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851 results for “turnover”
Data from: Evaluating temporal turnover in avian species richness in a Mediterranean semiarid region: different responses to elevation and forest cover
<p><span><strong>Aim</strong>.</span><span> When studying the effects of global change on biodiversity, it is far more common for the effects of climate change and land-use changes to be assessed separately rather than jointly. However, the effects of land-use changes in recent decades on species richness in areas affected by climate change have been less studied. </span><span>We assess the temporal turnover in species richness of an avian community between a historical period and a modern one as a consequence of global change.</span></p> <p><span><strong>Location</strong>. </span><span>Semiarid Mediterranean ecosystem (Southeastern Spain). </span></p> <p><span><strong>Method</strong>.</span><span> We fitted a hierarchical multi-species occupancy </span><span>model for each period (</span><span>1991-1992, and 2012-2017)</span><span>, obtaining avian species-specific estimates of occupancy probability in relation to environmental covariates </span><span>(elevation and forest cover)</span><span>. </span><span>We analyze the relationships between changes in the bird community and environmental variables, analysing the temporal turnover of the species richness and the richness-based species-exchange ratio.</span> </p> <p><span><strong>Results</strong>.</span> <span>The estimated species richness accounting for detectability was higher than observed species richness, and decreased in the </span><span>more recent </span><span>period. Following our hypotheses, we observed a dual pattern of species richness increase associated with different elevations, showing different species turnover rates due to the joint effects of climate change and land-use change. There is a trend toward greater species richness with higher elevations that is associated with climate change, where the species turnover rate is low. Also, species richness increased towards lower elevations, but with a high turnover rate. The latter can be due to species expansions through</span><span>ou</span><span>t new habitat configurations in bordering forest systems associated with anthropic land-use changes. </span></p> <p><span><strong>Conclusions</strong>.</span><span> Our study is of great interest to understand the temporal turnover of avian species richness associated with areas experiencing both climate and land-use change.</span></p>
Genome Database: Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers
<p>This repository contains the dataset used in the publication "Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers," which is currently under revision. A pre-print can be found <a href="https://doi.org/10.1101/2022.12.29.522137">here</a>. The database is based on previously published work to create a genomic database of honeybee gut microbes by Kirsten Ellegaard (2021), found <a href="https://zenodo.org/records/4661061">here.</a></p><p>The zipped folder deposited here after unzipping, should contain the following files and directories:</p><ul><li>honeybee_genome.fasta : fasta file containing the host (<i>Apis mellifera</i>) genome sequence</li><li>beebiome_db : fasta file of 198 concatenated genomes with one genome per entry (multi-line fasta) where the headers represent the genome identifier</li><li>beebiome_red_db : fasta file of 39 species representative genomes with one genome per entry (multi-line fasta) where the headers represent the genome identifier to be used for the analysis of intra-specific variation</li><li>fna_files : directory containing genome sequence files and concatenated files where the concatenated files contain one fasta entry renamed to the genome identifier and all contigs concatenated into one entry</li><li>ffn_files : directory containing one file per genome listing the nucleotide sequence of all the predicted genes</li><li>faa_files : directory containing one file per genome listing the amino acid sequence of all the predicted genes</li><li>bed_files : directory containing bed files where the location of each of the predicted genes are indicated based on their position in the concatenated genome file</li><li>single_ortho : directory containing one file per phylotype listing all the single-copy orthogroups (OGs) identified by orthofinder where each line represents an OG id followed by a list of genes from each of the genomes of that phylotype that belong to that OG and the corresponding sequences of these genes can be found in the ffn file belonging to the respective genome</li><li>red_bed_files : directory containing bed files for species representative genomes that only list the positions genes that belong to the core orthogroups of their phylotype</li></ul><p>Further information about how this genome database was used to analyze strain-level diversity can be found in the publication and accompanying code repository.</p>
Protists regulate microbially-mediated organic carbon turnover in soil aggregates
<p>Soil protists, the major predator of bacteria and fungi, shape the taxonomic and functional structure of soil microbiome via trophic regulation. However, how trophic interactions between protists and their prey influence microbially mediated soil organic carbon turnover remains largely unknown. Here, we investigated the protistan communities and microbial trophic interactions across different aggregates-size fractions in agricultural soil with long-term fertilization regimes. Our results showed that aggregate sizes significantly influenced the protistan community and microbial hierarchical interactions. Bacterivores were the predominant protistan functional group and were more abundant in macroaggregates and silt + clay than in microaggregates, while omnivores showed an opposite distribution pattern. Furthermore, partial least square path modeling revealed positive impacts of omnivores on the C-decomposition genes and soil organic matter (SOM) contents, while bacterivores displayed negative impacts. Microbial trophic interactions were intensive in macroaggregates and silt + clay but were restricted in microaggregates, as indicated by the intensity of protistan-bacterial associations and network complexity and connectivity. Cercozoan taxa were consistently identified as the keystone species in SOM degradation-related ecological clusters in macroaggregates and silt + clay, indicating the critical roles of protists in SOM degradation by regulating bacterial and fungal taxa. Chemical fertilization had a positive effect on soil C sequestration through suppressing SOM degradation-related ecological clusters in macroaggregate and silt + clay. Conversely, the associations between the trophic interactions and SOM contents were decoupled in microaggregates, suggesting limited microbial contributions to SOM turnovers. Our study demonstrates the importance of protists-driven trophic interactions on soil C cycling in agricultural ecosystems.</p>
Sex-biased gene content associates with sex chromosome turnover in Danaini butterflies
<p>Sex chromosomes play an outsized role in adaptation and speciation, and thus deserve particular attention in evolutionary genomics. In particular, fusions between sex chromosomes and autosomes can produce neo-sex chromosomes, which offer important insights into the evolutionary dynamics of sex chromosomes. Here we investigate the evolutionary origin of the previously reported <em>Danaus</em> neo-sex chromosome within the tribe Danaini. We assembled and annotated genomes of <em>Tirumala septentrionis</em> (subtribe Danaina), <em>Ideopsis similis</em> (Amaurina), <em>Idea leuconoe</em> (Euploeina), and <em>Lycorea halia</em> (Itunina) and identified their Z-linked scaffolds. We found that the <em>Danaus </em>neo-sex chromosome resulting from the fusion between a Z chromosome and an autosome corresponding to the <em>Melitaea cinxia</em> chromosome (McChr) 21 arose in a common ancestor of Danaina, Amaurina, and Euploina. We also identified two additional fusions as the W chromosome further fused with the synteny block McChr31 in <em>I. similis</em> and independent fusion occurred between the ancestral Z chromosome and McChr12 in <em>L. halia</em>. We further tested a possible role of sexually antagonistic selection in sex chromosome turnover by analyzing the genomic distribution of sex-biased genes in <em>I. leuconoe</em> and <em>L. halia</em>. The autosomes corresponding to McChr21 and McChr31 involved in the fusions are significantly enriched in female- and male-biased genes, respectively, which could have hypothetically facilitated fixation of the neo-sex chromosomes. This suggests a role of sexual antagonism in sex chromosome turnover in Lepidoptera. The neo-Z chromosomes of both <em>I. leuconoe</em> and <em>L. halia</em> appear fully compensated in somatic tissues, but the extent of dosage compensation for the ancestral Z is variable across tissues and species.</p>
Data and results for Sosiak et al. "Prolonged faunal turnover in earliest ants revealed by North American Cretaceous amber"
<p>Morphometric, fossil occurance, phylogenetic, and CT-scan data for Sosiak et al. publication "Prolonged faunal turnover in earliest ants revealed by North American Cretaceous amber"</p>
Incorporating plant phenological responses into species distribution models (SDMs) reduces estimates of future species loss and turnover
<p>Anthropogenetic climate change has caused distribution shifts of many species, and species distribution models (SDMs) are central for documenting this relationship. However, most SDMs rarely consider the evolution of climate-sensitive functional traits, such as phenology, which strongly affect species fitness. Using >120,000 herbarium specimens representing 360 plant species across the eastern United States, we developed a novel "phenology-informed" SDM that integrates dynamic phenological responses to changing climates. Compared to standard SDMs, our phenology-informed SDMs forecast lower species habitat loss and less species turnover under climate change. These results suggest that phenotypic plasticity or local adaptation in phenology may help species adjust their ecological niches and persist in their habitats under rapid environmental change. Our findings reveal how phenology variation mediates species distributions and affects regional biodiversity patterns. Our newly developed model also circumvents the need for mechanistic models, facilitating the deployment of trait-based SDMs across unprecedented spatial and taxonomic scales.</p>
Nectar values from: Turnover in floral composition explains species diversity and temporal stability in the nectar supply of urban residential gardens
<p>Residential gardens are a valuable habitat for insect pollinators worldwide, but differences in individual gardening practices substantially affect their floral composition. It is important to understand how the floral resource supply of gardens varies in both space and time so we can develop evidence-based management recommendations to support pollinator conservation in towns and cities.</p> <p>We surveyed 59 residential gardens in the city of Bristol, UK, at monthly intervals from March to October. For each of 472 garden surveys, we combined floral abundances with nectar sugar data to quantify the nectar production of each garden, investigating the magnitude, temporal stability, and diversity and composition of garden nectar supplies.</p> <p>We found that individual gardens differ markedly in the quantity of nectar sugar they supply (from 2 g to 1662 g), and nectar production is higher in more affluent neighbourhoods, but not in larger gardens. Nectar supply peaks in July (mid-summer), when more plant taxa are in flower, but temporal patterns vary among individual gardens. At larger spatial scales, temporal variability averages out through the portfolio effect, meaning insect pollinators foraging across many gardens in urban landscapes have access to a relatively stable and continuous supply of nectar through the year.</p> <p>Turnover in species composition among gardens leads to an extremely high overall plant richness, with 636 taxa recorded flowering. The nectar supply is dominated by non-natives, which provide 91% of all nectar sugar, while shrubs are the main plant life form contributing to nectar production (58%). Two thirds of nectar sugar is only available to relatively specialised pollinators, leaving just one third that is accessible to all.</p> <p><i>Synthesis and applications</i>. By measuring nectar supply in residential gardens, our study demonstrates that pollinator-friendly management, affecting garden quality, is more important than the size of a garden, giving every gardener an opportunity to contribute to pollinator conservation in urban areas. For gardeners interested in increasing the value of their land to foraging pollinators we recommend planting nectar-rich shrubs with complementary flowering periods and prioritising flowers with an open structure in late summer and autumn.</p>
Data from: Turnover in floral composition explains species diversity and temporal stability in the nectar supply of urban residential gardens
<p>Residential gardens are a valuable habitat for insect pollinators worldwide, but differences in individual gardening practices substantially affect their floral composition. It is important to understand how the floral resource supply of gardens varies in both space and time so we can develop evidence-based management recommendations to support pollinator conservation in towns and cities.</p> <p>We surveyed 59 residential gardens in the city of Bristol, UK, at monthly intervals from March to October. For each of 472 garden surveys, we combined floral abundances with nectar sugar data to quantify the nectar production of each garden, investigating the magnitude, temporal stability, and diversity and composition of garden nectar supplies.</p> <p>We found that individual gardens differ markedly in the quantity of nectar sugar they supply (from 2 g to 1662 g), and nectar production is higher in more affluent neighbourhoods, but not in larger gardens. Nectar supply peaks in July (mid-summer), when more plant taxa are in flower, but temporal patterns vary among individual gardens. At larger spatial scales, temporal variability averages out through the portfolio effect, meaning insect pollinators foraging across many gardens in urban landscapes have access to a relatively stable and continuous supply of nectar through the year.</p> <p>Turnover in species composition among gardens leads to an extremely high overall plant richness, with 636 taxa recorded flowering. The nectar supply is dominated by non-natives, which provide 91% of all nectar sugar, while shrubs are the main plant life form contributing to nectar production (58%). Two thirds of nectar sugar is only available to relatively specialised pollinators, leaving just one third that is accessible to all.</p> <p><i>Synthesis and applications</i>. By measuring nectar supply in residential gardens, our study demonstrates that pollinator-friendly management, affecting garden quality, is more important than the size of a garden, giving every gardener an opportunity to contribute to pollinator conservation in urban areas. For gardeners interested in increasing the value of their land to foraging pollinators we recommend planting nectar-rich shrubs with complementary flowering periods and prioritising flowers with an open structure in late summer and autumn.</p>
FIG. 36 in Vertebrate paleobiodiversity of the Early Cretaceous (Berriasian) Angeac-Charente Lagerstätte (southwestern France): implications for continental faunal turnover at the J/K boundary
FIG. 36. — Reconstruction of the Angeac-Charente landscape, 140 Million years ago, © Mazan.
Archive data supporting the results in the paper: Increase in carbon input by enhanced fine root turnover in a long-term warmed forest soil
<p>This is the archive data supporting the results in the paper: Increase in carbon input by enhanced fine root turnover in a long-term warmed forest soil; submitted to the Journal Science of the Total Environment.</p>
Data from: Helper plasticity in response to breeder turnover in gray wolves
<p>Nonbreeding helpers can greatly improve the survival of young and reproductive fitness of breeders in many cooperatively breeding species. Breeder turnover, in turn, can have profound effects on dispersal decisions made by helpers. Despite its importance in explaining group size and predicting population demography of cooperative breeders, our current understanding of how individual traits influence animal behavior after disruptions to social structure is incomplete particularly for terrestrial mammals. We used 12 years of genetic sampling and group pedigrees of gray wolves (<em>Canis lupus</em>) in Idaho, USA, to ask questions about how breeder turnover affected the apparent decisions by mature helpers (<u>></u>2-year-old) to stay or leave a group over a one-year time interval. We found that helpers showed plasticity in their responses to breeder turnover. Most notably, helpers varied by sex and appeared to base dispersal decisions on the sex of the breeder that was lost as well. Male and female helpers stayed in a group slightly more often when there was breeder turnover of the same sex, although males that stayed were often recent adoptees in the group. Males, however, appeared to remain in a group less often when there was breeding female turnover likely because such vacancies were typically filled by related females from the males' natal group (i.e., inbreeding avoidance). We show that helpers exploit instability in the breeding pair to secure future breeding opportunities for themselves. The confluence of breeder turnover, helper sex, and dispersal and breeding strategies merge to influence group composition in gray wolves.</p>
Fig. 1 in Species turnover between the northern and southern part of the South China Sea in the Elaphropeza Macquart mangrove fly communities of Hong Kong and Singapore (Insecta: Diptera: Hybotidae)
Fig. 1. Distribution of the Malaise traps around Hong Kong (map by C. Taylor and U. Chang).
Figure 4 in Revision of Eocene warm-water cassid gastropods from coastal southwestern North America: implications for paleobiogeographic distribution and faunal-turnover
Figure 4. See caption on the bottom of page 11.
Figure 3 in Revision of Eocene warm-water cassid gastropods from coastal southwestern North America: implications for paleobiogeographic distribution and faunal-turnover
Figure 3. See caption on the bottom of page 7.
Figure 1 in Revision of Eocene warm-water cassid gastropods from coastal southwestern North America: implications for paleobiogeographic distribution and faunal-turnover
Figure 1. Index map of the coastal southwestern North America (CSWNA) region.
Non-native vegetation encroachment drives functional turnover in island nematodes
<p>This community data matrix accompanies the manuscript "<span>Non-native vegetation encroachment drives functional turnover in island nematodes" by Adam Sharp, <span>Margarida Correia, Alan Gray, Rebecca Lawson, Martha Ledger, Noel Tawatao & Thomas Prior.</span></span></p>
The role of island physiography and oceanographic factors in shaping species richness and turnover of nesting seabird assemblages on islands across the southeastern Pacific
<p>For seabirds, food supplies and nest sites are largely driven by oceanographic gradients and island habitats, respectively. Research into seabirds' ecological roles in insular ecosystems is crucial to understanding processes that structure seabird nesting assemblages. We examined the influence of island physiography and oceanographic factors on the spatial variation in α and β-diversity of nesting seabird assemblages.<br> <br> <strong>Location</strong><br> Southeastern Pacific Ocean.<br> <br> <strong>Taxon</strong><br> Birds<br> <br> <strong>Methods</strong><br> We compiled data from 53 seabirds breeding on 41 coastal and oceanic islands using different sources: our field records, online databases, environmental reports, and literature. We used generalized linear models (GLM) to describe the effect of island physiography (area, elevation, and isolation) and oceanographic factors (surface temperature, salinity, and primary productivity) on seabird species richness (α-diversity). We applied multivariate GLM to test the effects of physiographic and oceanographic predictors on species composition (β-diversity). We used Jaccard dissimilarities on species occurrences per island to calculate β-diversity partitioned into turnover and nestedness. Polynomial models allowed us to model these metrics against geographical and environmental gradients and so analyze patterns in seabird β-diversity across spatial scales.<br> <br> <strong>Results </strong><br> Species richness was highest in Galápagos, Pitcairn, and Rapa Nui. Changes in seabird α-diversity across islands were determined by island area and distance to South America but not by oceanographic variables. Physiographic and oceanographic factors were significant in determining β-diversity. Changes in β-diversity were mostly due to species replacement (β-turnover) across three major island Systems (Galápagos Archipelago, Chilean coastal islands, and oceanic islands of the southeastern Pacific). The contribution of β-nestedness was restricted to small scales (within archipelagos).<br> <br> <strong>Main conclusions</strong><br> Physiographic and oceanographic factors explain species diversity of seabird assemblages on islands of the southeastern Pacific. Oceanographic variables did not affect species richness but significantly influenced species composition. Change in species composition reflects gradients across three marine biogeographical realms: Temperate South, Eastern Indo-Pacific, and Tropical Eastern Pacific. The low degree of species nestedness may reflect multiple evolutionary origins.</p>
Data from: Low species turnover of upland Amazonian birds in the absence of physical barriers
<p>Aim: One of the oldest and most powerful ways for ecologists to explain distinct biological communities is to invoke underlying environmental differences. But in hyper-diverse systems, which often display high species richness and low species abundance, these sorts of community comparisons are especially challenging. The classic view for Amazonian birds posits that riverine barriers and habitat specialization determine local and regional community composition. We test the tacit, complementary assumption that similar bird communities should therefore permeate uniform habitat between major rivers, regardless of distance.</p> <p>Location: Upland (terra firme) rainforests of central Amazonia.</p> <p>Results: In all, we detected 244 forest-dependent birds, with an average of 190 species (78%) per plot. Species turnover was negligible, no unique indicator species were found among plot pairs, and all documented species were already known from a complete inventory at one of the three sites.</p> <p>Main conclusions: Our study corroborates the classic biogeographical pattern and suggests that turnover contributes little to regional avian diversity within upland forests. Using a grain size of 100 ha, this implies that upland birds perceive the environment as uniform, at least over distances of ~60 km. Therefore, to maximize both local species richness and population persistence, our findings support the conservation of very large tracts of upland rainforest. Our analyses also revealed that the avifauna at Reserva Ducke, encroached by urban sprawl from the city of Manaus, shows the hallmarks of a disturbed community, with fewer vulnerable insectivores. This defaunation signals that even an enormous preserve (10 × 10 km) in lowland Amazonia is not insulated from anthropogenic degradation within the surrounding landscape.</p>
Mapping trait versus species turnover reveals spatiotemporal variation in functional redundancy and network robustness in a plant‐pollinator community
<p>1. Functional overlap among species (redundancy) is considered important in shaping competitive and mutualistic interactions that determine how communities respond to environmental change. Most studies view functional redundancy as static, yet traits within species – which ultimately shape functional redundancy – can vary over seasonal or spatial gradients. We therefore have limited understanding of how trait turnover within and between species could lead to changes in functional redundancy or how loss of traits could differentially impact mutualistic interactions depending on where and when the interactions occur in space and time.</p> <p>2. Using an Arctic bumblebee community as a case study, and 1,277 individual measures from 14 species over three annual seasons, we quantified how inter- and intraspecific body-size turnover compared to species turnover with elevation and over the season. Coupling every individual and their trait with a plant visitation, we investigated how grouping individuals by a morphological trait or by species identity altered our assessment of network structure and how this differed in space and time. Finally, we tested how the sensitivity of the network in space and time differed when simulating extinction of nodes representing either morphological trait similarity or traditional species groups. This allowed us to explore the degree to which trait-based groups increase or decrease interaction redundancy relative to species-based nodes.</p> <p>3. We found that i) groups of taxonomically and morphologically similar bees turn over in space and time independently from each other, with trait turnover being larger over the season; ii) networks composed of nodes representing species versus morphologically similar bees were structured differently; and iii) simulated loss of bee trait groups caused faster coextinction of bumblebee species and flowering plants than when bee taxonomic groups were lost. Crucially, the magnitude of these effects varied in space and time, highlighting the importance of considering spatiotemporal context when studying the relative importance of taxonomic and trait contributions to interaction network architecture.</p> <p>4. Our finding that functional redundancy varies spatiotemporally demonstrates how considering the traits of individuals within networks is needed to understand the impacts of environmental variation and extinction on ecosystem functioning and resilience.</p>
Data from: A case for the "Competitive exclusion – tolerance rule" as a general cause of species turnover along environmental gradients
<p><span>Closely-related, ecologically-similar species often segregate their distributions along environmental gradients of time, space, and resources, but previous research suggests diverse underlying causes. Here, we review reciprocal removal studies in nature that experimentally test the role of interactions among species in determining their turnover along environmental gradients. We find consistent evidence for asymmetric exclusion coupled with differences in environmental tolerance causing the segregation of species pairs, where a dominant species excludes a subordinate from benign regions of the gradient, but is unable to tolerate challenging regions to which the subordinate species is adapted. Subordinate species were consistently smaller and performed better in regions of the gradient typically occupied by the dominant species compared to their native distribution. These results extend previous ideas contrasting competitive ability with adaptation to abiotic stress to include a broader diversity of species interactions (intraguild predation, reproductive interference) and environmental gradients, including gradients of biotic challenge. Collectively, these findings suggest that adaptation to environmental challenge compromises performance in antagonistic interactions with ecologically-similar species. The consistency of this pattern across diverse organisms, environments, and biomes suggests generalizable processes structuring the segregation of ecologically-similar species along disparate environmental gradients, a phenomenon that we propose should be named the Competitive exclusion – tolerance rule.</span></p>
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OpenNeuro
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