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504 results for “ecological diversity”
Ecological divergence despite common mating sites: Genotypes and symbiotypes shed light on cryptic diversity in the black bean aphid species complex
<p>Different host plants represent ecologically dissimilar environments for phytophagous insects. The resulting divergent selection can promote the evolution of specialized host races, provided that gene flow is reduced between populations feeding on different plants. In black bean aphids belonging to the <em>Aphis fabae </em>complex, several morphologically cryptic taxa have been described based on their distinct host plant preferences. However, host choice and mate choice are largely decoupled in these insects: they are host-alternating and migrate between specific summer host plants and shared winter hosts, with mating occurring on the shared hosts. This provides a yearly opportunity for gene flow among aphids using different summer hosts, and raises the question if and to what extent the ecologically defined taxa are reproductively isolated. Here, we analyzed a geographically and temporally structured dataset of microsatellite genotypes from <em>A. fabae </em>that were mostly collected from their main winter host <em>Euonymus europaeus,</em> and additionally from another winter host and fourteen summer hosts. The data reveals multiple, strongly differentiated genetic clusters, which differ in their association with different summer and winter hosts. The clusters also differ in the frequency of infection with two heritable, facultative endosymbionts, separately hinting at reproductive isolation and divergent ecological selection. Furthermore, we found evidence for occasional hybridization among genetic clusters, with putative hybrids collected more frequently in spring than in autumn. This suggests that similar to host races in other phytophagous insects, both prezygotic and postzygotic barriers including selection against hybrids maintain genetic differentiation among <em>A. fabae </em>taxa, despite a common mating habitat.</p>
Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages
<p><strong>Background:</strong></p> <p>Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are still at the surface level. Among phages, some adopt the lysogenic mode of infection, where the genome integrates into the host cell genome, forming a prophage. Prophages enable viral genome replication without host cell lysis and often contribute novel and beneficial traits to the host genome. Despite their importance, research on prophages is limited. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles.</p> <p><strong>Results:</strong></p> <p>To bridge this gap, the creation of Prophage-DB, a prophage database, aims to address the limited knowledge of these crucial biological entities. To create the database, we identified lysogenic viruses from genomes in three publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster them, taxonomically classify them, and detect their respective AMGs. With our approach, we identified over 350,000 prophages and 35,000 auxiliary metabolic genes.</p> <p><strong>Conclusion:</strong></p> <p>By summarizing the collected information we have created a database with extensive metadata regarding phage and host taxonomy, host information, and auxiliary metabolic genes. We identified numerous phages, from a wide variety of archaeal and bacterial hosts, which show a wide environmental distribution. In addition, the identified auxiliary metabolic genes will improve our understanding of them given the context of our study. We estimate this comprehensive prophage database will be a valuable resource for advancing prophage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution. Its use promises to contribute towards understanding microbial ecosystems and unlocking the mysteries of microbial dark matter.</p>
Fig. 4 in A New Measure Of Conservation Value Combining Rarity And Ecological Diversity: A Case Study With Light Trap Collected Caddisflies (Insecta: Trichoptera)
Fig. 4. The relationship between diversity (D) and rarity (RAR-index) of the samples
Figure 1 in Preliminary study on distribution, diversity, and ecological characteristics of nonmarine Ostracoda (Crustacea) from the Erzincan region (Turkey)
Figure 1. Map illustrating the location of the 89 sampling sites randomly selected in Erzincan.
Figure 1 in A study on diversity and ecology of ichthyofauna of Rajouri district, Jammu and Kashmir, India
Figure 1. The highlighted areas in the map shows the sampling sites.
Fig. 6 in Evidence for cryptic diversity in the Neotropical water snake, Helicops angulatus (Linnaeus, 1758) (Dipsadidae, Hydropsini), with comments on its ecology, facultative reproductive mode, and conservation
Fig. 6. The lectotype of Natrix asper Wagler. Photos by Michael Franzen.
Fig. 7 in Evidence for cryptic diversity in the Neotropical water snake, Helicops angulatus (Linnaeus, 1758) (Dipsadidae, Hydropsini), with comments on its ecology, facultative reproductive mode, and conservation
Fig. 7. The holotype of Helicops fumigatus Cope, 1868. Photo by Ned Gilmore.
Fig. 4. NRM 17 in Evidence for cryptic diversity in the Neotropical water snake, Helicops angulatus (Linnaeus, 1758) (Dipsadidae, Hydropsini), with comments on its ecology, facultative reproductive mode, and conservation
Fig. 4. NRM 17, the holotype for Helicops angulatus. Photo courtesy of NRM.
Data from: Large-bodied sabre-toothed anchovies reveal unanticipated ecological diversity in early Palaeogene teleosts
<p>Many modern groups of marine fishes first appear in the fossil record during the early Palaeogene (66–40 million years ago), including iconic predatory lineages of spiny-rayed fishes that appear to have originated in response to ecological roles left empty after the Cretaceous/Palaeogene extinction. The hypothesis of extinction-mediated ecological release likewise predicts that other fish groups have adopted novel predatory ecologies. Here we report remarkable trophic innovation in early Palaeogene clupeiforms (herrings and allies), a group whose modern representatives are generally small-bodied planktivores. Two forms, the early Eocene (Ypresian) †<i>Clupeopsis </i>from Belgium and a new genus from the middle Eocene (Lutetian) of Pakistan, bear conspicuous features indicative of predatory ecology, including large size, long gapes, and caniniform dentition. Most remarkable is the presence of a single, massive vomerine fang offset from the midline in both. Numerous features of the neurocranium, suspensorium, and branchial skeleton place these taxa on the engraulid (anchovy) stem as the earliest known representatives of the clade. The identification of large-bodied, piscivorous anchovies contributes to an emerging picture of a phylogenetically diverse guild of predatory ray-finned fishes in early Palaeogene marine settings, which include completely extinct lineages alongside members of modern marine groups and taxa that are today restricted to freshwater or deep-sea environments.</p>
Ecology drives the evolution of diverse social strategies in Pseudomonas aeruginosa
<p><span>Bacteria often cooperate by secreting molecules that can be shared as public goods between cells. Because the production of public goods is subject to cheating by mutants that exploit the good without contributing to it, there has been great interest in elucidating the evolutionary forces that maintain cooperation. However, little is known on how bacterial cooperation evolves under conditions where cheating is unlikely of importance. Here we use experimental evolution to follow changes in the production of a model public good, the iron-scavenging siderophore pyoverdine, of the bacterium <i>Pseudomonas aeruginosa</i>. After 1200 generations of evolution in nine different environments, we observed that cheaters only reached high frequency in liquid medium with low iron availability. Conversely, when adding iron to reduce the cost of producing pyoverdine, we observed selection for pyoverdine hyper-producers. Similarly, hyper-producers also spread in populations evolved in highly viscous media, where relatedness between interacting individuals is increased. Whole-genome sequencing of evolved clones revealed that hyper-production is associated with mutations involving genes encoding quorum-sensing communication systems, while cheater clones had mutations in the iron-starvation sigma factor or in pyoverdine biosynthesis genes. Our findings demonstrate that bacterial social traits can evolve rapidly in divergent directions, with particularly strong selection for increased levels of cooperation occurring in environments where individual dispersal is reduced, as predicted by social evolution theory. Moreover, we establish a regulatory link between pyoverdine production and quorum-sensing, showing that increased cooperation with respect to one trait (pyoverdine) can be associated with the loss (quorum-sensing) of another social trait.Bacteria often cooperate by secreting molecules that can be shared as public goods between cells. Because the production of public goods is subject to cheating by mutants that exploit the good without contributing to it, there has been great interest in elucidating the evolutionary forces that maintain cooperation. However, little is known on how bacterial cooperation evolves under conditions where cheating is unlikely of importance. Here we use experimental evolution to follow changes in the production of a model public good, the iron-scavenging siderophore pyoverdine, of the bacterium <i>Pseudomonas aeruginosa</i>. After 1200 generations of evolution in nine different environments, we observed that cheaters only reached high frequency in liquid medium with low iron availability. Conversely, when adding iron to reduce the cost of producing pyoverdine, we observed selection for pyoverdine hyper-producers. Similarly, hyper-producers also spread in populations evolved in highly viscous media, where relatedness between interacting individuals is increased. Whole-genome sequencing of evolved clones revealed that hyper-production is associated with mutations involving genes encoding quorum-sensing communication systems, while cheater clones had mutations in the iron-starvation sigma factor or in pyoverdine biosynthesis genes. Our findings demonstrate that bacterial social traits can evolve rapidly in divergent directions, with particularly strong selection for increased levels of cooperation occurring in environments where individual dispersal is reduced, as predicted by social evolution theory. Moreover, we establish a regulatory link between pyoverdine production and quorum-sensing, showing that increased cooperation with respect to one trait (pyoverdine) can be associated with the loss (quorum-sensing) of another social trait.</span></p>
Airborne eDNA documents a diverse and ecologically complex tropical bat and other mammal community
<p><span>Environmental (e)DNA has rapidly become a powerful biomonitoring tool, particularly in aquatic ecosystems. This approach has not been as widely adopted in terrestrial communities where the methods of vertebrate eDNA collection have varied from the use of secondary collectors such as blood-feeding parasites and spider webs to washing surfaces of leaves and soil sampling. Recent studies have demonstrated the potential of direct collection of eDNA from air sampling, but none have tested how effective airborne eDNA sampling might be in a </span><span>biodiverse environment.</span> <span>We used three prototype samplers to actively sample a mixed neotropical bat community in a partially controlled environment. We assess whether airborne eDNA can accurately characterize a high-diversity community with skewed abundances and to determine if filter design impacts DNA collection and taxonomic recovery. Our study provides evidence for the accuracy of airborne eDNA as a detection tool and highlights its potential for monitoring high-density, diverse assemblages such as </span><span>bat roosts. </span><span>Analysis of air samples recovered >91% of the species present and some limited relationship between species abundance and read count. Our data suggest this method can accurately depict a diverse mixed mammal community, particularly when the location is contained (e.g., a roost, den or burrow) but also highlights the potential for secondary transfer of eDNA material on clothing and equipment. Our results also demonstrate that simple, inexpensive, battery-operated homemade air samplers can collect an abundance of eDNA from the air, opening the opportunity for sampling in remote environments. </span></p>
Impacts of ecological restoration on the genetic diversity of plant species: A global meta-analysis
<p>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.</p> <p>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).</p> <p>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.</p> <p>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.</p> <p>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.</p>
Data from: Chilean bee diversity: Contrasting patterns of species and phylogenetic turnover along a large-scale ecological gradient
<p>Title of dataset</p> <p>Data from: Chilean bee diversity: Contrasting patterns of species and phylogenetic turnover along a large-scale ecological gradient</p> <p>Authors of dataset</p> <p>Leon Marshall<sup>1,2</sup>, John S. Ascher<sup>3</sup>, Cristian Villagra<sup>4</sup>, Amaury Beaugendre<sup>1</sup>, Valentina Herrera<sup>4</sup>, Patricia Henríquez-Piskulich<sup>4</sup>, Alejandro Vera<sup>5</sup>, Nicolas J. Vereecken<sup>1</sup></p> <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> <p>Abstract</p> <p>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.</p> <p>Usage notes</p> <p>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>.</p> <p>Shapefiles, rasters, CSV files and code were all loaded and analyzed using R statistics software. </p> <p>Four files are included:</p> <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>
Remote sensing and ecological variables related to Influenza A prevalence and subtype diversity in wild birds in the Lluta wetland of northern Chile
<p>Supplemental material for manuscript, tables 1 and 2</p>
Ecological consequences of plant genotypic diversity within a foundation plant, Spartina alterniflora, are pervasive but not universal across multiple stress gradients
<ol> <li>Plant genotypic diversity can influence population- and community-level processes, yet we have a limited understanding of how these effects vary across environmental gradients that are ubiquitous in nature. </li> <li>We conducted a 2-year field experiment manipulating plant (<em>Spartina</em> <em>alterniflora</em>) genotypic diversity across a natural stress gradient in tidal elevation, both with and without the addition of nutrients. </li> <li> <em>Spartina</em> diversity increased stem production, but the magnitude of this effect was reduced at both the most stressful and most benign endpoints of the combined elevation and nutrient gradient, consistent with recent species diversity studies. Complementarity among individuals likely underpins the observed benefit of <em>Spartina</em> diversity. </li> <li> <em>Spartina</em> diversity also affected the associated marsh community, with higher consumer (<em>Littoraria</em> <em>irrorata</em>) abundance in more diverse plots, owing to both greater <em>Spartina</em> density and increased variation in <em>Spartina</em> traits.</li> <li> <em>Synthesis</em>: The positive effects of <em>Spartina</em> diversity on population- and community-level responses under most environmental conditions highlights the ecological importance of plant genotypic diversity for the maintenance of function across the marsh landscape. </li> </ol>
Eutrophication decreases ecological resilience by reducing species diversity and altering functional traits of submerged macrophytes
<p><span>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 (<em>MC</em>) and morphological plasticity (<em>MP</em>) are correlated with the stoichiometric homeostasis of phosphorus (<em>H<sub>P</sub></em>) 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<em> MC, MP,</em> and <em>H<sub>P</sub></em> 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.</span></p>
The data used for the paper "Adapting a multiscale approach to assess the compositional diversity of landscapes" (Landscape Ecology)
<p>The data consists of a single SimpleFeatures (sf) object with 267,813 rows, i.e. hexagons covering Hungary, and 89 variables. The following variables are contained by the data (Table 1.).</p> <table> <caption>Table 1. Main attributes of the variables. For explanation of the vegetation type codes implied in the table by "XX", see the Supplementary Material S2 of Konrád et al. 2023.</caption> <thead> <tr> <th scope="col">Variable</th> <th scope="col">Description</th> </tr> </thead> <tbody> <tr> <td>id</td> <td>unique id of hexagons</td> </tr> <tr> <td>Bakony</td> <td>logical mask for subsetting the landscape Bakony</td> </tr> <tr> <td>Baranya</td> <td>logical mask for subsetting the landscape Baranya Hills</td> </tr> <tr> <td>ExternalSomogy</td> <td>logical mask for subsetting the landscape External Somogy</td> </tr> <tr> <td>HunGreatPlain</td> <td>logical mask for subsetting the landscape Hungarian Great Plain</td> </tr> <tr> <td>KorosMarosInterfluve</td> <td>logical mask for subsetting the landscape Körös-Maros Interfluve</td> </tr> <tr> <td>Mezofold</td> <td>logical mask for subsetting the landscape Mezőföld & Velence Hills</td> </tr> <tr> <td>NorthernHunMountains</td> <td>logical mask for subsetting the landscape Northern Hungarian Mountains</td> </tr> <tr> <td>Orseg</td> <td>logical mask for subsetting the landscape Őrség</td> </tr> <tr> <td>SouthernBukk</td> <td>logical mask for subsetting the landscape Southern Bükk</td> </tr> <tr> <td>binarized_potential_XX</td> <td>binarized potential vegetation data of the XX vegetation type</td> </tr> <tr> <td>binarized_actual_XX</td> <td> <p>binarized potential vegetation data of the XX vegetation type</p> </td> </tr> </tbody> </table> <p> </p> <p><strong>References</strong><br> Konrád KD, Bede-Fazekas Á, Bartha S, Somodi I (2023) Adapting a multiscale approach to assess the compositional diversity of landscapes. <em>Landscape Ecology.</em></p> <p> </p>
Figure 1 in A review of amphidromous freshwater fishes of the Chocó biogeographical region (Colombia and Ecuador): diversity, ecology, fisheries and conservation
Figure 1. – Map of the Chocó Biogeographical Region in the Pacific of Colombia and Ecuador.
Foraging shifts and visual preadaptation in ecologically diverse bats
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Ecological data from: Combining botanical collections and ecological data to better describe plant community diversity
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.