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49 results for “alpha diversity”
Mesophotic coral ecosystems of French Polynesia are hotspots of alpha and beta generic diversity for scleractinian assemblages
<p>Revealing how diversity varies across the depth gradient is key to understanding the role of mesophotic coral ecosystems in the functioning of coral reefs. We examined how alpha and beta generic diversity of scleractinian coral assemblages vary across a wide depth gradient for coral reefs. We studied generic diversity patterns of scleractinian corals at sixteen sites in eight islands of three archipelagos in French Polynesia, as derived from the analysis of photo-quadrats, across the seafloor from shallow to lower mesophotic depths (6 to 120 m) and on a wide geographic scale. Our sampling considered quantitative coral cover to explore the patterns of alpha and beta components of diversity across depth and horizontal space. We show that in French Polynesia, mesophotic coral ecosystems host higher alpha and beta generic diversity than shallow reefs despite decreasing coral cover with depth. The variation of coral genus richness across the depth gradient is mainly driven by a mid-domain effect with a peak at 40 m depth. At the same time, we found that the turnover of coral genera across islands (i.e., spatial beta diversity) increased steadily along the depth gradient. Our findings report the first quantitative results of coral cover and diversity from mesophotic coral ecosystems in French Polynesia and also present one of the few existing studies to examine the broad breadth of the mesophotic depth gradient. We demonstrate that mesophotic depths can host unexpectedly high generic richness of scleractinian coral assemblages. At the same time, we showed that increasing depth increases the differences in generic diversity composition across islands, whereas shallow reefs are similar in between. While a single island could conserve shallow regional biodiversity, mesophotic depths containing the richest diversity require site-specific measures, suggesting that considering these mesophotic depths in conservation is necessary to maintain regional diversity.</p>
Data from: Temporal changes in taxonomic and functional alpha and beta diversity across tree communities in subtropical Atlantic forests
<h2><strong>The study is published in Oikos and available at: <a href="https://doi.org/10.1111/oik.10961">https://doi.org/10.1111/oik.10961</a></strong></h2> <p>Here we aim to assess temporal taxonomic and functional alpha and beta diversity of adult and juvenile tree communities across 11 sites in the subtropical Brazilian Atlantic Forest to infer about trends and drivers of biodiversity change. The tree communities were evaluated for temporal changes in: (1) taxonomic and functional alpha diversity, (2) taxonomic and functional composition (beta diversity), and (3) identifying potential abiotic and biotic drivers of these changes, considering three censuses across a period of 10 years.</p> <p> </p> <h2>Files description:</h2> <p><strong>traits-adults.csv</strong> - adult tree species and their functional traits values.</p> <p><strong>traits-juveniles.csv</strong> - juvenile tree species and their functional trait values.</p> <p><strong>abundance-adults_synthesis.csv</strong> - adult tree species abundance over the three time periods of forest surveys (T1, T2, and T3). Raw data on tree individual level is available at ForestPlots.net database (<a href="https://forestplots.net/">https://forestplots.net/</a>) under request.</p> <p><strong>abundance-juveniles_synthesis.csv</strong> - juvenile tree species abundance over the three time periods of forest surveys (T1, T2, and T3). Raw data on tree individual level is available at ForestPlots.net database (<a href="https://forestplots.net/">https://forestplots.net/</a>) under request.</p> <p>Functional traits abbreviations are defined as follows: LA = leaf area; SLA = specific leaf area; WD = wood density; SM = seed mass; range_temp = range of mean annual temperature; range_CWD = range of climatological water deficit; and biomes_distrib = number of Brazilian biomes that the species occur according to Flora and Funga do Brazil.</p> <p> </p> <h2><strong>Acknowledgments</strong></h2> <p>This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (CAPES) – Finance Code 001, through Portal de Periódicos and scholarships granted to JMFK, JK and RCP. The fieldwork was supported by Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS grant numbers 2218 – 2551/12-2 and 19/2551-0001698-0), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq/FAPERGS/PELD number 441590/2020-9), and the Instituto Nacional de Ciência e Tecnologia (INCT) in Ecology, Evolution and Biodiversity Conservation, supported by MCTIC/CNPq (grant number 465610/2014-5). KMB gratefully acknowledge the financial support by the National Institute of Science and Technology in Low Carbon Emission Agriculture (INCT-ABC) sponsored by Brazil’s National Council for Scientific and Technological Development (CNPq, grant no. 406635/2022-6), the Foundation for Research Support of the State of Rio Grande do Sul (Fapergs, grant no. 22/2551-0000392-3), and the Ministry of Agriculture (MAPA). SCM is supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq; grant number 309659/2019-1.</p> <p> </p> <h3><strong>Please find below the data used in the study.</strong></h3>
There and back to the present: a model-based framework to estimate phylogenetically constrained alpha diversity gradients
<p>The imprint left by niche evolution on the variation of biological diversity across spatial and environmental gradients is still debated among ecologists. Furthermore, understanding to what extent dispersal limitation may reinforce or blur such an imprint is still a gap in our ecological knowledge. In this article we introduce a simulation approach coupled to Approximate Bayesian Computation (ABC) that parameterizes both the adaptation rate of species' niche positions over the evolution of a monophyletic lineage and the intensity of dispersal limitation associated with the variation of species alpha diversity among assemblages distributed across spatial and environmental gradients. The analytical tool was implemented in the R package <em>mcfly</em>. We evaluated the statistical performance of the analytical framework using simulated datasets, which confirmed the suitability of the analysis to estimate the adaptation rate parameter but showed to be less precise in relation to the dispersal limitation parameter. Also, we found that increased dispersal limitation levels improved the parameterization of the adaptation rate of species' niche positions in simulated datasets. Further, we evaluated the role played by niche evolution and dispersal limitation on species alpha diversity variation of Phyllostomidae bats across the Neotropics. The framework proposed here sheds light on the links between niche evolution, dispersal limitation and gradients of biological diversity, and thereby improved our understanding of evolutionary imprints on current biological diversity patterns.</p>
Fig. 1 Insect alpha-diversity across tropical forest habitats. a in Mangroves are an overlooked hotspot of insect diversity despite low plant diversity
Fig. 1 Insect alpha-diversity across tropical forest habitats. a Mangroves treated as one habitat; b Comparison of mangrove sites: Pulau Ubin (PU), Sungei Buloh (SB), Pulau Semakau old-growth (SMO), Pulau Semakau new-growth (SMN), other smaller mangrove fragments (see Additional File 1: Table S13); solid lines = rarefaction; dotted = extrapolations. The arrow on the x-axis indicates the point of rarefaction where species richness comparisons were made (see bar charts for absolute numbers with 95% confidence intervals)
Mesophotic coral ecosystems of French Polynesia are hotspots of alpha and beta generic diversity for scleractinian assemblages
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There and back to the present: a model-based framework to estimate phylogenetically constrained alpha diversity gradients
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A novel method to assess the integrity of frozen archival DNA samples: Alpha-diversity ratios of short and long-read 16S rRNA gene sequences
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Plant invasion has limited impact on soil microbial alpha-diversity : a meta-analysis
<p>Plant invasion has proved to be a significant driver of ecosystem change, and with increased probability of invasion due to globalization, agricultural practices and other anthropogenic causes, it is crucial to understand its impact across multiple trophic levels. With the strong linkages between above and belowground processes, the response of soil microorganisms to plant invasion is the next logical step in developing our conceptual understanding of this complex system. In our study, we utilized a meta-analytical approach to better understand the impacts of plant invasion on soil microbial diversity. We synthesized 70 independent studies with 23 unique invaders across multiple ecosystem types to search for generalizable trends in soil microbial a-diversity following invasion. When possible, soil nutrient metrics were also collected in an attempt to understand the contribution of nutrient status shifts on microbial a-diversity. Our results show plant invasion to have highly heterogenous and limited impacts on microbial a-diversity. When taken together, our study indicates soil microbial a-diversity to remain constant following invasion, contrary to the aboveground counter parts. As our results suggest a decoupling in patterns of below and aboveground diversity, future work is needed to examine the drivers of microbial diversity patterns following invasion.</p>
Integrating data from different taxonomic resolutions to better estimate community alpha diversity
<p>Integrated distribution models (IDMs), in which datasets with different properties are analysed together, are becoming widely used to model species distributions and abundance in space and time. To date, the IDM literature has focused on technical and statistical issues, such as the precision of parameter estimates and mitigation of biases arising from unstructured data sources. However, IDMs have an unrealised potential to estimate ecological properties that could not be properly derived from the source datasets if analysed separately. We present a model that estimates community alpha diversity metrics by integrating one species-level dataset of presence-absence records with a co-located dataset of group-level counts (i.e. lacking information about species identity). We illustrate the ability of community IDMs to capture the true alpha diversity through simulation studies and apply the model to data from the UK Pollinator Monitoring Scheme, to describe spatial variation in the diversity of solitary bees, bumblebees and hoverflies. The simulation and case studies showed that the proposed IDM produced more precise estimates of the community diversity than the single models, and the analysis of the real dataset further showed that the alpha diversity estimates from the IDM were averages of the single models. Our findings also revealed that IDMs had a higher prediction accuracy for all the insect groups in most cases, with this performance linked to the information provided by a data source into the IDM.</p>
Data from: Metabarcoding of fecal pellets in wild muskox populations reveals negative relationships between microbiome and diet alpha diversity
<p>Microbiome diversity and diet composition concomitantly influence species health, fitness, immunity, and digestion. In environments where diet varies spatially and temporally, microbiome plasticity may promote rapid host adaptation to available resources. For northern ungulates in particular, metabarcoding of noninvasively collected fecal pellets presents unprecedented insights into their diverse ecological requirements and niches by clarifying the interrelationships of microbiomes, key to deriving nutrients, in context of altered forage availability in changing climates. Muskoxen (<em>Ovibos moschatus</em>) are Arctic-adapted species that experience fluctuating qualities and quantities of vegetation. Geography and seasonality have been noted to influence microbiome composition and diversity in muskoxen, yet it is unclear how their microbiomes intersect with diet. Following observations from other species, we hypothesized increasing diet diversity would result in higher microbiome diversity in muskoxen. We assessed diet composition in muskoxen using three common plant metabarcoding markers and explored correlations with microbiome data. Patterns of dietary diversity and composition were not fully concordant among the markers used, yet all reflected the primary consumption of willows and sedges. Individuals with similar diets had more similar microbiomes, yet in contrast to most literature, yielded negative relationships between microbiome and diet alpha diversity. This negative correlation may reflect the unique capacities of muskoxen to survive solely on high-fiber Arctic forage and provide insight into their resiliency to exploit changing dietary resources in a rapidly warming Arctic altering vegetation diversity.</p>
Discrepancies between the drivers of alpha and beta plant diversity in arable field margins
<p><span>Field margins are major habitats for biodiversity conservation and ecosystem functioning in agricultural landscapes, but biotic homogenization of plant communities threatens their ecological and agronomic functions. Our objective is to assess the effects of field margin structure and long-term management of herbaceous layer over 20 years (1995–2015) on the taxonomic and functional α- and β-diversity, and the functional composition of herbaceous plant communities. In 2015, we surveyed 302 field margins in bocage landscapes of Brittany (France). Results were very similar between taxonomic and functional diversity but revealed discrepancies between α- and β-diversity. Deep ditches, mowing, and grazing increased α-diversity but did not affect β-diversity. Denser hedgerows had lower α-diversity than other field margins but contributed to β-diversity by harboring more unique sets of species or life strategies. Long-term herbicide spraying in field margins and cropping intensity in adjacent habitats did not affect α-diversity, but had more complex effects on β-diversity and selected for common weeds. Preservation of dense hedgerows and abandonment of herbicide spraying are key measures to prevent the establishment of common weeds and biotic homogenization in field margins. Above all, our study shows how important it is to go beyond α-diversity to make robust conservation and restoration decisions.</span></p>
Integrating data from different taxonomic resolutions to better estimate community alpha diversity
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Discrepancies between the drivers of alpha and beta plant diversity in arable field margins
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Data from: Metabarcoding of fecal pellets in wild muskox populations reveals negative relationships between microbiome and diet alpha diversity
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Title: Partitioning plant spectral diversity into alpha and beta components
<p><span><span><span><span><span><span><span><span><span><span>Plant spectral diversity — how plants differentially interact with solar radiation — is an integrator of plant chemical, structural, and taxonomic diversity that can be remotely sensed. We propose to measure spectral diversity as spectral variance, which allows the partitioning of the spectral diversity of a region, called spectral <i>gamma</i> (<i>γ</i>) diversity, into additive alpha (<i>α</i>; within communities) and beta (<i>β</i>; among communities) components. Our method calculates the contributions of individual bands or spectral features to spectral <i>γ</i>-, <i>β</i>-, and <i>α</i>-diversity, as well as the contributions of individual plant communities to spectral diversity. We present two case studies illustrating how our approach can identify "hotspots" of spectral <i>α</i>-diversity within a region, and discover spectrally unique areas that contribute strongly to <i>β</i>-diversity. Partitioning spectral diversity and mapping its spatial components has many applications for conservation since high local diversity and distinctiveness in composition are two key criteria used to determine the ecological value of ecosystems.</span></span></span></span></span></span></span></span></span></span></p>
Mowing does not redress the negative effect of nutrient addition on alpha and beta diversity in a temperate grassland
<p>Species loss due to an increasing number of added nutrients has been explained by both light competition through biomass increase and by niche dimension reduction as a result of species specific limiting soil resources trade-offs. Disturbances, by reducing community biomass, species dominance and increasing light availability, may counteract above ground nutrient effects. However, it is unknown if diversity loss at local or spatial scales generated by increasing number of added nutrients can be redressed with canopy disturbance.</p> <p>We evaluated if local (alpha) and spatial scale (beta) diversity loss generated by the number of added nutrients can be reverted by disturbances in Flooding Pampa grasslands, Argentina. In a 4-yr replicated field experiment, we added soil resources combining nitrogen, phosphorus and potassium to obtain 0, 1, 2 or 3 nutrients and manipulated the regime of canopy disturbance by seasonal mowing and biomass removal.</p> <p>We found that the increasing number of added nutrients strongly reduced local and spatial plant diversity, despite biomass and light changes generated by mowing. In mown plots, nutrient driven local diversity loss was intensified along time, thus increasing species dominance. While mowing did not affect dominant species loss, increasing number of added nutrients promoted rare species loss and reduced spatial dissimilarity. Furthermore, mowing increased local and spatial diversity regardless light or biomass effects, suggesting alternative pathway effects for disturbance.</p> <p>Synthesis: Our results demonstrated that even when disturbance generated a positive effect on local and spatial diversity, it did not completely counteract the negative effect of number of added nutrients. Thus, the relative importance of above and belowground resource competition may change when chronic disturbances alter community dominance. Under low light availability, above-ground competition may drive species richness loss but when disturbance reduces light limitation, the increasing number of added nutrients may reduce niche dimensionality and thus species coexistence. In sum, faced with the need to manage eutrophized grasslands, our study showed that disturbance may not completely mitigate the negative effect of multiple nutrient inputs on local and spatial grassland diversi</p>
Ephemeral habitat supports high alpha and beta diversity during drought in a subtropical semiarid wetland
<p>Globally, the number of rivers with intermittent flow is increasing due to climate change and water abstraction for human consumption. Currently, our understanding of how hydrology in subtropical rivers with intermittent flow affects the structure and dynamics of aquatic communities is poorly understood. Here, we investigated how fish α and β-diversity patterns in intermittent channels in the lower reaches of the Okavango Delta respond to seasonal flooding and drought. Under low-flow conditions, ephemeral habitat had higher α-diversity, and this was influenced by a combination of fish aggregation and apparent transient legacy effects as habitat patches became smaller and more isolated. Investigation of changes in fish assemblage structure across different hydrological periods and habitat types showed significant species turnover when water levels fell, suggesting a strong influence from species sorting. During high-water periods, species assemblages were homogenized both at local and regional scales, suggesting a greater influence of mass effects. Our findings support hydrology as a major factor regulating diversity patterns in intermittent rivers of a major wetland in a semiarid region of subtropical Africa. We infer from these findings that maintenance of a relatively natural flow regime will be necessary for conserving aquatic ecosystem structure and function in this system.</p>
Data from: Drivers of tropical rainforest composition and alpha diversity patterns over a 2,520 m altitudinal gradient
We determined the relationship of forest composition and alpha diversity (species diversity of a local assemblage) to altitude, soil and spatial factors over a 440 - 2950 ma.s.l gradient. Altitudinal gradient on the Atlantic slope of the Talamanca Cordillera, Costa Rica. We measured and identified all stems > 10 cm dbh in 32 0.25-ha undisturbed rain forest plots over the gradient. We determined compositional patterns using Non-Metric Multidimensional Scaling (NMS) ordination, and used linear regressions to explore the relationship between four alpha diversity metrics and altitude. With variation partitioning (VARPART) we determined the compositional variation explained by altitude, soil and spatial variables quantified using Principle Components of Neighbour matrices. We identified 425 species. NMS axis 1 separated a lowland zone (440-1120 m asl) from a transitional one dominated by holarctic Oreomunnea mexicana (1400-1600 m asl) and Quercus-dominated forests at altitudes >2100 m asl. The lowland zone was separated into two clusters of plots on NMS axis 2, the first in the 430-620 m asl range and the second at 1000-1120 masl. . Regressions showed that alpha diversity metrics were strongly negatively related to altitude (R2>0.78). Overall adjusted R2 from VARPART was 0.43, with 0.30, 0.21 and 0.17 for altitude, soil and space respectively. The respective adjusted R2 of individual matrices, on controlling for the other two, were 0.06, 0.05 and 0.09 (p<0.001). There are two well-defined forest compositional zones on this gradient – lowlands and montane forests – with a transitional zone at 1400-1600 m asl where lowland tropical and montane holarctic species are found together. Montane forests are very distinct in their composition and low alpha diversity. Vegetation and soil respond to altitude, and therefore temperature, as an integrated system, a model that goes beyond niche assembly as shown by the significant effect of space in the VARPART.
Data from: Effects of water level and grassland management on alpha and beta diversity of wet grassland birds in restored wetlands
Nearly 60% of European wetlands have been lost to drainage or to the cessation of grassland management. Large amounts of resources are put into wetland restoration with the aim to recover biodiversity. However, few studies have simultaneously evaluated effects of management, wetness and flooding dynamics on biodiversity of restored wetlands such as seasonally flooded wet grasslands. We inventoried bird communities over 4 years at 137 sites (each 3·1 ha) within five restored wet grassland areas in Sweden to investigate whether species richness and occurrence of 12 common wet grassland species were related to (i) local conditions such as management (grazing, mowing and unmanaged areas), basic wetness and spring flooding dynamics. Further, we investigated whether (ii) the composition of the adjacent landscape (20 ha) related to local bird diversity and (iii) species turnover (i.e. beta diversity) differed between sites characterized by their basic wetness, degree of flooding and predominant management regime. Local species richness was positively linked to degree of flooding and basic wetness of grasslands but not to type of grassland management. Species richness tended also to be negatively linked to proportion of forest at the landscape scale. Although variable, the same results were also true concerning the probability of the occurrence of a single species at the local scale. Species turnover between sites, and thus total species richness, was distinctly higher in (i) grazed as compared to mowed grasslands except in dry non-flooded grasslands and (ii) flooded as compared to non-flooded sites. Similar patterns held for the subset of 12 red-listed species. We suggest that the high beta diversity in grazed and flooded grasslands is driven by the heterogeneous vegetation structure, resulting in good conditions for foraging and nesting for several wet grassland bird species. Synthesis and applications. The selection of wetlands for conserving wet grassland birds should prioritize temporary flooded grasslands of moderate wetness, preferably far from forest edges. Restoration and management of wet grasslands should include water level management, removal of shrubs and trees, and low-intensity grazing, whereas mowing could be used in non-flooded grasslands of low basic wetness.
The role of bracket fungi in creating alpha diversity of invertebrates in the Białowieża National Park, Poland
<p>Bracket fungi are seen mainly as the cause of economic losses in forestry and their role as creators of biodiversity is relatively poorly understood. The effect of this group of fungi on the modification of biodiversity of invertebrates (spiders – Aranae, Opiliones – Opiliones, pseudoscorpions – Pseudoscorpionida, two groups of mites – Mesostigmata, and Oribatida, springtails – Collembola, and insects – Insecta) was investigated by analyzing 100 fruiting bodies of 10 species of bracket fungi divided into four DD classes. As well as defining the manner in which the degree of decay (DD) of the fruiting bodies determines the character of the invertebrate assemblages colonising them were the aims of this study. The material was collected at Białowieża National Park, which is considered to be the largest area of natural forests in the North European Plain. 16 068 invertebrate individuals classified into 224 species were obtained. Oribatid mites (12 543 individuals) constituted the largest group of individuals which were classified into 115 species with the most numerous <i>Carabodes femoralis </i>(8811 individuals). Representatives of this group of mites have been reported previously in the publications on bracket fungi, however, the contributions of Oribatida and other groups of invertebrates were not broadly compared. Moreover, the species such as <i>Hoploseius mariae</i> and <i>H. oblongus</i>, which were predominantly found in fruiting bodies of bracket fungi, have also been discerned. The invertebrate fauna differs depending on DD of the samples: in the more decayed samples a higher number of both individuals and species were recorded compared to the samples with lower DDs; however, this trend proved to be non-linear. The DCA analysis and cluster analysis revealed a similarity of the invertebrate assemblages from the 2 DD and 4 DD samples. They also indicated that the group 3 DD differed the most from all the other samples. The indicator species analysis identified species characteristic to individual DDs: for group 1 DD it was e.g. <i>Hoploseius oblongus</i>, for 2 DD – <i>Orchesella bifasciata</i>, for 3 DD – <i>Chernes cimicoides</i>, while for 4 DD – <i>Dinychus perforatus.</i></p>
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Allen Brain Atlas
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