Find research datasets worth reusing

opencc-by-4.0Feb 2023View details →

Tampere - Biodiversity surveys and species diversity

Results of the biodiversity surveys and corresponding evaluation of the diversity of species in Tampere.

opencc-by-4.0Apr 2013View details →

Fig. 28 in Terrestrial mollusc species richness and diversity in Omo Forest Reserve, Ogun State, Nigeria

Fig. 28. Dendrogram of Bray-Curtis similarity between plots in sites I and II.

opencc-by-4.0Apr 2013View details →

Fig. 2 in Terrestrial mollusc species richness and diversity in Omo Forest Reserve, Ogun State, Nigeria

Fig. 2. Rank abundance curve for terrestrial snails from Omo Forest Reserve in Ogun State, Nigeria.

opencc-zeroMar 2023View details →

Impacts of ecological restoration on the genetic diversity of plant species: A global meta-analysis

1. In contrast to the depth of knowledge available for the enhancement of plant species diversity and ecosystem services through ecological restoration, our understanding of how ecological restoration impacts genetic diversity (GD) of plant species has not yet been synthesized. 2. We performed a global meta-analysis to examine whether ecological restoration improved GD of plant species in restored populations. First, we compared the GD of restored populations with reference or degraded populations. Second, we explored whether the influence of ecological restoration on plant GD varies between species with different characteristics (life form and threat status), between different restoration strategies (active/passive, seeding/planting, mixture/non-mixture) or between different restoration times (<50 and ≥50 years; with an average of 29.3 years). 3. The GD of restored populations was significantly lower (HE, 1.06%; PPB, 5.10%, and SWI, 4.95%) than in reference populations but was comparable to degraded populations. The inbreeding coefficient (FIS, the proportion by which the heterozygosity of an individual is reduced by inbreeding) was consistently comparable between restored populations and reference or degraded populations. 4. Woody species but not herbs had significantly lower GD in restored populations than in reference populations. Forest but not grassland ecosystem had significantly lower GD in restored populations than in reference populations. Passive but not active restoration, seeding rather than planting, and mixing materials from different sources rather than using a single source, all significantly increased the GD of restored populations. When the restoration time was ≥50 years, in contrast to <50 years, GD was comparable between the restored and reference populations. 5. Synthesis and applications. In general, ecological restoration did not significantly improve the GD of plant species compared to reference or degraded populations. This might be due in part to the relatively short restoration time. Using passive restoration, seeding, and mixed sources could significantly increase the GD of restored populations. We emphasize that GD should not be treated as a minor cobenefit of ecological restoration for other purposes and that the recovery of GD should be listed as a vital goal in future ecological restoration with plant species.

openother-openApr 2023View details →

Data from: Chilean bee diversity: Contrasting patterns of species and phylogenetic turnover along a large-scale ecological gradient

Title of dataset Data from: Chilean bee diversity: Contrasting patterns of species and phylogenetic turnover along a large-scale ecological gradient Authors of dataset Leon Marshall1,2, John S. Ascher3, Cristian Villagra4, Amaury Beaugendre1, Valentina Herrera4, Patricia Henríquez-Piskulich4, Alejandro Vera5, Nicolas J. Vereecken1 <ol> <li>Agroecology Lab, Université libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/2, B 1050 Brussels, Belgium</li> <li>Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands</li> <li>Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore</li> <li>Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Región Metropolitana, Chile</li> <li>Departamento de Biología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Región Metropolitana, Chile</li> </ol> Abstract Chile's isolation and varied climates have driven the evolution of a unique biodiversity with a high degree of endemism. As a result, Chile encompasses diverse environments, including the Mediterranean-type ecosystem, a global biodiversity hotspot. These environments are currently threatened by anthropogenic land use change impacting the integrity of local biomes and associated species. This area is the most intensively sampled of the country with high endemicity of native bee species. Characterising habitat requirements of bees is a pressing priority to safeguard these insects and the ecosystem services they provide. We investigated broad-scale patterns of bee (Hymenoptera: Apoidea: Anthophila) diversity using newly accessible expert-validated datasets comprising digitized specimen records from Chilean and US collections, and novel expert-validated type specimen data for the bees of Chile. We used a generalised dissimilarity modelling (GDM) approach to explore both compositional and phylogenetic β-diversity patterns across latitudinal, altitudinal, climate and habitat gradients in well-sampled bee assemblages in Central Chile. Using the GDM measures of increasing compositional and environmental dissimilarity we categorised and compared the most important drivers of these patterns and used them to classify 'wild bee ecoregions' (WBE) representing unique assemblages. Turnover of bee assemblages was explained primarily by latitudinal variation (proxy for climate) from south to north in Chile. However, temperature variations, precipitation and the presence of bare soil also significantly explained turnover in bee assemblages. In comparison, we observed less turnover in phylogenetic biodiversity corresponding to spatial gradients. We identified six de novo ecoregions (WBE), all with distinct taxa, endemic lineages, and representative species. The WBE represent distinct spatial classifications but have similarities to existing biogeographical classifications, ecosystems and bioclimatic zones. This approach establishes the baseline needed to prioritise bee species conservation efforts across this global biodiversity hotspot. We discuss the novelty of this classification considering previous biogeographical characterisations and their relevance in assessing conservation priorities for bee conservation. We argue that Chile's WBE highlight areas in need of funding for bee species surveys and description, distribution mapping and strengthening of conservation policies. Usage notes The dataset contains species occurrence data of chilean bees aggregated to a 5 x 5 km grid shapefile. The shapefile of the grid and the raster mask of the Central Chilean study area are also included. Finally, a database of type specimen data used to supplement the dataset is included here.  The code for the analysis can be found at: <a href="https://github.com/lmar116/ChileanBeeDiversity">https://github.com/lmar116/ChileanBeeDiversity</a>. Shapefiles, rasters, CSV files and code were all loaded and analyzed using R statistics software.  Four files are included: <ol> <li>Marshall-et-al-2023_Ecosphere_DataTable_bee_grid: contains all species occurrence data used in GDM analysis, Grid column refers to cl.5km.shp.</li> <li>cl.5km.shp (and associated files): 5 x 5 km grid shapefile of the Central Chilean study area</li> <li>chile.mask.tif: raster outline of the Central Chilean study area</li> <li>Marshall-et-al-2023_Ecosphere_CentralChileTypeSpecimens.xlsx: contains type specimen data used to supplement species occurrence dataset.</li> </ol>

opencc-by-4.0Nov 2023View details →

UAV-Based Height Measurement and Height-Diameter Model integrating Taxonomic Effects: Exploring Vertical Structure of Aboveground Biomass and Species Diversity in a Malaysian Tropical Forest

These Excel files are the dataset used for the analysis in the submitted paper Dataset S1: Data for 6-ha pot in Pasoh Forest Researve Dataset S2: Data for height–diameter (HD) models

opencc-zeroMay 2023View details →

Data for: Patterns of species diversity in a network of artificial wetlands

Aim Artificial island habitats such as human-made wetlands are emerging novel ecosystems. Understanding the drivers of diversity in such artificial systems is essential for balancing the goals of biodiversity conservation and human socio-economic needs. Location Telangana State, India. Methods We surveyed water birds in a network of 57 artificial wetlands and assessed four macroecological biodiversity patterns: spatial beta diversity, temporal beta diversity, species-abundance distributions (SADs), and the species–area relationship (SAR). We employed a mix of phenomenological and mechanistic models to examine the four macro-ecological patterns. We hypothesised that the wetland bird communities are primarily structured by immigration–extinction dynamics and thus that spatial and temporal beta diversity would be high, the within-wetland SADs would exhibit a large number of rare species and a monotonically declining overall shape, and that the SAR across wetlands would be strongly increasing. Results Spatial and temporal beta diversity were both high and mostly attributable to turnover rather than nestedness. While the pooled SAD exhibited an interior mode, the SAD for individual wetlands was generally log-series distributed, consistent with a model in which immigration among wetlands is high. The SAR exhibited an increasing trend, with the "small-island effect", which reflects constraints on immigration and is often observed for true island archipelagos, being absent. Main Conclusions We tentatively conclude that bird diversity in this network of artificial wetlands is mainly structured by immigration–extinction dynamics, although we acknowledge that some of the patterns are also consistent with niche dynamics and future research should measure relevant biotic and abiotic variables in these wetlands. We encourage future work in which our rich data set is used to fit dynamic models that permit more detailed quantitative inferences about mechanisms structuring diversity in this novel ecosystem, which can ultimately also inform conservation management.

opencc-zeroMay 2023View details →

Genetic diversity varies with species traits and latitude in predatory soil arthropods (Myriapoda: Chilopoda)

Aim To investigate the drivers of intra-specific genetic diversity in centipedes, a group of ancient predatory soil arthropods. Location Asia, Australasia and Europe Time period Present Major taxa studied Centipedes (Class: Chilopoda) Methods We assembled a database of 1245 mitochondrial cytochrome c oxidase subunit I sequences representing 128 centipede species from all five orders of Chilopoda. This sequence dataset was used to estimate genetic diversity for centipede species and compare its distribution with estimates from other arthropod groups. We studied the variation in centipede genetic diversity with species traits and biogeography using a beta regression framework, controlling for the effect of shared evolutionary history within a family. Results A wide variation in genetic diversity across centipede species (0 to 0.1713) falls towards the higher end of values among arthropods. Overall, 27.57% of the variation in mitochondrial COI genetic diversity in centipedes was explained by a combination of predictors related to life history and biogeography. Genetic diversity decreased with body size and latitudinal position of sampled localities, was greater in species showing maternal care and increased with geographic distance among conspecifics. Main conclusions Centipedes fall towards the higher end of genetic diversity among arthropods, which may be related to their long evolutionary history and low dispersal ability. In centipedes, the negative association of body size with genetic diversity may be mediated by its influence on local abundance or the influence of ecological strategy on long-term population history. Species with maternal care had higher genetic diversity, which goes against expectations and needs further scrutiny. Hemispheric differences in genetic diversity can be due to historic climatic stability and lower seasonality in the southern hemisphere. Overall, we find that despite the differences in mean genetic diversity among animals, similar processes related to life history strategy and biogeography are associated with the variation within them.

opencc-zeroJun 2023View details →

Effects of tree species diversity and conspecific seedling density on insect herbivory and pathogen infection on big-leaf mahogany seedlings

The Janzen-Connell Hypothesis (JCH) predicts that attack by specialist enemies on seedlings increases with conspecific seedling density, but studies have rarely experimentally tested for the contingency of such effects on tree community context (e.g., diversity, composition) and measured responses by different enemies (e.g. herbivores, pathogens). We conducted a field study in a large-scale system evaluating tree species diversity and conspecific density effects on leaf damage on mahogany (Swietenia macrophylla) seedlings. We established quadrats of eight levels of seedling density across mahogany tree monocultures and species polycultures including mahogany, and recorded percent leaf damage by insects and percent leaf necrosis by a pathogenic fungus on mahogany seedlings. We found contrasting effects of tree species diversity on insects and pathogens. Whereas diversity did not affect leaf damage by insects, it had a significant negative effect on leaf necrosis by pathogens. On average, percent leaf necrosis on mahogany seedlings in polyculture was half of that observed in monoculture. We discuss the potential influences of changes in mahogany tree density vs. frequency (relative to other tree species) driving this diversity effect. Unexpectedly, we found no effect of seedling conspecific density on either leaf insect or pathogen damage (i.e., density-independent attack). Likewise, we found no significant tree diversity by seedling density interaction, indicating that attackers were consistently unresponsive to variation in seedling density across two levels of tree diversity. Overall, this study provides a unique test of the JCH by experimentally evaluating seedling density and tree diversity effects on contrasting plant enemies, shedding light on enemy controls over plant recruitment.

opencc-by-4.0Jun 2023View details →

Fig. 7 in The discovery of two new species in the Cyrtodactylus irregularis group highlights that hidden diversity remains in the largest clade of the mega-diverse genus Cyrtodactylus

Fig. 7. Cyrtodactylus arndti sp. nov., paratypes ♂♂ (IEBR R.4931, IEBR R.4932), in life.

opencc-by-4.0Jun 2023View details →

Fig. 3 in The discovery of two new species in the Cyrtodactylus irregularis group highlights that hidden diversity remains in the largest clade of the mega-diverse genus Cyrtodactylus

Fig. 3. Cyrtodactylus chumuensis sp. nov., holotype, ♂ (IEBR R.4928), in life.

opencc-by-4.0Jun 2023View details →

Fig. 6 in The discovery of two new species in the Cyrtodactylus irregularis group highlights that hidden diversity remains in the largest clade of the mega-diverse genus Cyrtodactylus

Fig. 6. Cyrtodactylus arndti sp. nov., holotype, ♂ (IEBR R.4930), in life.

opencc-zeroJul 2023View details →

Data for: Increases in functional diversity of mountain plant communities is mainly driven by species turnover under climate change

Warming in mountain regions is projected to be three times faster than the global average. Pronounced climate change will likely lead to species reshuffling in mountain plant communities and consequently change ecosystem resilience and functioning. Yet, little is known about the role of inter- versus intraspecific changes of plant traits and their consequences for functional richness and evenness of mountain plant communities under climate change. We performed a downslope translocation experiment of intact plant-soil mesocosms from an alpine pasture and a subalpine grassland in the Swiss and Austrian Alps to simulate an abrupt shift in climate and removal of dispersal barriers. Translocated plant communities experienced warmer and dryer climatic conditions. We found a considerable shift from resource conservative to resource acquisitive leaf-economy in the two climate change scenarios. However, shifts in leaf-economy were mainly attributable to species turnover, namely colonization by novel lowland species with trait expressions for a wider range of resource use. We also found an increase in vegetative height of the warmed and drought-affected alpine plant community, while trait plasticity to warming and drought was limited to few graminoid species of the subalpine plant community. Our results highlight the contrast between the strong competitive potential of novel lowland species in quickly occupying available niche space and native species' lack of both the intraspecific trait variability and the plant functional trait expressions needed to increase functional richness under warming and drought. This is particularly important for the trailing range of many mountain species (i.e. subalpine zone) where upward moving lowland species are becoming more abundant and abiotic climate stressors are likely to become more frequent in the near future. Our study emphasizes mountain plant communities' vulnerability to novel climates and biotic interactions under climate change and highlights graminoid species as potential winners of a warmer and dryer future.

opencc-zeroJul 2023View details →

Eutrophication decreases ecological resilience by reducing species diversity and altering functional traits of submerged macrophytes

Positive feedback is key to producing alternative stable states and largely determines ecological resilience in response to external perturbations. Understanding the positive feedback mechanisms in macrophyte-dominated lakes is crucial for resilience-based management and restoration. Based on the field investigation of submerged macrophyte communities in 35 lakes in China, we found that morphological complexity (MC) and morphological plasticity (MP) are correlated with the stoichiometric homeostasis of phosphorus (HP) and are related to ecosystem structure, functioning, and stability. We also found that the positive feedback strength of lakes dominated by macrophytes is biomass- and diversity-dependent. Eutrophication can decrease the community biomass by decreasing community MC, MP, and HP and the species diversity through low-light availability, ultimately decreasing the positive feedback strength and resilience of clear-water states. We argue that functional traits and species diversity should be considered to build more resilient ecosystems in future changing environment scenarios.

opencc-by-4.0Jul 2023View details →

The isolation of novel species expands the genomic diversity of Lachnospiraceae

A comprehensive understanding of the diversity of Lachnospiraceae, one of the most promising next-generation probiotics, is currently lacking, which limits the selection of strains for subsequent applications. To address this, we performed an in-depth genomic and functional analysis of 1,868 high-quality isolated genomes by integrating data from public databases and our new isolates, representing 387 colonization selective species-level clusters, of which 9 genera represent multi-lineage clusters. Pan-genome analysis, single nucleotide polymorphism (SNP) identification, and probiotic functional predictions revealed that species taxonomy, habitats, and geography shape the functional diversity of Lachnospiraceae. Finally, analyses of associations with atherosclerotic cardiovascular disease (ACVD) indicated that many strains of the potentially novel species can reduce the abundance of opportunistic pathogens. Together, the large-scale genomics diversity analysis of Lachnospiraceae highlights the importance of potentially novel species and provides the ability for strain-level metagenomic association analysis to guide the selection of strains for the next-generation probiotics.

opencc-zeroJul 2023View details →

Diversity of mitochondrial DNA in three species of great whales before and after modern whaling

The 20th-century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for three great whales in the South Atlantic, the blue, humpback and fin whale. Pre-whaling diversity is described from mtDNA extracted from bones collected near abandoned whaling stations, primarily from the South Atlantic island of South Georgia. These bones are known to represent the first stage of 20th-century whaling and thus pre-whaling diversity of these populations. Post-whaling diversity is described from previously published studies reporting large-scale sampling of living whales in the Southern Hemisphere. Despite relatively high levels of surviving genetic diversity in the post-whaling populations, we found evidence of a probable loss of mtDNA lineages in all three species. This is evidenced by the detection of a large number of haplotypes found in the pre-whaling samples that are not present in the post-whaling samples. A rarefaction analysis further supports a loss of haplotypes in the South Atlantic humpback and Antarctic blue whale populations. The bones from former whaling stations in the South Atlantic represent a remarkable molecular archive for further investigation of the decline and ongoing recovery in the great whales of the Southern Hemisphere.

Functional identity of dominant species in a predator community prevails over functional diversity in shaping the top-down control of herbivores

<ol> <li>Decline in species richness as well as changes in community evenness or functional diversity have been hypothesized to jointly affect ecosystem functioning. However, disentangling the relative effects of these changes in community structure is hard as these different aspects often covary with species richness in real-world ecosystems. In this study, we investigated the individual and interactive effects of functional diversity and community evenness of predators on the level of control of herbivorous prey. </li> <li>Using a highly-replicated mesocosm experiment, we crossed three levels of functional diversity of arthropod predators with two levels of community evenness while controlling for the effect of species richness. Using this experimental setting, we hypothesized that the effect size of functional diversity of predators depends on community evenness. We expected a positive effect of functional diversity of predators on top-down control at a high level of community evenness while we thought that species identity and their associated traits should drive most of the effect on top-down control at a low level of community evenness. </li> <li>Our results did not provide any evidence for an interaction between functional diversity and community evenness nor any beneficial effect of increased functional diversity overall on predation rates of herbivorous prey. In addition, our results revealed that species and functional identity drives most of the effects of predator community composition on top-down control of their prey in our study system. Assemblages composed of active hunters with low handling time and no starvation ability tended to have the highest impacts on prey biomass.</li> <li>By indicating that top-down control of herbivorous prey by arthropod predators is mainly driven by species and functional identity and not by functional diversity, our study provides insights into the consequences of ongoing species loss on ecosystem functioning. Future research should now explore the predictability of trophic interactions based on functional traits of predator and herbivorous prey to anticipate the consequences of changes in species composition on ecosystem functioning.</li> </ol>

Avian species functional diversity and habitat use the role of forest structural attributes and tree diversity in the Midlands Mistbelt forests of KwaZulu-Natal, South Africa

Forest transformation has major impacts on biodiversity and ecosystem functioning. Identifying the influence of forest habitat structure and composition on avian functional communities is important for conserving and managing forest systems. This study investigated the effect of forest structure and composition characteristics on bird species community structure, habitat use, and functional diversity in 14 Mistbelt forest patches of the Midlands of KwaZulu-Natal in South Africa. We surveyed bird communities using point counts. We quantified bird functional diversity for each forest patch using three diversity indices: functional richness, functional evenness, and functional divergence. We further assessed species-specific responses by focusing on three avian forest specialists, orange ground-thrush Geokichla gurneyi, forest canary Crithagra scotops, and Cape parrot Poicephalus robustus. We found that bird community and forest-specialist species responses to forest structure and tree species diversity differed. Also, forest structural complexity, canopy cover, and tree species richness were the main forest characteristics better at explaining microhabitat influence on bird functional diversity. Forest patches with relatively high structural complexity and tree species richness had higher functional richness. Different structural characteristics influenced habitat use by the three forest specialists. Tree species diversity influenced C. scotops and G. gurneyi positively, while P. robustus responded negatively to forest patches with high tree species richness. Our study showed that site-scale forest structure and composition characteristics are important for bird species richness and functional richness. Forest patches with high tree species diversity and structural complexity should be maintained to conserve forest specialists, bird species richness, and functional richness.

Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA

Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population-level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population-level genetic data from sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species with a circumpolar distribution and three lineages for present-day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primers to target these. Initial multiplex PCR testing resulted in a final set of 38 primers. These primers were used to analyse 20 lake sedaDNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V. uliginosum lineages in these regions and all primers could be recovered from the sedaDNA data, where for each sample 28.1 primers containing 34.15 variant sequences were obtained on average. All sediment samples were dominated by a single lineage, except three alpine samples which had co-occurrence of two different lineages. Furthermore, lineage turnover was observed in the Alps and northern Norway, suggesting that present-day phylogeographical studies may overlook past genetic patterns. Multiplexing primers is a promising tool for generating population-level genetic information from sedaDNA. The relatively simple method, combined with high sensitivity, provides a scalable method that will allow researchers to track populations through time and space using environmental DNA.

Testing the links between bird diversity, alien species and disturbance within a human-modified landscape

Introduced alien species are associated with lower taxonomic, functional and phylogenetic diversity of native communities and negative impacts on ecosystem functioning. This is particularly evident in habitats where human disturbance may favour alien species, posing an additional stressor on native communities. Following the community resistance hypothesis (higher diversity promotes higher resistance to invasion), we predicted: i) higher taxonomic, functional and phylogenetic diversity (TD, FD and PD respectively) in non-invaded bird communities (i.e. no alien bird species); and, ii) higher diversity and resistance to invasion in less human-disturbed areas. We surveyed bird communities in a modified Mediterranean landscape subject to varying levels of human disturbance. We tested whether TD, FD and PD were significantly different between non-invaded and invaded bird communities, and assessed the effect of land classes (forest, agriculture, urban), landscape composition and heterogeneity on these metrics. We found that non-invaded communities retained higher TD and FD, but not PD, than invaded communities. Alien birds occupied marginal niches in invaded communities, and did not fully compensate for the taxonomic and functional diversity loss caused by the absence of native species. These results were consistent across different land classes, suggesting weak environmental filtering of communities. Generally, less human-modified and more heterogeneous areas supported higher TD regardless of the presence of alien species. FD and PD of invaded communities decreased with increases in human-modified areas, whereas non-invaded communities were not affected. Our results suggest that even within a human-modified landscape, invaded community diversity is more affected by, and thus has a lower resilience to, disturbance. Restoring and protecting natural habitats within human-modified landscapes is likely to increase the resilience of native species.