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5,864 results for “species diversity”
Data from: How diverse is Mitopus morio? Integrative taxonomy detects cryptic species in a small-scale sample of a widespread harvestman
Mitopus morio is a widespread harvestman species occurring in most of Europe and in moderate and cold-moderate zones of Asia and North America. The species is characterized by extreme variability in body size and leg length. As leg length is correlated with habitat temperature, M. morio has been considered as an example of Allen's rule. Recently, observations for a single location in Tyrol, Austria, indicated the absence of mating between short- and long-legged individuals. This study examines for signs of putative cryptic species in M. morio using an integrative approach that combines mating trials, amplified fragment length polymorphism whole-genome scans, mitochondrial sequences and morphometrics. The mating trials did not corroborate the initial hypothesis of a reproductive barrier associated with leg size. Both types of genetic data revealed the existence of three distinct groups, in line with the mating results but largely unrelated to leg morphology and geographical origin of specimens. Morphometric characters supporting the findings of the other disciplines were identified using a supervised approach. We infer from all data together the existence of strongly diverged cryptic lineages among the analysed individuals, cautiously interpret them as three sympatric species and conclude that in these harvestmen Allen's rule applies at different levels. Due to the unexpected amount of differentiation found within a geographical scale very small compared with the distribution of M. morio, we suggest a thorough revision of the genus prior to formal taxonomic changes. Our case study underlines the general applicability of the integrative taxonomic protocol used and highlights the relevance of several rationales implemented in the protocol.
Data from: Diversity patterns of native and exotic fish species suggest homogenization processes, but partly fail to highlight extinction threats
Exotic species are a major threat to biodiversity and have modified native communities worldwide. Invasion processes have been extensively studied, but studies on species richness and beta diversity patterns of exotic and native species are rare. We investigate such patterns among exotic and native fish communities in upland and lowland rivers to explore their relationship with environmental drivers. Location: Northern Italy. Exotic and native fish beta diversity patterns were investigated separately in lowland and upland sites using Local Contribution to Beta Diversity (LCBD) and Species Contribution to Beta Diversity (SCBD) analyses. To examine the main environmental variables affecting the LCBD, a Boosted Regression Trees (BRT) method was used. Community dispersion among and within stream orders was investigated with the PERMDISP test. In lowland sites, exotic species richness was higher than native species richness, especially in large rivers and drainage canals. An opposite trend was found in upland sites, where native species richness was higher than exotic species richness, especially in large rivers. No clear LCBD patterns were found along stream orders in the lowland, whereas higher stream orders in the upland showed the highest LCBD. Its patterns in upland and lowland sites were related with a number of factors, such as total suspended solids and total phosphorus. Community dispersion among stream orders did not show a relationship with environmental heterogeneity. SCBD values were positively correlated with species occupancy in the study area and native species showed higher SCBD values than exotic species only in the uplands. Main conclusions: Large rivers in the uplands are important in maintaining native fish diversity and should be protected against invasive fish. In contrast, most lowland rivers have suffered from biological homogenization. Some rare native species can show low contribution to beta diversity, but still need conservation actions due to their risk of local extinction.
Figure 2 in Diversity of Diptera species associated with pig carcasses in a Brazilian city exposed to high rates of homicide
Figure 2. Dominance ranking for dipterans species according to the season (Dry or Rainy).
Data from: Habitat diversity associated with island size and environmental filtering control the species richness of rock-savanna plants in neotropical inselbergs
Disentangling the multiple factors controlling species diversity is a major challenge in ecology. Island biogeography and environmental filtering are two influential theories emphasizing respectively island size and isolation, and the abiotic environment, as key drivers of species richness. However, few attempts have been made to quantify their relative importance and investigate their mechanistic basis. Here, we applied structural equation modelling, a powerful method allowing test of complex hypotheses involving multiple and indirect effects, on an island-like system of 22 French Guianan neotropical inselbergs covered with rock-savanna. We separated the effects of size (rock-savanna area), isolation (density of surrounding inselbergs), environmental filtering (rainfall, altitude) and dispersal filtering (forest-matrix openness) on the species richness of all plants and of various ecological groups (terrestrial versus epiphytic, small-scale versus large-scale dispersal species). We showed that the species richness of all plants and terrestrial species was mainly explained by the size of rock-savanna vegetation patches, with increasing richness associated with higher rock-savanna area, while inselberg isolation and forest-matrix openness had no measurable effect. This size effect was mediated by an increase in terrestrial-habitat diversity, even after accounting for increased sampling effort. The richness of epiphytic species was mainly explained by environmental filtering, with a positive effect of rainfall and altitude, but also by a positive size effect mediated by enhanced woody-plant species richness. Inselberg size and environmental filtering both explained the richness of small-scale and large-scale dispersal species, but these ecological groups responded in opposite directions to altitude and rainfall, that is positively for large-scale and negatively for small-scale dispersal species. Our study revealed both habitat diversity associated with island size and environmental filtering as major drivers of neotropical inselberg plant diversity and showed the importance of plant species growth form and dispersal ability to explain the relative importance of each driver.
Data from: Fire-sensitive species dominate seed rain in a long unburned Cerrado: implications for plant community diversity and woody encroachment in savannas
Woody encroachment is becoming common in tropical savannas. Seed rain data and seed addition experiments in a long unburned Brazilian savanna indicate that abundant seed rain of fire-sensitive species can surpass limitations to recruitment and lead to woody encroachment. Thus, active fire management may be required to maintain savanna diversity.
Data from: Supporting local diversity of habitats and species on farmland: a comparison of three wildlife-friendly schemes
Restoration and maintenance of habitat diversity have been suggested as conservation priorities in farmed landscapes, but how this should be achieved and at what scale are unclear. This study makes a novel comparison of the effectiveness of three wildlife-friendly farming schemes for supporting local habitat diversity and species richness on 12 farms in England. The schemes were: (i) Conservation Grade (Conservation Grade: a prescriptive, non-organic, biodiversity-focused scheme), (ii) organic agriculture and (iii) a baseline of Entry Level Stewardship (Entry Level Stewardship: a flexible widespread government scheme). Conservation Grade farms supported a quarter higher habitat diversity at the 100-m radius scale compared to Entry Level Stewardship farms. Conservation Grade and organic farms both supported a fifth higher habitat diversity at the 250-m radius scale compared to Entry Level Stewardship farms. Habitat diversity at the 100-m and 250-m scales significantly predicted species richness of butterflies and plants. Habitat diversity at the 100-m scale also significantly predicted species richness of birds in winter and solitary bees. There were no significant relationships between habitat diversity and species richness for bumblebees or birds in summer. Butterfly species richness was significantly higher on organic farms (50% higher) and marginally higher on Conservation Grade farms (20% higher), compared with farms in Entry Level Stewardship. Organic farms supported significantly more plant species than Entry Level Stewardship farms (70% higher) but Conservation Grade farms did not (10% higher). There were no significant differences between the three schemes for species richness of bumblebees, solitary bees or birds. Policy implications. The wildlife-friendly farming schemes which included compulsory changes in management, Conservation Grade and organic, were more effective at increasing local habitat diversity and species richness compared with the less prescriptive Entry Level Stewardship scheme. We recommend that wildlife-friendly farming schemes should aim to enhance and maintain high local habitat diversity, through mechanisms such as option packages, where farmers are required to deliver a combination of several habitats.
Data from: Burning savanna for avian species richness and functional diversity
<p><span>Prescribed fire is used throughout fire-prone landscapes to conserve biodiversity. Current best practice in managing savanna systems advocates methods based on the assumption that increased fire-mediated landscape heterogeneity (pyrodiversity) will promote biodiversity. However, considerable knowledge gaps remain in our understanding of how savanna wildlife responds to the composition and configuration of pyrodiverse landscapes. The effects of pyrodiversity on functional diversity has rarely been quantified and assessing this relationship at a landscape scale which is commensurate with fire management is important for understanding mechanisms underlying ecosystem resilience. Here, we assess the impact of spatiotemporal variation in a long-term fire regime on avian diversity in North West Province, South Africa. <a name="_Hlk12800642">We examined the relationship between (a) species richness, (b) three indices of functional diversity</a> (i.e., functional richness, functional evenness and functional dispersion) and four measures of pyrodiversity, the spatial extents of fire age-classes, and habitat type at the landscape-scale. We then used null models to assess differences between observed and expected functional diversity. <a name="_Hlk23757785">We found that the proportion of newly-burned (<1-year post-fire), old, unburned (≥10 years post-fire), and woodland habitat on the landscape predicted species and functional richness. </a><a name="_Hlk535845085">Species richness also increased with the degree of edge contrast between patches of varying fire age, while functional dispersion increased with the degree of patch shape complexity. Lower than expected levels of functional richness suggest that habitat filtering is occurring, resulting in functional redundancy across our study sites. </a>We demonstrate that evaluating functional diversity and redundancy is an important component of conservation planning as they may contribute to previously reported fire resilience. Our findings suggest that it is the type and configuration, rather than the diversity, of fire patches on the landscape that promote avian diversity and conserve ecological functions. A management approach is needed that includes significant coverage of adjacent newly-burned and older, unburned savanna habitat; the latter, in particular, is inadequately represented under current burning practices.</span></p>
Data from: Genome-wide assessment of diversity and divergence among extant Galápagos giant tortoise species
Genome-wide assessments allow for fuller characterization of genetic diversity, finer-scale population delineation, and better detection of demographically significant units to guide conservation compared to those based on "traditional" markers. Galapagos giant tortoises (Chelonoidis spp.) have long provided a case study for how evolutionary genetics may be applied to advance species conservation. Ongoing efforts to bolster tortoise populations, which have declined by 90%, have been informed by analyses of mitochondrial DNA sequence and microsatellite genotypic data, but could benefit from genome-wide markers. Taking this next step, we used double-digest restriction-site associated DNA sequencing to collect genotypic data at >26,000 single nucleotide polymorphisms (SNPs) for 117 individuals representing all recognized extant Galapagos giant tortoise species. We then quantified genetic diversity, population structure, and compared results to estimates from mitochondrial DNA and microsatellite loci. Our analyses detected 12 genetic lineages concordant with the 11 named species as well as previously described structure within one species, C. becki. Furthermore, the SNPs provided increased resolution, detecting admixture in four individuals. SNP-based estimates of diversity and differentiation were significantly correlated with those derived from nuclear microsatellite loci and mitochondrial DNA sequences. The SNP toolkit presented here will serve as a resource for advancing efforts to understand tortoise evolution, species radiations, and aid conservation of the Galapagos tortoise species complex.
Data from: A phylogenetic perspective on species diversity, β-diversity, and biogeography for the microbial world
There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high altitude lakes district dataset to describe phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled eighteen lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within a small geographical area. The results showed highly diverse communities non-randomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity approach shared similar patterns and were primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies for microorganisms.
Data from: Species asynchrony and response diversity determine multifunctional stability of natural grasslands
1. A growing body of empirical evidence has suggested that biodiversity affects the simultaneous performance of multiple ecosystem functions (that is, ecosystem multifunctionality). Given increasing environmental variability and uncertainty under global change, an emerging question is how biodiversity influences the stability of multiple functions (that is, multifunctional stability). We currently know little, however, about the determinants and mechanisms of multifunctional stability, which is of practical importance for ensuring the sustainable provision of multiple functions. 2. Here we examined mechanisms contributing to stability (quantified as the ratio of the mean to the standard deviation) of multiple functions related to ecosystem productivity and carbon sequestration, including plant aboveground and belowground productivity, litter production, gross primary productivity, and ecosystem respiration, in a large grassland biodiversity experiment in Inner Mongolia. 3. We found that community-wide species asynchrony was a strong driver to stabilize multiple functions. Community-wide asynchrony mediated the positive effects of species richness and response diversity (describing how species with similar effects on ecosystem function respond differently to environmental change) on multifunctional stability. However, species richness had a negative direct effect on multifunctional stability because, although it increased the averaged temporal mean of multiple functions, it strongly increased the averaged temporal standard deviation of multiple functions. The overall effects of species richness on multifunctional stability were thus negative, whereas those of response diversity were positive. 4. Synthesis. The studied ecosystem functions related to ecosystem productivity and carbon sequestration are important in natural grasslands across the world. We conclude that species asynchrony and response diversity, rather than species richness, are key to the ecosystem multifunctional stability. The loss of response diversity and compensatory mechanisms would likely reduce the long-term sustainability of grasslands in the face of global change.
Data from: Genomic patterns of diversity and divergence of two introduced salmonid species in Patagonia, South America
Invasive species have become widespread in aquatic environments throughout the world, yet there are few studies that have examined genomic variation of multiple introduced species in newly colonized environments. In this study, we contrast genomic variation in two salmonid species (anadromous Chinook Salmon, Oncorhynchus tshawytscha, 11,579 SNPs and resident Brook Charr Salvelinus fontinalis, 13,522 SNPs) with differing invasion success after introduction to new environments in South America relative to populations from their native range in North America. Estimates of genetic diversity were not significantly different between introduced and source populations for either species, indicative of propagule pressure that has been shown to maintain diversity in founding populations relative to their native range. Introduced populations also demonstrated higher connectivity and gene flow than those in their native range. Evidence for candidate loci under divergent selection was observed, but was limited to specific introduced populations and was not widely evident. Patterns of genomic variation were consistent with general dispersal potential of each species and therefore also the notion that life history variation may contribute to both invasion success and subsequent genetic structure of these two salmonids in Patagonia.
Data from: Impacts of grazing by different large herbivores in grassland depend on plant species diversity
1. It is well documented that large herbivores have pronounced effects on plant communities in grassland ecosystems, and the extent and course of their effects can largely depend on both plant and herbivore characteristics. Previous studies highlighted the importance of plant productivity in predicting the impact of herbivores on grasslands. Yet, there has been little consideration of how different herbivores affect plant communities that, in turn, differ in plant diversity. 2. In a 2-year grazing experiment, we tested the effects of large herbivores (cattle or sheep, or both together) on plant communities under high and low plant diversity levels in eastern Eurasian steppe. 3. We found that, for high plant diversity grassland, mixed grazing by cattle and sheep significantly increases plant diversity, but we found no effect of grazing by cattle or sheep alone. Grazing by cattle or sheep alone or mixed grazing by cattle and sheep did not significantly affect plant biomass in the high diversity grassland. However, for low plant diversity grassland, grazing by cattle alone and mixed grazing by cattle and sheep significantly increased plant diversity, but significantly decreased plant biomass. There was no significant impact on both plant diversity and biomass from sheep grazing. 4. Synthesis and applications. We conclude that the effects of grazing in grassland strongly depend on herbivore assemblages and pre-grazing plant diversity. Herbivore grazing might contribute more to the maintenance of grassland structure and ecosystem functioning under high plant diversity compared with low plant diversity. Furthermore, our data suggest that multiple-species mixed grazing regimes in grassland systems with high plant diversity could represent the optimal protocol for grazing management. This study emphasizes the importance of maintaining both plant and herbivore diversity to optimize ecosystem functioning.
Data from: Barcoding snakeheads (Teleostei, Channidae) revisited: discovering greater species diversity and resolving perpetuated taxonomic confusions
Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group.
Data from: Conservation of old individual trees and small populations is integral to maintain species' genetic diversity of a historically fragmented woody perennial
Historically fragmented and specialised habitats such as granite outcrops are understudied globally unique hotspots of plant evolution. In contrast to predictions based on mainstream population genetics theory, some granite outcrop plants appear to have persisted as very small populations despite prolonged geographic and genetic isolation. Eucalyptus caesia Benth. is a long-lived lignotuberous tree endemic with a naturally fragmented distribution on granite outcrops in south-western Australia. To quantify population to landscape level genetic structure we employed microsatellite genotyping at 14 loci of all plants in 18 stands of E. caesia. Sampled stands were characterised by low levels of genetic diversity, small absolute population sizes, localised clonality and strong fine-scale genetic sub-division. There was no significant relationship between population size and levels of heterozygosity. At the landscape scale, high levels of population genetic differentiation were most pronounced among representatives of the two subspecies in E. caesia as originally circumscribed. Past genetic interconnection was evident between some geographical neighbours separated by up to 20 kilometres. Paradoxically, other pairs of neighbouring stands as little as 7 kilometres apart were genetically distinct. There was no consistent pattern of isolation by distance across the 280 km range of E. caesia. Low levels of gene flow, together with strong drift within stands, provides some explanation of the patterns of genetic differentiation we observed. Individual genet longevity via the ability to repeatedly re-sprout and expand from a lignotuber may enhance the persistence of some woody perennial endemic plants despite small population size, minimal genetic interconnection and low heterozygosity.
Data from: Designed habitat heterogeneity on green roofs increases seedling survival but not plant species diversity
Urban areas benefit from the ecosystem services provided by low input green roofs. However, limited substrate depth on these green roofs creates challenging conditions for plant establishment and survival, leading to industry reliance on non-native succulents. Through a green roof and glasshouse study, we assessed the impact of simple design modifications to the green roof surface, including redistribution of substrate and addition of logs and pebble piles, on both substrate temperature and moisture content. We added seeds of 26 native species and quantified seedling density, species richness and composition over a single growing season. Overall effects of microsite heterogeneity on species diversity were assessed using species accumulation curves. The modifications altered substrate temperature and moisture. Deep substrate (10-12 cm) and the presence of surface features reduced temperature by 14.6°C and, while surface features had mixed effects on substrate moisture on the green roof, pebble piles slowed moisture loss during a six-week drought in the glasshouse. Following drought conditions, seedling density and species richness was greatest, relative to seeded controls, where substrate was deep on the green roof and where pebbles were present in glasshouse modules, despite high mortality overall. Design modifications did not result in differentiation of seedling communities among different microsite types. Species accumulation curves showed no difference in species richness between aggregates of modified vs. unaltered microsites. Synthesis and applications. Redistribution of green roof substrate and the addition of logs and pebble piles altered microsite conditions and created habitat heterogeneity on a green roof. These design modifications represent a minimalist strategy to ameliorate growing conditions, improve seedling survival and decrease species loss on shallow substrate green roofs.
FIGURE 37 in On the diversity of Terebellides (Annelida, Trichobranchidae) in West Africa, seven new species and the redescription of T. africana Augener, 1918 stat. prom.
FIGURE 37. Body staining patterns—following Schüller & Hutchings (2010)—in ventral view of the species described in this work; chaetigers indicated in Arabic numbers.
FIGURE 33 in On the diversity of Terebellides (Annelida, Trichobranchidae) in West Africa, seven new species and the redescription of T. africana Augener, 1918 stat. prom.
FIGURE 33. (A–B) Terebellides ramili sp. nov. Stereomicroscope images of holotype MNCN 16.01/186013. (A) full specimen, right lateral view; (B) anterior end, left lateral view. Terebellides af. ramili (NHMD-231438): (C) anterior end, right lateral view. Abbreviations: bldl—branchial left dorsal lobe; blvl—branchial left ventral lobe; brdl—branchial right dorsal lobe; brvl—branchial right ventral lobe; bvltf—branchial ventral lobe terminal filament; gc—geniculate chaetae; loli—lower lip; ooc—oocytes; SG—segment; TC—thoracic chaetiger; tm—tentacular membrane.
FIGURE 36 in On the diversity of Terebellides (Annelida, Trichobranchidae) in West Africa, seven new species and the redescription of T. africana Augener, 1918 stat. prom.
FIGURE 36. Summary of the size, number and arrangement of denticles in uncinal capitium and its relative length in relation to rostrum, corresponding to the types of thoracic uncini, as defined for the species of Terebellides described in this work.
FIGURE 34 in On the diversity of Terebellides (Annelida, Trichobranchidae) in West Africa, seven new species and the redescription of T. africana Augener, 1918 stat. prom.
FIGURE 34. Terebellides ramili sp. nov. SEM micrographs of the paratype MNCN 16.01/18614. (A) TC6 geniculate chaetae; (B–D) thoracic uncini in latero-frontal, lateral and upper view; (E–F) abdominal uncini, fronto-lateral view. Circle in (D) showing number of teeth on capitium. Abbreviations: cap—capitium; ros—rostrum.
FIGURE 31 in On the diversity of Terebellides (Annelida, Trichobranchidae) in West Africa, seven new species and the redescription of T. africana Augener, 1918 stat. prom.
FIGURE 31. Terebellides nkossa sp. nov. SEM micrographs of the paratype MNCN 16.01/18601. (A) TC6, two geniculate chaetae; (B) row of thoracic uncini row and detail of geniculate chaeta capitium (framed in (A); (C) two thoracic uncini, lateroupper view; (D) three abdominal uncinigers in dorsal view; (E-F) abdominal uncini, anterior and fronto-upper view. Circles in (C) and (F) showing number of teeth on capitium. Abbreviations: cap—capitium; ros—rostrum.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.