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61 results for “habitat specialists”
Data and Code for "Why are generalists the 'winners' of habitat loss? Unveiling the process underlying specialist-generalist replacements in fragmented landscapes"
<p><span>Data and R-based workflow for the study "Why are generalists the ‘winners’ of habitat loss? Unveiling the process underlying specialist-generalist replacements in fragmented landscapes".</span></p>
Supplementary data and code from: Significant decline in habitat specialists in semi-dry grasslands over four decades
<h2>Supplementary code and data to the article:</h2><p>Klinkovská K., Sperandii M. G., Trávníček B. & Chytrý M. (2023) Significant decline in habitat specialists in semi-dry grasslands over four decades. Biodiversity and Conservation. <a href="https://doi.org/10.1007/s10531-023-02740-6">https://doi.org/10.1007/s10531-023-02740-6</a></p><h3>Data</h3><p>The data contain plant species composition data from resurveyed vegetation plots in the Central Moravian Carpathians (Czech Republic, 49°06'04''–49°13'31''N, 16°56'58''–17°20'47''E). The dataset comprises 90 vegetation plots first surveyed in 1985 and 1986 by Bohumil Trávníček (Trávníček 1987), and resurveyed in 2022 by Klára Klinkovská. Of these, 40 were inside protected areas and 50 were outside. To locate the historical plots as accurately as possible, a description of the location of each plot was used along with information on slope, aspect, elevation, and dominant species. In 2022, the geographical coordinates of each plot were measured using GPS with a location uncertainty of 3–5 m. All plots were squares of 16 m2.</p><p>The total percentage cover of vascular plants and bryophytes was recorded in each plot, and cover of individual vascular plant species was estimated using the seven-grade Braun-Blanquet scale in the 1980s and the nine-grade Braun-Blanquet scale in 2022 (Westhoff and van der Maarel 1978). The nine-grade scale divides degree 2 of the seven-grade scale into three grades, while the scales remain compatible.</p><p>In 2022, soil samples were collected from four places approximately in the middle of each quarter of the plot, below the litter layer at a depth of 5–10 cm. Mixed samples from each vegetation plot were dried at room temperature and sieved. A suspension with distilled water (weight ratio 1:2.5) was shaken in the Biosan PSU-10i orbital shaker for 5 minutes at 280 rpm and, after 5 hours, soil pH was measured using the HACH HQ40D digital multimeter.</p><p>The header data structure follows that of the ReSurveyEurope Database (<a href="http://euroveg.org/eva-database-re-survey-europe">http://euroveg.org/eva-database-re-survey-europe</a>).</p><p>The data on species composition and environmental variables are provided in two formats:</p><p>Turboveg 2 database (see <a href="https://www.synbiosys.alterra.nl/turboveg/">https://www.synbiosys.alterra.nl/turboveg/</a>) TurbovegDbBackup_Cz_0019_47.zip (<a href="https://euroveg.org/resurvey_metadata/CZ_0019_047.pdf">https://euroveg.org/resurvey_metadata/CZ_0019_047.pdf</a>). For using this dataset in Turboveg, the database dictionary (TurbovegDdBackup_Default_dictionary.zip) and the species list (TurbovegSlBackup_Czechia_slovakia_2015.zip) must be installed.</p><p>Three CSV files with columns separated by commas:</p><p>Klinkovska_et_al_semi_dry_grasslands_S_Moravia_species.csv contains the percentage covers of plant species in the plots, which are mid-values for cover-abundance categories of the seven-grade Braun-Blanquet scale. Plant nomenclature was harmonised according to Danihelka et al. (2012).</p><p>Klinkovska_et_al_semi_dry_grasslands_S_Moravia_species_data.csv contains ecological indicator values and information on the Red List status (Grulich 2017), alien species (Pyšek et al. 2022) and species diagnostic for the alliances Cirsio-Brachypodion pinnati and Bromion erecti (Chytrý et al. 2007).</p><p>Klinkovska_et_al_semi_dry_grasslands_S_Moravia_head.csv contains header data for the vegetation plots.</p><p>These data are also stored in the Czech National Phytosociological Database (Chytrý & Rafajová 2003; <a href="https://botzool.cz/vegsci/phytosociologicalDb">https://botzool.cz/vegsci/phytosociologicalDb</a>) and the ReSurveyEurope database (Knollová et al. 2023; <a href="http://euroveg.org/eva-database-re-survey-europe">http://euroveg.org/eva-database-re-survey-europe</a>).</p><h3>Scripts</h3><ul><li>Script_1.R: Transitions between vegetation types, changes in species richness, proportions of threatened species, specialists and alien species per plot</li><li>Script_2.R: Changes in species composition and ecological indicator values</li><li>Script_3.R: Temporal beta-diversity indices</li></ul>
Figure 1 in Specialist and generalist species in habitat use: implications for conservation assessment in snakes
Figure 1. Relationship between the diversity scores in habitat use and the number of citations (log transformed) for each snake species in the study area. Each point is one snake species: Ca, Coronella austriaca, Cg, Coronella girondica, Hh, Hemorrhois hippocrepis, Mb, Macroprotodon brevis, Mm, Malpolon monspessulanus, Nn, Natrix natrix, Rh, Rhinechis scalaris, Vl, Vipera latastei.
Figure 2 in Specialist and generalist species in habitat use: implications for conservation assessment in snakes
Figure 2. Principal components plot for different snake species. The percentage of the variance explained by the two main factors is indicated on the axes. Three separate groups of species are indicated. Ca, Coronella austriaca, Cg, Coronella girondica, Hh, Hemorrhois hippocrepis, Mb, Macroprotodon brevis, Mm, Malpolon monspessulanus, Nn, Natrix natrix, Rs, Rhinechis scalaris, Vl, Vipera latastei.
Data from: Insights into the population genetics of an extreme habitat specialist, the wood ant commensal Formicoxenus nitidulus
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Small fish, large river: surprisingly minimal genetic structure in a dispersal-limited, habitat specialist fish
<p>Genetic connectivity is expected to be lower in species with limited dispersal ability and a high degree of habitat specialization (intrinsic factors). Also, gene flow is predicted to be limited by habitat conditions such as physical barriers and geographic distance (extrinsic factors). We investigated the effects of distance, intervening pools, and rapids on gene flow in a species, the Tuxedo Darter (<i>Etheostoma lemniscatum</i>), a habitat specialist that is presumed to be dispersal-limited. We predicted that the interplay between these intrinsic and extrinsic factors would limit dispersal and lead to genetic structure even at the small spatial scale of the species range (a 38.6 km river reach). The simple linear distribution of <i>E. lemniscatum </i>allowed for an ideal test of how these factors acted on gene flow and allowed us to test expectations (e.g., isolation-by-distance) of linearly distributed species. Using 20 microsatellites from 163 individuals collected from 18 habitat patches, we observed low levels of genetic structure that were related to geographic distance and rapids, though these factors were not barriers to gene flow. Pools separating habitat patches did not contribute to any observed genetic structure. Overall, <i>E. lemniscatum</i> maintains gene flow across its range and is comprised of a single population. Due to the linear distribution of the species, a stepping stone model of dispersal best explains the maintenance of gene flow across its small range. In general, our observation of higher than expected connectivity likely stems from an adaptation to disperse due to temporally unstable and patchy habitat.</p>
Patch quality and habitat fragmentation shape the foraging patterns of a specialist folivore
<p><span>Research on use of foraging patches has focused on why herbivores visit or quit patches, yet little is known about visits to patches over time. Food quality, as reflected by higher nutritional quality and lower plant defences, and physical patch characteristics, which offer protection from predators and weather, affect patch use and hence should influence their revisitation. Due to the potentially high costs of moving between patches, fragmented habitats are predicted to complicate foraging decisions of many animals. We aimed to determine how food quality, shelter availability and habitat fragmentation influence tree reuse by a specialist folivore, the koala, in a fragmented agricultural landscape. We GPS- tracked 23 koalas in northern New South Wales, Australia and collated number of revisits, average residence time, and average time-to-return to each tree. We measured tree characteristics including food quality (foliar nitrogen and toxic formylated phloroglucinol compounds, FPCs concentrations), tree size and tree connectedness. We also modelled the costs of locomotion between trees. Koalas re-visited isolated trees with high leaf nitrogen disproportionately often. They spent longer time in trees with high leaf nitrogen, and in large trees used for shelter. They took longer to return to trees with low leaf nitrogen. Tree connectivity reduced travel costs between patches, being either individual or groups of trees. FPC levels had no detectable effect on patch revisitation. We conclude that food quality and shelter drive koala tree re-visits. Scattered, isolated trees with nutrient-rich leaves are valuable resource patches for koalas despite movement costs to reach them. </span></p>
Patch quality and habitat fragmentation shape the foraging patterns of a specialist folivore
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Warm winters lead to early breeding, increased breeding effort, but lower reproductive success, in a threatened habitat specialist
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Data from: Red pandas on the move: Weather and disturbance effects on habitat specialists
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Habitat management interventions for a specialist mid- successional grassland butterfly, the Lulworth Skipper
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Data from: Adaptation and divergence in edaphic specialists and generalists: serpentine soil endemics in the California flora occur in barer serpentine habitats with lower soil calcium levels than serpentine tolerators
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Small fish, large river: surprisingly minimal genetic structure in a dispersal-limited, habitat specialist fish
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Data from: Microbiomes of a specialist caterpillar are consistent across different habitats but also resemble the local soil microbial communities
<p><b>Background</b>: Insect-associated microorganisms can provide a wide range of benefits to their host, but insect dependency on these microbes varies greatly. The origin and functionality of insect microbiomes is not well understood. Many caterpillars can harbor symbionts in their gut that impact host metabolism, nutrient uptake and pathogen protection. Despite our lack of knowledge on the ecological factors driving microbiome assemblages of wild caterpillars, they seem to be highly variable and influenced by diet and environment. Several recent studies have shown that shoot-feeding caterpillars acquire part of their microbiome from the soil. Here, we examine microbiomes of a monophagous caterpillar (<i>Tyria jacobaeae</i>) collected from its natural host plant (<i>Jacobaeae vulgaris</i>) growing in three different environments: coastal dunes, natural inland grasslands and riverine grasslands, and compare the bacterial communities of the wild caterpillars to those of soil samples collected from underneath each of the host plants from which the caterpillars were collected.</p> <p><b>Results</b>: The microbiomes of the caterpillars were dominated by Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. Only 5% of the total bacterial diversity represented 86.2% of the total caterpillar's microbiome. Interestingly, we found a high consistency of dominant bacteria within the family Burkholderiaceae in all caterpillar samples across the three habitats. There was one amplicon sequence variant belonging to the genus <i>Ralstonia</i> that represented on average 53% of total community composition across all caterpillars. On average, one quarter of the caterpillar microbiome was shared with the soil.</p> <p><b>Conclusions</b>: We found that the monophagous caterpillars collected from fields located more than 100 kilometers apart were all dominated by a single <i>Ralstonia</i>. The remainder of the bacterial communities that were present resembled the local microbial communities in the soil in which the host plant was growing. Our findings provide an example of a caterpillar that has just a few key associated bacteria, but that also contains a community of low abundant bacteria characteristic of soil communities.</p>
Data from: Age‐dependent habitat relationships of a burned forest specialist emphasise the role of pyrodiversity in fire management
1. Variation in fire characteristics, termed pyrodiversity, plays an important role in structuring post-fire communities, but little is known about the importance of pyrodiversity for individual species. The availability of diverse post-fire habitats may be key for fire-associated species if they require different resources at different life history stages. 2. We tested for age-specific habitat relationships in the black-backed woodpecker, a post-fire specialist. We used radio-telemetry to track fledgling and adult woodpeckers in burned forests and built resource selection functions to compare the effect of stand-, tree-, and snag-level covariates between adults and fledglings. 3. Fledgling black-backed woodpeckers selected habitat with more live trees than adults, and used more heterogeneous habitats burned at lower severity, illustrating strong age-dependent effects on habitat selection. Within selected stands, fledglings were less likely to use snags and more likely to use live trees when compared to adults, but both age classes showed strong positive selection for larger-diameter trees (live and dead). Over the 60 days after leaving their nests, fledglings showed an increasing propensity to use snags rather than live trees. 4. Our results provide evidence that the predation–starvation hypothesis, which posits a trade-off between foraging efficiency and the need to minimize predation risk, plays a role in structuring the age-dependent habitat use of a burned forest specialist. Adult black-backed woodpeckers selected resources associated with food availability, but these resources occurred in relatively open, exposed habitat. Fledglings selected habitat that provided increased cover, perhaps as a strategy to reduce predation risk. 5. Synthesis and applications. Globally, fires are increasing in severity and extent, leading to increased focus on fire-associated species that play keystone roles in facilitating biodiversity resilience. Our findings suggest that a diversity of patches burned at different severities may benefit post-fire specialists like the black-backed woodpecker at multiple life history stages. The increasing prevalence of large, homogeneously high-severity "megafires" may present an emerging threat even to post-fire specialists, and we urge land managers to consider opportunities to promote pyrodiversity in the face of novel fire regimes.
Data from: Habitat choice meets thermal specialization: competition with specialists may drive suboptimal habitat preferences in generalists
Limited dispersal is classically considered as a prerequisite for ecological specialization to evolve, such that generalists are expected to show greater dispersal propensity compared with specialists. However, when individuals choose habitats that maximize their performance instead of dispersing randomly, theory predicts dispersal with habitat choice to evolve in specialists, while generalists should disperse more randomly. We tested whether habitat choice is associated with thermal niche specialization using microcosms of the ciliate Tetrahymena thermophila, a species that performs active dispersal and habitat choice. We found that thermal specialists preferred optimal habitats as predicted by theory, a link that should make specialists more likely to track suitable conditions under environmental changes than expected under the random dispersal assumption. Surprisingly, generalists also performed habitat choice but with a preference for suboptimal habitats. Since this result challenges current theory, we developed a simple metapopulation model to understand under which circumstances such a preference for suboptimal habitats should evolve. We showed that competition between generalists and specialists may favor a preference for niche margins in generalists under environmental variability. Our results demonstrate that the behavioral dimension of dispersal—here, habitat choice—fundamentally alters our predictions of how dispersal evolve with niche specialization, making dispersal behaviors crucial for ecological forecasting facing environmental changes.
Data from: Hierarchical analysis of genetic structure in the habitat-specialist Eastern Sand Darter (Ammocrypta pellucida)
Quantifying spatial genetic structure can reveal the relative influences of contemporary and historic factors underlying localized and regional patterns of genetic diversity and gene flow – important considerations for the development of effective conservation efforts. Using 10 polymorphic microsatellite loci, we characterize genetic variation among populations across the range of the Eastern Sand Darter (Ammocrypta pellucida), a small riverine percid that is highly dependent on sandy substrate microhabitats. We tested for fine scale, regional, and historic patterns of genetic structure. As expected, significant differentiation was detected among rivers within drainages and among drainages. At finer scales, an unexpected lack of within-river genetic structure among fragmented sandy microhabitats suggests that stratified dispersal resulting from unstable sand bar habitat degradation (natural and anthropogenic) may preclude substantial genetic differentiation within rivers. Among-drainage genetic structure indicates that postglacial (14 kya) drainage connectivity continues to influence contemporary genetic structure among Eastern Sand Darter populations in southern Ontario. These results provide an unexpected contrast to other benthic riverine fish in the Great Lakes drainage and suggest that habitat-specific fishes, such as the Eastern Sand Darter, can evolve dispersal strategies that overcome fragmented and temporally unstable habitats.
Data from: The success of a habitat specialist biological control agent in the face of disturbance
<p class="MsoNormal">A field study was conducted in alfalfa fields in the Arlington Agricultural Research Station, Dane County, Wisconsin, USA.</p> <p class="MsoNormal">Three fields were studied. Each field was divided into three sections and in each section a one of three treatments was implemented:</p> <p class="MsoListParagraphCxSpFirst"><span><span>1.<span> </span></span></span>Control – harvesting normally, once a month (medium disturbance)</p> <p class="MsoListParagraphCxSpMiddle"><span><span>2.<span> </span></span></span>Insecticide – harvesting as in the control + implementing insecticide spray (permethrin insecticide Pounce 32 EC (8 oz/ac)) immediately after harvest (high disturbance)</p> <p class="MsoListParagraphCxSpLast"><span><span>3.<span> </span></span></span>Strips – harvesting in strips (low disturbance)</p> <p class="MsoNormal">In each field and each section insects were collected during the summer of 2001 (exact dates are in the files). Insects were collected with sweep nets, the number of sweeps changed in according to the number of aphids in the field, and is given in the files for each sample. Mummies of Apidius ervi were collected by visual searches of three minutes.</p>
Bringing Back the Manchester Argus Coenonympha tullia ssp. davus (Fabricius 1777): Quantifying the habitat resource requirements to inform the successful reintroduction of a specialist peatland butterfly
<p>2021-30 has been designated the UN decade of ecosystem restoration. A landscape scale peatland restoration project is being undertaken on Chat Moss, Greater Manchester, UK, with conservation translocations an important component of this work. The Manchester Argus Coenonympha tullia ssp. davus, a specialist butterfly of lowland raised bogs in the northwest of England, UK is under threat due to severe habitat loss and degradation. A species reintroduction was planned for spring 2020. </p> <p>This study aimed to quantify the resource thresholds for C. tullia, in order to assess potential risks for the project. Thirteen peatland habitat patches with either recent historic or current C. tullia populations were surveyed for biotic and abiotic factors based on previous qualitative research on the species' requirements. </p> <p>Percentage cover of two habitat resources were found to be the strongest predictors in models of C. tullia presence: cross-leaved heath Erica tetralix and hair's-tail cotton-sedge Eriophorum vaginatum. </p> <p>Critical inflection points on logistic regression curves were used to make quantitative estimates of the minimum requirement of each resource for population survival and the near-optimum abundance of each resource. </p> <p>The results of this study improve our understanding of C. tullia's ecology and the restoration of peatlands for its reintroduction. Additionally, the method has wider utility for the quantitative assessment of habitat readiness before attempting species reintroductions.</p>
Recent population differentiation in the habitat specialist Glossy Antshrike (Aves: Thamnophilidae) across Amazonian seasonally flooded forests: Complete matrix
<p>We assessed population structure and the spatio-temporal pattern of diversification in the Glossy Antshrike <i>Sakesphorus luctuosus</i> (Aves, Thamnophilidae) to understand the processes shaping the evolutionary history of Amazonian floodplains and address unresolved taxonomic controversies surrounding its species limits. By targeting ultraconserved elements (UCEs) from 32 specimens of <i>S. luctuosus</i>, we identified independent lineages and estimated their differentiation, divergence times and migration rates. We also estimated current and past demographic histories for each recovered lineage. We found evidence confirming that <i>S. luctuosus</i> consists of a single species, comprising at least four populations, with some highly admixed individuals and overall similar levels of migration between populations. We confirmed the differentiation of the Araguaia River basin population (<i>S. l.</i> <i>araguayae</i>), and gathered circumstantial evidence indicating that the taxon <i>S. hagmanni</i> may represent a highly introgressed population between 3 distinct phylogroups of <i>S. luctuosus</i>. Divergence time estimates between populations seem to be recent, occurring during the last 183 kya. Signs of population expansions were detected for populations attributed to subspecies <i>S. l. luctuosus</i>, but the <i>S. l. araguayae </i>population had probably maintained its effective size through time. Our results support<b> </b>that <i>S. luctuosus</i> has had a complex population history, resulting from a high dependence on southeastern "clear-water" habitats and their availability through time. Spatial and demographic expansions towards the western "white water" flooded forests might still be ongoing. Our study reinforces the view that isolation due to absence of suitable habitat has been an important driver of population differentiation within Amazonian flooded forests, but also that differences between <i>várzeas</i> ("white water" floodplains, mostly in southwestern Amazonia) and <i>igapós</i> ("clear- water" floodplains, especially located in the east) should be further explored as powerful drivers of micro-evolution.</p>
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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)
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DANDI Archive for NWB datasets
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