the Quaternary glaciations. The mtDNA data supported multiple glacial refugia across the Mediterranean, the largest of which were found in the Ibero-Maghreb region and an eastern location (Anatolia/Middle East)-that were used by R. hipposideros during the most recent glacial cycles. Finally, microsatellites provided the most recent information on these species' movements since the Last Glacial Maximum and suggested that lineages that had diverged into glacial refugia, such as in the Ibero-Maghreb region, have remained isolated. These findings should be used to inform future conservation management strategies for R. hipposideros and show the power of using a multimarker data set for phylogeographic studies.

Diversity of Malaysian insectivorous bat assemblages revisited

To what extent tropical forest persisted in the Malay-Thai Peninsula during the Last Glacial Maximum, or contracted southwards with subsequent post-glacial expansion, has long been debated. These competing scenarios might be expected to have left contrasting broad spatial patterns of diversity of forest-dependent taxa. To test for a post-glacial northward spread of forest, we examined latitudinal clines of forest-dependent bat species at 15 forest sites across Peninsular Malaysia. From captures of 3776 insectivorous forest bats, we found that low richness characterized the north of the study area: predicted richness of 9–16 species, compared with 21–23 in the south. Predicted species richness decreased significantly with increasing latitude, but showed no relationship with either seasonality or peninsula width. Analyses of beta-diversity showed that differences between communities were not related to geographical distance, although there was evidence of greater differences in species numbers between the most distant sites. Assemblages were consistently dominated by six cave-roosting species from the families Rhinolophidae and Hipposideridae, while another 16 species were consistently rare. We suggest that these observed patterns are consistent with the hypothesized northward expansion of tropical rain forest since the Last Glacial Maximum, but emphasize that more surveys in the extreme north and south of the peninsula are required to support this assertion.

Unveiling a mechanism for species decline in fragmented habitats: fragmentation induced reduction in encounter rates

Several studies have reported that fragmentation (e.g. of anthropogenic origin) of habitats often leads to a decrease in the number of species in the region. An important mechanism causing this adverse ecological impact is the change in the encounter rates (i.e. the rates at which individuals meet other organisms of the same or different species). Yet, how fragmentation can change encounter rates is poorly understood. To gain insight into the problem, here we ask how landscape fragmentation affects encounter rates when all other relevant variables remain fixed. We present strong numerical evidence that fragmentation decreases search efficiencies thus encounter rates. What is surprising is that it falls even when the global average densities of interacting organisms are held constant. In other words, fragmentation per se can reduce encounter rates. As encounter rates are fundamental for biological interactions, it can explain part of the observed diminishing in animal biodiversity. Neglecting this effect may underestimate the negative outcomes of fragmentation. Partial deforestation and roads that cut through forests, for instance, might be responsible for far greater damage than thought. Preservation policies should take into account this previously overlooked scientific fact.