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2,399 results for “fragmentation”
Disentangling fragmentation effects on herbivory in understory plants of longleaf pine savanna
Habitat fragmentation affects species and their interactions through intertwined mechanisms that include changes to fragment area, shape, connectivity and distance to edge. Disentangling these pathways is a fundamental challenge of landscape ecology and will help identify ecological processes important for management of rare species or restoration of fragmented habitats. In a landscape experiment that manipulated connectivity, fragment shape, and distance to edge while holding fragment area constant, we examined how fragmentation impacts herbivory and growth of nine plant species in longleaf pine savanna. Probability of herbivory in open habitat was strongly dependent on proximity to forest edge for every species, increasing with distance to edge in six species (primarily grasses and annual forbs) and decreasing in three species (perennial forbs and a shrub). In the two species of perennial forbs, these edge effects were dependent on fragment shape; herbivory strongly decreased with distance to edge in fragments of two shapes, but not in a third shape. For most species, however, probability of herbivory was unrelated to connectivity or fragment shape. Growth was generally determined more strongly by leaf herbivory than by distance to edge, fragment shape, or connectivity. Taken together, these results demonstrate consistently strong edge effects on herbivory, one of the most important biotic factors determining plant growth and demography. Our results contrast with the generally inconsistent results of observational studies, likely because our experimental approach enabled us to tease apart landscape processes that are typically confounded.
Edge-mediated patterns of seed removal in experimentally connected and fragmented landscapes
While biological reserves remain central to biodiversity conservation, the amount of area available for terrestrial reserves may be inadequate for many taxa. Biodiversity spillover-the promotion of diversity in matrix areas surrounding reserves-might help address this shortfall in reserve area. However, the mechanistic underpinning of spillover remains uninvestigated. Two fundamental processes-seed dispersal and establishment-might generate plant biodiversity spillover. Here, we investigate the role of establishment in promoting spillover by assessing post-dispersal seed predation, a key component of establishment, in the matrix of a replicated, large-scale habitat fragmentation experiment, where spillover is elevated around patches connected by landscape corridors. Our results show that matrix seed predation may constrain the distance of this spillover effect by reducing establishment: seed removal was least at the matrix edge and increased further into the matrix. We found some support for matrix seed predation underpinning previously reported landscape-level variation in spillover. Of the three species we investigated, two showed evidence for elevated seed predation in the matrix surrounding the unconnected patches around which the lowest levels of spillover occur. However, seed predation did not explain connectivity-enhanced spillover, suggesting that seed dispersal likely drives this pattern. Management activities that increase seed deposition in the matrix may have beneficial effects via spillover. Our work also illustrates that matrix-mediated gradients in seed predation may be widespread, but likely vary depending upon matrix composition and the ecological system under consideration. In fragmented landscapes, this gradient could impact the distribution, abundance, and spread of plant species.
Landscape Corridors Promote Long Distance Seed Dispersal by Birds During Winter but Not During Summer at an Experimentally Fragmented Restoration Site
In fragmented landscapes, plant population persistence and community diversity can hinge upon plants dispersing seeds long distances between isolated patches of habitat. Landscape corridors, which connect otherwise isolated patches, have been shown to increase seed dispersal by birds moving between patch fragments. However, because bird behaviors change seasonally, the strength of this "corridor effect" may also change. We assessed the utility of corridors for promoting seed dispersal by birds during both summer and winter in a well-replicated corridor experiment conducted in early successional longleaf pine (Pinus palustris) savannah habitat at the Savannah River Site in South Carolina, USA. We used a single species of bird-dispersed fruiting plant, American black nightshade (Solanum americanum), and controlled the timing and number of fruits available to birds during summer and winter. Corridors increased long-distance seed dispersal during winter but not during summer, indicating that the effectiveness of corridors for promoting long-distance seed dispersal can depend upon plant reproductive timing and seasonal differences in bird movement. A better understanding of the seasonality of plant-animal interactions will permit better predictions about whether and how corridors provide connectivity for plants.
Data from : Fragmentation promotes the role of dispersal in determining 10 intermittent headwater stream metacommunities
<p>Dispersal, defined as the movement of individuals among local communities in a landscape, is a regional process determining metacommunity dynamics in ecosystems. Whereas both natural and anthropogenic ecosystem fragmentations can limit dispersal, previous attempts to measure such limitation have faced considerable context-dependency, due to a combination of spatial extent and associated environmental variability, the wide range of dispersal modes and abilities of organisms or variation in network topologies. Therefore, it is today unclear what role dispersal plays compared to local environmental filtering in explaining metacommunity dynamics in dendritic ecosystems. We quantified alpha and beta-diversity components of invertebrate metacommunities across ten fragmented headwater stream networks and tested the hypothesis that dispersal is the primary determinant of biodiversity organisation in these dynamic and spatially-constrained ecosystems. Alpha-diversity was much lower at intermittent reaches compared to perennial’s, including long upon rewetting, indicating an overwhelming effect of drying including a legacy on local communities. Beta-diversity was never correlated with environmental distances but predominantly explained by spatial distances accounting for river network fragmentation. The nestedness proportion of beta-diversity was considerable and echoed compositional differences that communities from intermittent reaches were subsets of perennial ones. Altogether, these results indicate dispersal is the primary process shaping metacommunity dynamics in these ten headwater stream networks, where local communities recurrently undergo extinction and recolonization events. This challenges previous conceptual views that local environment filtering is the main driver of headwater stream metacommunities. As the fragmentation of river networks is increasing due to global change, our results suggest that some freshwater ecosystems currently driven by local environment filtering could gradually become dispersal-limited. In this perspective, shifts from perennial to intermittent flow regimes represent tipping points that should not be crossed to not jeopardise river biodiversity, functional integrity and the ecosystem services they provide to society.</p>
Solvated Protein Fragments (QCArchive View Formatted)
<p>Data curated by the QCArchive team, originally sourced from quantum-machine.org.</p> <p>Water-solvated protein fragments with up to 8 heavy atoms. Configurations are generated from MD, evaluated at the revPBE-D3(BJ)/def2-TZVP level of theory. Also included are fragment dimers and clusters of up to 40 water molecules.</p> <p>For more information, see http://qcarchive.molssi.org/apps/ml_datasets/.</p>
Synthetic dataset for the PFC3D simulation of fragmentable blocks sliding experiments
<p>Dataset 1 - The raw data of numerical simulations, including deposit parameters of all simulations, fragments size distribution of all simulations, impact force of D1, breakage bond number of D1, velocity of D1.</p> <p>Simulation code - all the PFC3D simulation code for the fragmentable blocks sliding experiments.</p>
Dataset for laboratory experiments of fragmenting rockfalls and rockslides
<p>This data set provides movies for impact-fragmentation of sliding blocks recorded using high-speed camera during laboratory experiments, which can be useful for a thorough understanding of the evolutions of internal rock damages. The calculated data of area covered by deposit, aspect ratio of deposit, the travel distance of the center of mass on the horizontal plane, the travel distance of sliding mass on the horizontal plane, and the relative breakage ratio are also provided. In addition, we also provided the data of velocity profiles of blocks with different structures at t=0.1 s from x=0 m to x = 0.8 m.</p> <p>Dataset_S1. Data of area covered by deposit, aspect ratio of deposit, the travel distance of the center of mass on the horizontal plane, the travel distance of sliding mass on the horizontal plane, and the relative breakage ratio. The velocities of each tests derived from the pictures took by high speed camera (PIVLab code in Matlab is used for those calculation). The deposit parameters was calculated based on digital surface model (DSM) of deposit.</p> <p><br> Dataset_S2. Videos of all tests.</p> <p><br> Dataset_S3. Orthophotos and DSM of deposits for all tests.</p>
Fragmentation cross-sections for cosmic ray nuclei in the interstellar medium
<p>Table of the cumulative (included ghost nuclei) and direct fragmentation cross sections <strong>on H target</strong> generated with the <a href="https://github.com/carmeloevoli/XS4GCR">XS4GCR</a> code.</p> <p>More than 3800 channels are included from Ni64 to H1.</p> <ul> <li>Tables are saved as txt files with ' ' as delimiter.</li> <li>For each row the first 4 integers represent: fragment Z, fragment A, projectile Z and projectile A</li> <li>The following 160 values are the cross sections (in mbarn) as a function of the projectile kinetic energy per nucleon</li> <li>The first row is identified with 0 0 0 0 as the first 4 values and contains the values of the kinetic energy per nucleon (log spaced between 10 MeV/n and 1 TeV/n) at which the cross sections are computed.</li> </ul>
al-Qurʼān: Kufic fragment [IO Loth 1] القرآن الكريم
<ul> <li>al-Qurʼān القرآن الكريم : Kufic fragment</li> <li><strong>This manuscript was 38A in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), here with notations and hyperlinks]</strong>.</li> </ul> <p> </p> <p>1.</p> <p><strong>38 A</strong>. Size 3<sup>1/4</sup> in. by 5 in.; foll. 64. Five lines in a page.</p> <p>A <a href="https://en.wikipedia.org/wiki/Kufic">Kûfic</a> MS. on parchment, containing fragments of <a href="https://en.wikipedia.org/wiki/Surah">Sûrah</a><strong> <a href="https://quran.com/36">36</a>-<a href="https://quran.com/39">39</a>,</strong> viz. (foll. 2v.-6) Sû. <strong>36</strong>, 26-40; (foll. 13-18, 7-8)<sup>1</sup> 47-71; (foll. 9-11) 74 to the end; (foll. 12, 19-20) Sû. <strong>37</strong>, 1-15; (foll. 21-28) 20-64; (foll. 29-31) 71-90; (foll. 32-38) 102-145; (foll. 39-47) 151 to Sû. <strong>38</strong>, 13; (foll. 48-59) 16-50; (foll. 60-61) 59-65; (fol. 62) 85 to the end, and the title of Sû. <strong>39</strong>; (fol. 63, in four lines and in another handwriting) Sû. <strong>39</strong>, 31-32, with the words کتبه علی ابوطالب (sic).</p> <p>Round characters; wide spaces; occasional red dots for vowels. Verses divided by gold ornaments; every tenth verse likewise marked by larger ones. The titles of the Sûrahs have not been filled in. The whole MS. has more recently been bordered with thick paper, which is entirely gilt and ornamented. At the beginning (foll. 1 and 2r.) Sûrah 1; at the end the usual epilogue, صدق الله الخ, both within ornaments. Bound in leather, and covered with silk.</p> <p>This MS. is said to have been “[Arabian books] brought into Hindostan by Tamerlane, and sent from Lahore to Paris.” [<strong>ed. note</strong>: this according to an eighteenth-century note on the flyleaf, which also says "Koran Kufic" and is signed "Charles."]</p> <p>----------------------------------------</p> <p>Note 1: The first eighteen leaves have been misplaced in binding.</p> <ul> <li>[<strong>ed note</strong>: Catalogued in the library as IO Loth 1]</li> </ul> <p> </p> <p> </p>
• al-Qurʼān: Kufic fragment [IO Loth 5] القرآن الكريم
<p>القرآن الكريم al-Qurʼān: Kufic fragment</p> <ul> <li><strong>This manuscript is now IO Islamic 42A in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><a href="http://doi.org/10.5281/zenodo.3923636"><em><strong>A Catalogue of the Arabic Manuscripts in the Library of the India Office</strong></em></a><strong>, (volume 1), here with notations and hyperlinks]</strong></li> </ul> <p><a href="https://archive.org/details/in.gov.ignca.35737/page/1/mode/2up"><strong>5</strong></a>.</p> <p>42A. Size 63/4 in. by 91/2 in.; foll. 181. Sixteen lines in a page.</p> <p>A large fragment of a <a href="https://de.wikipedia.org/wiki/Kufi">Kûfic</a> <a href="https://www.wikidata.org/wiki/Q428">Koran</a>, containing (foll. 13-20)2 <a href="https://de.wikipedia.org/wiki/Liste_der_Koransuren">Sûrah</a>. <a href="https://quran.com/5"><strong>5</strong></a>, 112-6, 95; (foll. 25-34) <a href="https://quran.com/6"><strong>6</strong></a>, 108-7, 63 (fol. 36) <a href="https://quran.com/7"><strong>7</strong></a>, 104-126; (foll. 37-38) 7, 138-160; (fol. 35) <a href="https://quran.com/8"><strong>8</strong></a>, 20-34; (fol. 39) <a href="https://quran.com/9"><strong>9</strong></a>, 7-19; (fol. 21) 9, 38-51; (fol. 41) 9, 74-86; (fol. 42) 9, 108-118; (fol. 24) <a href="https://quran.com/10"><strong>10</strong></a>, 12-23; (fol. 22) 10, 34-50; (fol. 23) <a href="https://quran.com/11"><strong>11</strong></a>, 29-44; (foll. 1-4) <a href="https://quran.com/15"><strong>15</strong></a>, 99-16, 70; (foll. 5-12) <a href="https://quran.com/20"><strong>20</strong></a>, 34-21, 68; (foll. 66-75, 116-125, 86-105, 76-85) <a href="https://quran.com/21"><strong>21</strong></a>, 88-31, 38; (foll. 40, 44-51, 43, 53, 140-147, 56, 63) <a href="https://quran.com/34"><strong>34</strong></a>, 18-39, 63; (foll. 57-64) <a href="https://quran.com/41"><strong>41</strong></a>, 20-43, 37; (foll. 65, 54, 134-136) <a href="https://quran.com/43"><strong>43</strong></a>, 86-46, 11; (foll. 137-139, 55, 126) <a href="https://quran.com/46"><strong>46</strong></a>, 35-48, 26; (foll. 163-166, 162) <a href="https://quran.com/50"><strong>50</strong></a>, 1-53, 7; (foll. 133, 127-129, 148-151, 130-132, 152-161, 106-115, 167-176) <a href="https://quran.com/53"><strong>53</strong></a>, 36-89, 3; (foll. 177-181) <a href="https://quran.com/93"><strong>93</strong></a>, 10 to the end.</p> <p>Written in rather slender characters, approaching to <a href="https://de.wikipedia.org/wiki/Nasch%C4%AB">Naskh</a>. Frequent red dots for vowels. Titles of Sûrahs, in a still more cursive character, and in red, are regularly inserted, but often differ from the usual names, being always derived from the first word. Every tenth verse is marked with the letters serving for figures, according to the older or Maghribî order. Also every two hundredth verse is marked on the margin.</p> <p>At the end, in the same hand, کتبه عثمان بن عفان. [See <a href="https://www.wikidata.org/wiki/Q37731">ʿUthmān b. ʿAffān</a>]</p> <p>Seal and signature of <a href="https://www.wikidata.org/wiki/Q8597">Akbar </a>[1542-1605] and others on the last page. "Presented to the Library of the <a href="https://en.wikipedia.org/wiki/East_India_House">East India House</a> by <a href="https://en.wikipedia.org/wiki/Sir_Henry_Rawlinson,_1st_Baronet">Major Rawlinson</a>, C. B., the Hon. Company's Political Agent in Turkish Arabia, and H. M.'s Consul at Baghdad, March, 1845."</p> <p>----------------------------</p> <p>2 The leaves have been entirely misplaced in binding.</p> <p> </p> <p> </p> <p> </p>
Data from: Effects of Habitat Structure and Adjacent Habitats on Birds in Tropical Rainforest Fragments and Shaded Plantations in the Western Ghats, India
<p>This dataset includes bird community, habitat structure, and vegetation data from the following publication:</p> <p>Raman, T.R.S. 2006. Effects of Habitat Structure and Adjacent Habitats on Birds in Tropical Rainforest Fragments and Shaded Plantations in the Western Ghats, India. <em>Biodiversity and Conservation</em> 15: 1577–1607. https://doi.org/10.1007/s10531-005-2352-5</p> <p><strong>Abstract: </strong>As large nature reserves occupy only a fraction of the earth's land surface, conservation biologists are critically examining the role of private lands, habitat fragments, and plantations for conservation. This study in a biodiversity hotspot and endemic bird area, the Western Ghats mountains of India, examined the effects of habitat structure, floristics, and adjacent habitats on bird communities in shade-coffee and cardamom plantations and tropical rainforest fragments. Habitat and birds were sampled in 13 sites: six fragments (three relatively isolated and three with canopy connectivity with adjoining shade-coffee plantations and forests), six plantations differing in canopy tree species composition (five coffee and one cardamom), and one undisturbed primary rainforest control site in the Anamalai hills. Around 3300 detections of 6000 individual birds belonging to 106 species were obtained. The coffee plantations were poorer than rainforest in rainforest bird species, particularly endemic species, but the rustic cardamom plantation with diverse, native rainforest shade trees, had bird species richness and abundance comparable to primary rainforest. Plantations and fragments that adjoined habitats providing greater tree canopy connectivity supported more rainforest and fewer open-forest bird species and individuals than sites that lacked such connectivity. These effects were mediated by strong positive effects of vegetation structure, particularly woody plant variables, cane, and bamboo, on bird community structure. Bird community composition was however positively correlated only to floristic (tree species) composition of sites. The maintenance or restoration of habitat structure and (shade) tree species composition in shade-coffee and cardamom plantations and rainforest fragments can aid in rainforest bird conservation in the regional landscape.</p>
Data from: Effects of restoration on tree communities and carbon storage in rainforest fragments of the Western Ghats, India
Ecological restoration is a leading strategy for reversing biodiversity losses and enhancing terrestrial carbon sequestration in degraded tropical forests. There have been few comprehensive assessments of recovery following restoration in fragmented forest landscapes, and the efficacy of active versus passive (i.e., natural regeneration) restoration remains unclear. We examined 11 indicators of forest structure, tree diversity and composition (adult and sapling), and aboveground carbon storage in 25 pairs of actively restored (AR; 7–15 yr after weed removal and mixed-native tree species planting) and naturally regenerating (NR) plots within degraded rainforest fragments, and in 17 less-disturbed benchmark (BM) rainforest plots in the Western Ghats, India. We assessed the effects of active restoration on the 11 indicators and tested the hypothesis that active restoration effects increase with isolation from contiguous and relatively intact rainforests. Active restoration significantly increased canopy cover, adult tree and sapling density, adult and sapling species density (overall and late successional), compositional similarity to benchmarks, and aboveground carbon storage, which recovered 14–82% toward BM targets relative to NR baselines. By contrast, tree height–diameter ratios and the proportion of native saplings did not recover consistently in actively restored forests. The effects of active restoration on canopy cover, species density (adult), late successional species density (adult and sapling), and species composition, but not carbon storage, increased with isolation across the fragmented landscape. Our findings show that active restoration can promote recovery of forest structure, composition, and carbon storage within 7–15 yr of restoration in degraded tropical rainforest fragments, although the benefits of active over passive restoration across fragmented landscapes would depend on indicator type and may increase with site isolation. These findings on early stages of recovery suggest that active restoration in ubiquitous fragmented landscapes of the tropics could complement passive restoration of degraded forests in less fragmented landscapes, and protection of intact forests, as a key strategy for conserving biodiversity and mitigating climate change.
SIRAH-CoV2 initiative: S2 Spike core fragment in postfusion state (PDB id:6M1V)
<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Spike S2 fragment in its postfusion form (PDB id: 6M1V). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. </p> <p>The files 6M1V_SIRAHcg_rawdata_0-5us.tar, and 6M1V_SIRAHcg_rawdata_5-10us.tar, contain all the raw information required to visualize (on VMD 1.9.3), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file 6M1V_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6LU7_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6M1V_SIRAHcg_10us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD 1.9.3 using the command line:</p> <p>vmd 6M1V_SIRAHcg_prot.prmtop 6M1V_SIRAHcg_prot.ncrst 6M1V_SIRAHcg_10us_prot_skip10ns.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
Data for: Fragmentation and disturbance drive montane mixed-flock species roles and interaction strength
Mixed-species flocks are a key facilitative interaction for tropical birds. Forest fragmentation leads to species loss and spatial turnover in these flocks, yet it is unknown how these changes to composition influence within-flock species interactions. We used network analysis to characterize flocking interactions along a fragment-size gradient in the Colombian Western Andes. We asked (1) how patch size, edge density, and vegetation structure explained network measures indicative of flock cohesion, (2) whether changes were driven by flocking species turnover or changes to the frequency of species co-occurrence, and (3) whether nuclear species, those that maintain flock stability and cohesion, changed in importance across the gradient. We constructed weighted social networks from flock compositions observed on 500-meter transects, and then calculated global network measures and the centrality of six nuclear species. Patch size and edge density did not correlate with interspecific co-occurrence patterns, but interaction strength increased with canopy height. Flocks contained numerous, weak interactions and there were no flock sub-types, suggesting flock composition was dynamic and unstructured. Several redundant nuclear species were present and varied in importance based on ecological conditions. A chlorospingus (Passerellidae) was most central in old-growth forest, whereas several tanager (Thraupidae) species became more central in smaller fragments and disturbed forest. When partitioning network dissimilarity, we found that 66% of dissimilarity resulted from species turnover, whereas only 34% resulted from changes to species co-occurrence. This finding suggests that coherence of flocking behavior itself is maintained even as extensive species turnover occurs from continuous forest to small fragments.
The interacting effect of habitat amount, habitat diversity and fragmentation on insect diversity along elevational gradients.
Aim: Elevational gradients are a useful approach to evaluate how environmental factors affect animal diversity. Decades of studies on the elevation-diversity gradient have revealed that this gradient varies greatly with taxa and geographic regions. One potential explanation for this may be the dependence of the relationship on landscape features. We explore the impact of fragmentation, habitat diversity and habitat amount on insect diversity (alpha and beta) and abundance along elevational gradients. We hypothesize that insect diversity and abundance will relate negatively with elevation, but positively with these landscape features. We also hypothesize that landscape features will interact in a way that the positive effect of a given variable on insect diversity may be offset by the others. Location: Reunion Island (Indian Ocean) Taxon: The insect order thrips (Thysanoptera) Methods: Insects were sampled along replicated elevational gradients, and at each sampling plot landscape features and abiotic variables were estimated within buffers surrounding the site. Insect alpha diversity was estimated using abundance-based rarefaction methods, whereas beta diversity was estimated calculating the "local contributions to beta diversity" metric. The effect of elevation, rainfall, landscape features and their interactions was assessed on insect alpha and beta diversity and abundance during two consecutive seasons using linear mixed effects models. Results: We found that thrips alpha and beta diversity was negatively related with elevation, but the relationship varied between seasons and rainfall regimes. Among the different landscape features considered, we found that habitat amount had the strongest effect on diversity. The effect of habitat amount on diversity, however, was offset in areas of low habitat (or land cover) diversity. Main conclusions: Generalizing the factors that underlie the elevation diversity gradient has become a cornerstone in ecological theory because it can help to understand the impact of human activities on diversity. Here we show that taking landscape information into account may help to fulfil this objective because landscape effects co-vary with elevation with often intricate consequences for diversity.
Tick microbiomes in neotropical forest fragments are best explained by tick-associated and environmental factors rather than host blood source
<p>The composition of tick microbiomes varies both within and among tick species. Whether this variation is intrinsic (related to tick characteristics), or extrinsic (related to vertebrate host and habitat) is poorly understood but important, as microbiota can influence the reproductive success and vector competence of ticks. We aimed to uncover what intrinsic and extrinsic factors best explain the microbial composition and taxon richness of 11 species of Neotropical ticks, collected from eight species of small mammals in 18 forest fragments across central Panama. Microbial richness varied among tick species, life stages, and collection sites, but was not related to host blood source. Microbiome composition was best explained by tick life stage, with bacterial assemblages of larvae being a subset of those of nymphs. Collection site explained most of the bacterial taxa with differential abundance across intrinsic and extrinsic factors. <i>Francisella </i>and <i>Rickettsia </i>were highly prevalent, but their proportional abundance differed greatly among tick species and we found both positive and negative co-occurrence between members of these two genera. Other tick endosymbionts (e.g. <i>Coxiella</i>, <i>Rickettsiella</i>) were associated with specific tick species. In addition, we detected <i>Anaplasma</i> and <i>Bartonella </i>in several tick species. Our results indicate that the microbial composition and richness of Neotropical ticks are principally related to intrinsic factors (tick species, life stage) and collection site. Taken together, our analysis informs how tick microbiomes are structured and can help anchor our understanding of tick microbiomes from tropical environments more broadly.</p>
Patch size and vegetation structure drive changes to mixed-species flock diversity and composition across a gradient of fragment sizes in the Western Andes of Colombia
<p>This data set represents a series of 502 mixed-species bird flock compositions, and derived taxonomic, functional, and phylogenetic diversity indices, that were gathered along a gradient of forest fragment sizes (range = 10-173 ha) in the Colombian Western Andes. We sampled mixed-species flocks using transect surveys along 14 transects in 8 fragments and a continuous forest reference site in the same landscape and at the same elevation (~1900-2200 m.a.s.l.). We also used buffer analysis to quantify the proportion of forest cover and forest edge within 1 km of each transect, and calculated local vegetation density and complexity, as well as distance from edge, for each 100-meter transect segment (<em>n</em> = 70 segments). Flock composition data observed on a transect were used to calculate overall species richness and flock size as well as two indices of functional and phylogenetic diversity; we calculated the stadardized effect size (SES) of each measure to account for the correlation between these measures and species richness. We also provide the raw counts of each species for each flock composition. These data were used for the analyses in Jones and Robinson (2020). </p>
Data from: Forest fragmentation and loss reduce richness, availability, and specialization in tropical hummingbird communities
Hummingbirds are important pollinators of many native Neotropical plants but their abundance and diversity in landscapes dominated by intensive human uses such as agriculture have rarely been examined, despite such land-uses prevailing in the tropics. We examined how tropical deforestation affects hummingbird community structure in premontane forest patches embedded in a tropical countryside of Coto Brus Canton, Costa Rica. We captured hummingbirds in fourteen landscapes representing a gradient in patch size and forest amount, and tested for the effects of these variables on (1) hummingbird captures at flowers (pollinator availability); (2) species richness; and (3) filtering of functional traits. After accounting for sampling effects, both hummingbird availability and species richness declined by 40% and 50%, respectively, across the gradient in deforestation that we observed (9–66% forest within 1000 m). Focal patch size was the strongest predictor, even after statistically accounting for the amount of forest and matrix composition of landscapes. These reductions in availability and richness were well predicted by functional traits; morphologically specialized species with the capacity to transport long-distance outcrossed pollen and low functional redundancy within the pollinator network showed the greatest sensitivity to landscape change. We hypothesize that declines in hummingbird availability, diversity, and functional traits are important mechanisms driving the observed pollen limitation of ornithophilous flowers in fragmented tropical landscapes. Efforts to conserve large forest patches and enhance matrix permeability are critical for maintaining forest hummingbird communities and pollination services under current and predicted deforestation regimes.
Data from: Seed-dispersal networks in tropical forest fragments: area effects, remnant species, and interaction diversity
<p>Seed dispersal interactions involve key ecological processes in tropical forests that help to maintain ecosystem functioning. Yet this functionality may be threatened by increasing habitat loss, defaunation and fragmentation. However, generalist species, and their interactions, can benefit from the habitat change caused by human disturbance while more specialized interactions mostly disappear. Therefore changes in the structure of the local, within fragment, networks can be expected. Here we investigated how the structure of seed-dispersal networks changes along a gradient of increasing habitat fragmentation. We analysed 16 bird seed-dispersal assemblages from forest fragments of a biodiversity-rich ecosystem. We found significant species-, interaction- and network-area relationships, yet the later was determined by the number of species remaining in each community. The number of frugivorous bird and plant species, their interactions, and the number of links per species decreases as area is lost in the fragmented landscape. In contrast, network nestedness has a negative relationship with fragment area, suggesting an increasing generalization of the network structure in the gradient of fragmentation. Network specialization was not significantly affected by area, indicating that some network properties may be invariant to disturbance. Still, the local extinction of partner species, paralleled by a loss of interactions and specialist-specialist bird-plant seed dispersal associations suggests the functional homogenization of the system as area is lost. Our study provides empirical evidence for network-area relationships driven by the presence/absence of remnant species and the interactions they perform.</p>
Figure 4 in Notes on the bionomy of two spider wasp species in an urban forest fragment in Brazil
Figure 4. Nest of Auplopus cf. brasiliensis. The third cell broke during handling. Note the arrangement of the cells forming a cluster, the papillated surface suggesting the employment of several mud pellets to construct the cells. Scale bar = 0.5 cm.
ScienceDex guides
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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.