Diversity — Open Access Journal

In Europe, the interest in introducing megaherbivores to achieve ambitious habitat restoration goals is increasing. In this study, we present the results of a one-year monitoring program in a rewilding project in Germany (Doeberitzer Heide), where European bison (Bison bonasus) and Przewalski’s horses (Equus ferus przewalskii) were introduced for ecological restoration purposes. Our objectives were to investigate diet and habitat preferences of Przewalski’s horses and European bison under free-choice conditions without fodder supplementation. In a random forest classification approach, we used multitemporal RapidEye time series imagery to map the diversity of available habitats within the study area. This spatially explicit habitat distribution from satellite imagery was combined with direct field observations of seasonal diet preferences of both species. In line with the availability of preferred forage plants, European bison and Przewalski’s horses both showed seasonal habitat preferences. Because of their different preferences for forage plants, they did not overlap in habitat use except for a short time in the colder season. European bison used open habitats and especially wet open habitats more than expected based on available habitats in the study area. Comparative foraging and feeding niches should be considered in the establishment of multispecies projects to maximize the outcome of restoration processes. Full article

Genetic diversity and its distribution, both within and between populations, may be determined by micro-evolutionary processes, such as the demographic history of populations, natural selection, and gene flow. In plants, indices of genetic diversity (e.g., k, h and π) and structure (e.g., F_ST) are typically inferred from sequences of chloroplast markers. Given the recent advances and popularization of molecular techniques for research in population genetics, phylogenetics, phylogeography, and ecology, we adopted a scientometric approach to compile evidence on the recent trends in the use of cpDNA sequences as markers for the analysis of genetic diversity in botanical studies, over the years. We also used phylogenetic modeling to assess the relative contribution of relatedness or ecological and reproductive characters to the genetic diversity of plants. We postulated that genetic diversity could be defined not only by microevolutionary factors and life history traits, but also by relatedness, so that species more closely related phylogenetically would have similar genetic diversities. We found a clear tendency for an increase in the number of studies over time, confirming the hypothesis that the advances in the area of molecular genetics have supported the accumulation of data on the genetic diversity of plants. However, we found that the vast majority of these data have been produced by Chinese authors, and refer specifically to populations of Chinese plants. Most of the data on genetic diversity have been obtained for species in the International Union for Conservation of Nature (IUCN) category NE (Not Evaluated), which indicates a relative lack of attention on threatened species. In general, we observed very high F_ST values in the groups analyzed and, as we focused primarily on species that have not been evaluated by the IUCN, the number of plant species that are threatened with extinction may be much greater than that indicated by the listing of this organization. We also found that the number of haplotypes (k) was influenced by the type of geographic distribution of the plant, while haplotype diversity (h) was affected by the type of flower, and the fixation index (F_ST), by the type of habitat. The plant species most closely-related phylogenetically have similar levels of genetic diversity. Overall, then, it will important to consider phylogenetic dependence in future studies that evaluate the effects of life-history traits on plant genetic diversity. Full article

Land-use change from natural to managed agricultural ecosystems significantly impacts soil bacterial diversity and function. The Eastern Free State (EFS) is one of the most productive agricultural regions in South Africa. However, no studies aiming to understand the changes in bacterial diversity, composition and function due to land-use change in this area have been conducted. This study investigated, using high-throughput 16S rRNA gene amplicon sequencing, the effects of long-term agriculture on bacterial diversity, composition and putative function in the EFS by comparing microbiomes from lands that have been under agronomic activity for over 50 years to those from uncultivated land. Results indicate that agriculture increased bacterial diversity. Soil chemical analysis showed that land-use shifted soils from being oligotrophic to copiotrophic, which changed bacterial communities from being Actinobacteria dominated to Proteobacteria dominated. Predictive functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that agricultural soil was abundant in genes associated with plant fitness and plant growth promotion, while non-agricultural soil was abundant in genes related to organic matter degradation. Together, these results suggest that edaphic factors induced by long-term agriculture resulted in shifts in bacterial diversity and putative function in the EFS. Full article

The amount of energy invested in sexual reproduction by scleractinian corals depends on their life history strategies (i.e., allocation of energy between growth, reproduction, and maintenance). However, energy allocated to reproduction will also be affected by the amount of energy acquired and prevailing environmental conditions. Coral fecundity is therefore likely to vary spatially, especially along marked gradients in environmental conditions. One of the foremost gradients in reef structure and environmental conditions occurs with distance from the coast, whereby inner-shelf or near shore reefs are generally subject to higher levels of nutrients, sediments and pollutants, which often adversely affect reef-building corals. This study quantified fecundity (oocytes per polyp) for three species, Acropora nasuta, A. spathulata, and A. hyacinthus, at six locations in the northern Great Barrier Reef (GBR), encompassing inner-, mid- and outer-shelf reefs. Replicate colonies were sampled at each location prior to the predicted date of spawning in 2013 and 2014. Both shelf position and year were important factors explaining variation in fecundity for each of the three coral species. Most notably, there were clear and consistent declines in the number of oocytes between 2013 and 2014, coinciding with the incidence of category 4 Cylone Ita in early 2014. Contrary to expectations, polyp-level fecundity was no lower (and in some cases substantially higher) on inner-shelf reefs, compared to conspecifics growing on mid-shelf or outer-shelf reefs. The observed patterns are much more complicated than anticipated, necessitating further research to understand differential population dynamics of corals on inner-shelf versus mid- and outer-shelf reefs. Full article

Lichens have important ecological functions in black pine forests, such as nitrogen fixation and nutrient cycling. Understanding lichen diversity could provide a better understanding of black pine ecosystems. The aim of this study was to identify the factors affecting the composition of lichen communities and their specific diversity in Mediterranean black pine forests. Research was conducted in 48 sampling plots. For the analysis, presence–absence and frequency data of lichen species were used. For stand level analysis, four community composition tables were created. We used bioclimate, topography, stand, and parent rock as variables. A total of 33 epiphytic lichen species were identified in the black pine forests from 282 sampled trees. Indicator lichen species were determined according to geographic region and stand age classes. Hypocenomyce scalaris was found to be an indicator species for old forests. Frequency data were more useful for revealing lichen species composition than presence–absence data. Of the topographic variables, elevation was the most prominent and had the highest explanation ratio for the composition of lichen species with a coefficient of correlation (R²) value of 0.49. Significantly positive (p < 0.001) relationships were found between epiphytic lichen richness and tree crown height, tree height, and bark pH. Our results revealed that to retain the trees in the stands rich in lichen species diversity is recommended in the managed forests. Full article

The Paradise Parrot, Psephotellus pulcherrimus, was a charismatic Australian bird that became extinct around 1928. While many extrinsic factors have been proposed to explain its disappearance, it remains unclear as to what extent genetic erosion might have contributed to the species’ demise. In this study, we use whole-genome resequencing to reconstruct a 15x coverage genome based on a historical museum specimen and shed further light on the evolutionary history that preceded the extinction of the Paradise Parrot. By comparing the genetic diversity of this genome with genomes from extant endangered birds, we show that during the species’ dramatic decline in the second half of the 19th century, the Paradise Parrot was genetically more diverse than individuals from species that are currently classified as endangered. Furthermore, demographic analyses suggest that the population size of the Paradise Parrot changed with temperature fluctuations during the last glacial cycle. We also confirm that the Golden-shouldered Parrot, Psephotellus chrysopterygius, is the closest living relative of this extinct parrot. Overall, our study highlights the importance of museum collections as repositories of biodiversity across time and demonstrates how historical specimens can provide a broader context on the circumstances that lead to species extinctions. Full article

Coral communities display spatial patterns. These patterns can manifest along a coastline as well as across the continental shelf due to ecological interactions and environmental gradients. Several abiotic surrogates for environmental variables are hypothesised to structure high-latitude coral communities in South Africa along and across its narrow shelf and were investigated using a correlative approach that considered spatial autocorrelation. Surveys of sessile communities were conducted on 17 reefs and related to depth, distance to high tide, distance to the continental shelf edge and to submarine canyons. All four environmental variables were found to correlate significantly with community composition, even after the effects of space were removed. The environmental variables accounted for 13% of the variation in communities; 77% of this variation was spatially structured. Spatially structured environmental variation unrelated to the environmental variables accounted for 39% of the community variation. The Northern Reef Complex appears to be less affected by oceanic factors and may undergo less temperature variability than the Central and Southern Complexes; the first is mentioned because it had the lowest canyon effect and was furthest from the continental shelf, whilst the latter complexes had the highest canyon effects and were closest to the shelf edge. These characteristics may be responsible for the spatial differences in the coral communities. Full article

Southern bull kelps (Durvillaea spp., Fucales) are ‘primary’ foundation species that control community structures and ecosystem functions on temperate wave-exposed rocky reefs. However, these large foundation species are threatened by disturbances and stressors, including invasive species, sedimentation and heatwaves. It is unknown whether ‘alternative’ foundation species can replace lost southern bull kelps and its associated communities and networks. We compared community structure (by quantifying abundances of different species) and attachment-interaction networks (by quantifying which species were attached to other species) among plots dominated by Durvillaea spp. and plots where Durvillaea spp. were lost either through long-term repeated experimental removals or by recent stress from a marine heatwave. Long-term experimental removal plots were dominated by ‘alternative’ foundation species, the canopy-forming Cystophora spp. (Fucales), whereas the recent heatwave stressed plots were dominated by the invasive kelp Undaria pinnatifida (Laminariales). A network analysis of attachment interactions showed that communities differed among plots dominated by either Durvillaea spp., Cystophora spp. or U. pinnatifida, with different relationships between the primary, or alternative, foundation species and attached epiphytic ‘secondary’ foundation species. For example, native Cystophora spp. were more important as hosts for secondary foundation species compared to Durvillaea spp. and U. pinnatifida. Instead, Durvillaea spp. facilitated encrusting algae, which in turn provided habitat for gastropods. We conclude that (a) repeated disturbances and strong stressors can reveal ecological differences between primary and alternative foundation species, (b) analyses of abundances and attachment-networks are supplementary methods to identify linkages between primary, alternative and secondary foundation species, and (c) interspersed habitats dominated by different types of foundation species increase system-level biodiversity by supporting different species-abundance patterns and species-attachment networks. Full article

Urban environments are densely populated areas buzzing with a wide range of anthropic activities that cause disturbances like air pollution or the heat island effect, threatening both human and environmental health. Mitigating its impacts implies understanding the integrated effects that those disturbances exert on urban environments. Lichen biodiversity is frequently used as an ecological indicator, being able to integrate its effects in a quantifiable way. The poleotolerance response trait classifies lichens according to their tolerance to human disturbance, but it was developed for Italy’s flora and has seldom been applied outside Italy or in urban context studies. The aim of this work was to assess this trait suitability as an indicator of urban anthropic disturbance and test it outside Italy. For that, we sampled lichen diversity in 41 green spaces in Lisbon. Lichens were classified into the respective poleotolerance trait functional groups and their community weighted mean related with three type of environmental variables used as surrogates of urban disturbance. We showed that disturbance-tolerant functional groups could be used as an ecological indicator of the integrated effects of environmental disturbances. Some species were clearly misclassified, so we propose reclassification for those. Natural and seminatural functional groups did not behave as expected. Nevertheless, disturbance-tolerant functional groups have the potential to be used in in other Southern European cities. Full article

This paper provides an overview of bioclimatic models applied to lichen species, supporting their potential use in this context as indicators of climate change risk. First, it provides a brief summary of climate change risk, pointing to the relevance of lichens as a topic area. Second, it reviews the past use of lichen bioclimatic models, applied for a range of purposes with respect to baseline climate, and the application of data sources, statistical methods, model extents and resolution and choice of predictor variables. Third, it explores additional challenges to the use of lichen bioclimatic models, including: 1. The assumption of climatically controlled lichen distributions, 2. The projection to climate change scenarios, and 3. The issue of nonanalogue climates and model transferability. Fourth, the paper provides a reminder that bioclimatic models estimate change in the extent or range of a species suitable climate space, and that an outcome will be determined by vulnerability responses, including potential for migration, adaptation, and acclimation, within the context of landscape habitat quality. The degree of exposure to climate change, estimated using bioclimatic models, can help to inform an understanding of whether vulnerability responses are sufficient for species resilience. Fifth, the paper draws conclusions based on its overview, highlighting the relevance of bioclimatic models to conservation, support received from observational data, and pointing the way towards mechanistic approaches that align with field-scale climate change experiments. Full article

Transitional areas between two or more different biomes—ecotones—are clearly visible due to the sudden changes in vegetation structures and patterns. However, much is still unknown about the crucial soil factors that control such vegetational changes across ecotones and how different soil properties vary across ecotones. In this study, we try to understand the spatial variation in soil properties across a clearly defined ecotone from a forest stand to meadow field at the Training Forest Enterprise (T.F.E), Masaryk Forest Křtiny, Czechia. Thirteen sampling sites were selected: six in the forest region, six in the meadow and one in the ecotone zone between forest and meadow. Soil samples were taken at 5 cm below the soil surface once every month from April to November. All the collected soil samples were examined for minimal air capacity, actual and potential soil reaction and maximum capillary water. The results showed a pattern of soil acidity decreasing from the forest stand towards the meadow field but that increased sharply at the ecotone zone. The water holding capacity showed a decreasing trend approaching the ecotone zone from the meadow region and markedly decreased from the meadow site closest to the ecotone zone. The minimum air capacity showed an increasing trend from the forest region but suddenly declined at the ecotone region. Full article

Nematodes are ideal biological indicators to monitor soil biodiversity and ecosystem functioning. For this reason, they have been receiving increasing attention from a broad range of scientists. The main method to characterize soil nematode communities until at least genus level is still based on microscopic observations of nematode morphology. Such an approach is time-consuming, labor-intensive, and requires specialized personnel. The first studies on the potential use of DNA-metabarcoding to characterize nematode communities showed some shortcomings: under- or overestimation of species richness caused by failure to detect a number of nematode species or caused by intraspecific sequence variants increasing the number of OTUs (operational taxonomic units) or ‘molecular’ species, and flaws in quantification. We set up experiments to optimize this metabarcoding approach. Our results provided new insights such as the drastic effect of different DNA-extraction methods on nematode species richness due to variation in lysis efficacy. Our newly designed primer set (18S rRNA gene, V4-V5 region) showed in silico an improved taxonomic coverage compared with a published primer set (18S rRNA gene, V6-V8 region). However, results of DNA-metabarcoding with the new primer set showed less taxonomic coverage, and more non-nematode reads. Thus, the new primer set might be more suitable for whole soil faunal analysis. Species-specific correction factors calculated from a mock community with equal amounts of different nematode species were applied on another mock community with different amounts of the same nematode species and on a biological sample spiked with four selected nematode species. Results showed an improved molecular quantification. In conclusion, DNA-metabarcoding of soil nematode communities is useful for monitoring shifts in nematode composition but the technique still needs further optimization to enhance its precision. Full article

Epiphytic richness is continuously declining due to forest fragmentation, logging, burning, agriculture, and livestock. The rate of species loss caused by habitat degradation and loss is more pronounced in Central and South America. Considering the extreme difficulty and time required to identify the more inconspicuous species, rapid diversity assessment methods need to be extrapolated throughout the world. This study correlated lichen growth forms and total epiphytic abundance across 119 forests located in Europe and Central-South America. A total of 54 papers were selected from specific databases focused on lichens. Additionally, data from several unpublished ecological studies were included. Linear regression models showed that epiphytic lichen abundance was highly and positively correlated with the number of growth forms at all geographical levels considered (i.e., Central-South American and European forests, and the combination of both). Thus, the use of growth forms may provide an alternative and complementary way to evaluate epiphytic diversity because most growth forms have cosmopolitan distribution and are easily recognizable. Full article

Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, and present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have shown mixed results in detecting the presence of these animals under field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored non-avian reptile eDNA quantification by sampling four lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months to detect differences in eDNA using a qPCR assay amplifying the COI gene of the mtDNA genome. Only one sample of the highest-density pond amplified eDNA for a positive detection. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present the “shedding hypothesis”—the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms—as a potential challenge for eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles. Full article

Chondrichthyes (sharks, rays, skates and chimaeras) are among the oldest extant predators and are vital to top-down regulation of oceanic ecosystems. They are an ecologically diverse group occupying a wide range of habitats and are thus, exploited by coastal, pelagic and deep-water fishing industries. Chondrichthyes are among the most data deficient vertebrate species groups making design and implementation of regulatory and conservation measures challenging. High-throughput sequencing technologies have significantly propelled ecological investigations and understanding of marine and terrestrial species’ populations, but there remains a paucity of NGS based research on chondrichthyan populations. We present a brief review of current methods to access genomic and metagenomic data from Chondrichthyes and discuss applications of these datasets to increase our understanding of chondrichthyan taxonomy, evolution, ecology and population structures. Last, we consider opportunities and challenges offered by genomic studies for conservation and management of chondrichthyan populations. Full article

Climate change and the overall increase of seawater temperature are causing a poleward shift in species distribution, which includes a phenomenon described as the tropicalization of temperate regions. This work aims to report the first records of four species off the southwestern Iberian Peninsula, namely, the oceanic puffer Lagocephalus lagocephalus (Linnaeus, 1758), the Madeira rockfish Scorpaena maderensis Valenciennes, 1833, the ornate wrasse Thalassoma pavo (Linnaeus, 1758), and the bearded fireworm Hermodice carunculata (Pallas, 1766). These last three species, along with other occurrences of aquatic fauna and flora along the Portuguese coast, reveal an ongoing process of poleward expansion of several species, which urgently necessitates a comprehensive survey along the entire Iberian Peninsula. The putative origins of these subtropical and tropical species off continental Portugal are discussed, as well as the potential public health problems that two of the four reported species may cause. Full article

Few reports have been published on detection distances of bat calls because the evaluation of detection distance is complicated. Several of the approaches used to measure detection distances are based on the researcher’s experience and judgment. More recently, multiple microphones have been used to model flight path. In this study, the validity of a low-cost and simple detectability metric was tested. We hypothesize that the duration of an echolocating-bat-pass within the area of an ultrasonic bat detector is correlated with the distance of detection. Two independent datasets from a large-scale acoustic bat survey—a total of 25,786 bat-passes from 20 taxa (18 species and two genera)—were measured. We found a strong relationship between these measures of bat-pass duration and published detection distances. The advantages of bat-pass duration measures are that, for each study, experimenters easily produce their own proxy for the distance of detection. This indirect measure of the distance of detection could be mobilized to monitor the loss in microphone sensitivity used to monitor long-term population trends. Finally, the possibility of producing an index for distance of detection provides a weight for each bat species’ activity when they are aggregated to produce a bat community metric, such as the widely used “total activity”. Full article

Many coral reef systems are shelf-based and consist of reefs that are arranged in rows parallel to the coastline. They usually show an increase in species richness in the offshore direction, coinciding with decreasing terrigenous impact and a deeper seafloor. These two conditions usually concur, which makes it less easy to distinguish how each of them influences coral diversity separately. Since reefs off Jakarta (in the Thousand Islands archipelago) are arranged in an 80 km long string perpendicular to the coastline in south-to-north direction, with a maximum shelf depth halfway along (instead of at the end of) the string, this archipelago is very suitable for studies on inshore–offshore gradients. In the present study, mushroom corals (Fungiidae; n = 31) were used to examine diversity patterns on 38 reef sites along such a gradient, involving species richness over their entire depth range from reef flat to reef base (2–30 m) and separately at shallow depths (2–6 m). Total species diversity was highest in the central part of the archipelago, with unique species occurring in deep habitats. Diversity at shallow depths was only slightly higher here than at reefs located more nearshore and offshore, which both had less clear water. Therefore, shelf depth and distance from the mainland can be considered separate determinants of coral diversity off Jakarta. Full article

Climate change and the anthropic emission of pollutants are likely to have an accelerated impact in high-elevation mountain areas. This phenomenon could have negative consequences on alpine habitats and for species of conservation in relative proximity to dense human populations. This premise implies that the crucial task is in the early detection of warning signals of ecological changes. In alpine landscapes, high-elevation forests provide a unique environment for taking full advantage of epiphytic lichens as sensitive indicators of climate change and air pollution. This literature review is intended to provide a starting point for developing practical biomonitoring tools that elucidate the potential of hair-lichens, associated with high-elevation forests, as ecological indicators of global change in the European Alps. We found support for the practical use of hair-lichens to detect the impact of climate change and nitrogen pollution in high-elevation forest habitats. The use of these organisms as ecological indicators presents an opportunity to expand monitoring activities and develop predictive tools that support decisions on how to mitigate the effects of global change in the Alps. Full article