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opencc-zeroDec 2016View details →

Data from: Specialized specialists and the narrow niche fallacy: a tale of scale-feeding fishes

Although rare within the context of 30,000 species of extant fishes, scale-feeding as an ecological strategy has evolved repeatedly across the teleost tree of life. Scale-feeding (lepidophagous) fishes are diverse in terms of their ecology, behavior, and specialized morphologies for grazing on scales and mucus of sympatric species. Despite this diversity, the underlying ontogenetic changes in functional and biomechanical properties of associated feeding morphologies in lepidophagous fishes are less understood. We examined the ontogeny of feeding mechanics in two evolutionary lineages of scale-feeding fishes: Roeboides, a characin, and Catoprion, a piranha. We compare these two scale-feeding taxa to their nearest, non-lepidophagous taxa to identify traits held in common among scale-feeding fishes. We use a combination of micro-computed tomography scanning and iodine staining to measure biomechanical predictors of feeding behavior such as tooth shape, jaw lever mechanics, and jaw musculature. We recover a stark contrast between the feeding morphology of scale-feeding and non-scale-feeding taxa, with lepidophagous fishes displaying some paedomorphic characters through to adulthood. Few traits are shared between lepidophagous characins and piranhas, except for their highly-modified, stout dentition. Given such variability in development, morphology, and behavior, ecological diversity within lepidophagous fishes has been underestimated.

opencc-zeroDec 2014View details →

Data from: Description and preliminary results from a structured specialist behavioural weight management group intervention: Specialist Lifestyle Management (SLiM) Programme

Background: Specialist Lifestyle Management (SLiM) is a structured patient education and self-management group weight management programme. Each session is run monthly over a 6-month period providing a less intensive long-term approach. The groups are patient-centred incorporating educational, motivational, behavioural and cognitive elements. The theoretical background, programme structure and preliminary results of SLiM are presented. Subjects/methods: The study was a pragmatic service evaluation of obese patients with a body mass index (BMI) ≥35 kg/m2 with comorbidity or ≥40 kg/m2 without comorbidity referred to a specialist weight management service in the West Midlands, UK. 828 patients were enrolled within SLiM over a 48-month period. Trained facilitators delivered the programme. Preliminary anonymised data were analysed using the intention-to-treat principle. The primary outcome measure was weight loss at 3 and 6 months with comparisons between completers and non-completers performed. The last observation carried forward was used for missing data. Results: Of the 828 enrolled within SLiM, 464 completed the programme (56%). The mean baseline weight was 135 kg (BMI=49.1 kg/m2) with 87.2% of patients having a BMI≥40 kg/m2 and 12.4% with BMI≥60 kg/m2. The mean weight change of all patients enrolled was −4.1 kg (95% CI −3.6 to −4.6 kg, p=0.0001) at the end of SLiM, with completers (n=464) achieving −5.5 kg (95% CI −4.2 to −6.2 kg, p=0.0001) and non-completers achieving −2.3 kg (p=0.0001). The majority (78.6%) who attended the 6-month programme achieved weight loss with 32.3% achieving a ≥5% weight loss. Conclusions: The SLiM programme is an effective group intervention for the management of severe and complex obesity.

opencc-zeroDec 2014View details →

Data from: Patterns and predictors of β-diversity in the fragmented Brazilian Atlantic forest: a multiscale analysis of forest specialist and generalist birds

1. Biodiversity maintenance in human-altered landscapes (HALs) depends on the species turnover among localities, but the patterns and determinants of β-diversity in HALs are poorly known. In fact, declines, increases, and neutral shifts in β-diversity have all been documented, depending on the landscape, ecological group and spatial scale of analysis. 2. We shed some light on this controversy by assessing the patterns and predictors of bird β-diversity across multiple spatial scales considering forest specialist and habitat generalist bird assemblages. 3. We surveyed birds from 144 point counts in 36 different forest sites across two landscapes with different amount of forest cover in the Brazilian Atlantic forest. We analysed β-diversity among points, among sites, and between landscapes with multiplicative diversity partitioning of Hill numbers. We tested whether β-diversity among points was related to within-site variations in vegetation structure, and if β-diversity among sites was related to site location and/or to differences among sites in vegetation structure and landscape composition (i.e. percent forest and pasture cover surrounding each site). 4. β-diversity between landscapes was lower than among sites and among points in both bird assemblages. In forest specialist birds, the landscape with less forest cover showed the highest β-diversity among sites (bird differentiation among sites), but generalist birds showed the opposite pattern. At the local scale, however, the less forested landscape showed the lowest β-diversity among points (bird homogenisation within sites), independently of the bird assemblage. β-diversity among points was weakly related to vegetation structure, but higher β-diversity values were recorded among sites that were more isolated from each other, and among sites with higher differences in landscape composition, particularly in the less forested landscape. 5. Our findings indicate that patterns of bird β-diversity vary across scales and are strongly related to landscape composition. Bird assemblages are shaped by both environmental filtering and dispersal limitation, particularly in less forested landscapes. Conservation and management strategies should therefore prevent deforestation in this biodiversity hotspot.

opencc-by-4.0Feb 2021View details →

Data from: A sink host allows a specialist herbivore to persist in a seasonal source

Filename: 1_Population_growth_rate.xlsx Variables: 1. Source host - the plant species from which experimental females were transferred  2. Target host - the plant species to which experimental females were transferred 3. Generations - tested time period, in generations 4. N0 - the number of females placed at the beginning of the experiment 5. N - the number of mites (being a progeny of N0 females) counted after each tested time period Filename: 2_Emigration_dispersal.xlsx Variables: 1. Source host - the plant species infested by mites and exposed to wind 2. Target host - the plant species toward which mites could disperse 3. N - population size on the source host 4. D - the number of individuals that dispersed from the source host Filename: 3_Emigration_acceptance.xlsx Variables: 1. Source host - the plant species from which experimental females were transferred  2. Target host - the plant species to which experimental females were transferred 3. N - the number of females placed on the experimental arena 4. R - the number of females that stayed on the experimental arena after incubation  Filename: 4_Experimental_evolution.xlsx Variables: 1. Regime - host selection regime (W - wheat; B - brome; WB - wheat-brome alternating each three generations on each host species) 2. Generations - the number of generations the population survived 3. Status - 0 - censored observation; 1 - observed event of extinction Filename: 5_Field_database.xlsx Variables: 1. Sampling date - date of plant collection in the field 2. Day - the day of the year when the sample was collected 3. Year - the year of the sample collection 4. Database - N: the sample collected during 2012-2014 surveys; O: the sample collected during 2007-2014 surveys 5. Host - the plant species collected 6. GPS lat. [N] - the latitude in the northern hemisphere 7. GPS long. [E] - the longitude in the eastern hemisphere 8. n - the number of all plant shoots examined 9. k - the number of plant shoots infested

opencc-zeroDec 2018View details →

Data from: Genomic reconstruction of 100 000-year grassland history in a forested country: population dynamics of specialist forbs

Grassland ecosystems worldwide have been extensively converted to other land uses and are globally imperiled. Because many grasslands have been maintained by human activities, understanding their origin and history is fundamentally important to better contemporary management. However, existing methods to reconstruct past vegetation can produce contrasting views on grassland history. Here, we inferred demographic histories of 40 populations of four grassland forb species throughout Japan using high-resolution genome sequences and model-flexible demographic simulation based on the site frequency spectrum. Although two species showed a slight decline in population size between 100 000–10 000 years ago, our results suggest that population sizes of studied species have been maintained within the range of 0.5–2.0 times the most recent estimates for at least 100 000 years across Japan. Our results suggest that greater than 90% declines in Japanese grasslands and subsequent losses of grassland species in the last 100 years are geologically and biologically important and will have substantial consequences for Japanese biota and culture. People have had critical roles in maintaining disturbance-dependent grassland ecosystems and biota in this warm and wet forested country. In these contexts, disturbances associated with forest harvesting and traditional extensive farming have the potential to maintain grassland ecosystems and can provide important opportunities to reconcile resource production and conservation of grassland biodiversity.

Figure 5 in Breeding biology of the threatened Campo Miner Geositta poeciloptera (Aves: Scleruridae), a Neotropical grassland specialist

Figure 5. Relationship between the time spent on building activity (including digging and platform construction) and the date of nest initiation in 24 nests of the Campo Miner monitored in southeastern Brazil during the 2014 breeding season.

Figure 4 in Breeding biology of the threatened Campo Miner Geositta poeciloptera (Aves: Scleruridae), a Neotropical grassland specialist

Figure 4. (a) Entrance hole of a nest of the Campo Miner dug in a dirt bank along a dirt road; (b) the nest chamber (opened after being partially damaged by cattle activity); (c) materials used to line the nest, clockwise from left, mammal faeces, grass and other plant fragments, mammal hairs and charcoal fragments; (d) eggs. Photographs by TLSSM.

Figure 3 in Breeding biology of the threatened Campo Miner Geositta poeciloptera (Aves: Scleruridae), a Neotropical grassland specialist

Figure 3. Relationship between cavity area, cavity depth, and relative position in the soil profile of 70 nest of the Campo Miner found during the 2014 to 2016 breeding seasons in the municipality of São João del-Rei, south-eastern Brazil.

Figure 1 in Breeding biology of the threatened Campo Miner Geositta poeciloptera (Aves: Scleruridae), a Neotropical grassland specialist

Figure 1. (a) Location of the study area. (b) Detail of the study area, depicting the Rio Grande. Grey areas are above 900 m asl. (c) Detail of the study area, depicting the limits of the municipality of São João del-Rei and the remaining patches of natural grasslands according to Carvalho and Scolforo (2008). Records of the Campo Miner for other municipalities were not depicted.

Figure 2 in Breeding biology of the threatened Campo Miner Geositta poeciloptera (Aves: Scleruridae), a Neotropical grassland specialist

Figure 2. Number of active nests of the Campo Miner found during the 2014 to 2016 breeding seasons in São João del-Rei, south-eastern Brazil. Each month was subdivided in three periods of 10 days each (I, II and III) and each nest was counted only once during each stage: nest with eggs (day of laying of the first egg) and nest with nestlings (day of hatching of the first egg). Each nest was counted only once for tallying the number of active nests.

opencc-zeroAug 2021View details →

Specialist predation covaries with colour polymorphism in tawny owls

Understanding intraspecific phenotypic variation in prey specialisation can help to predict how long-term changes in prey availability affect the viability of these phenotypes and their persistence. Generalists are favoured when the main food resources are unpredictable compared to specialists, which track the availability of the main prey and are more vulnerable to changes in the main food resource. Intraspecific heritable melanin-based colour polymorphism is considered to reflect adaptations to different environments. We studied colour morph-specific diet specialisation in a generalist predator, tawny owl (Strix aluco), during offspring food provisioning in relation to mammal prey density. We hypothesised that the grey morph, with higher fitness than the brown in Northern boreal conditions, is more specialised in mammalian prey than the brown morph, which in turn has higher fitness than the grey in the temperate zone. We found a higher diversity of prey delivered to the nest by brown fathers compared to grey ones, which also depended on the overall mammalian prey availability. Brown fathers provided proportionally fewer mammalian prey than grey in poor, but not in favourable mammal prey years. Our results suggest that the brown morph is more generalistic and reacts more strongly to variations in food supply than the grey morph, which may be a beneficial strategy in an unpredictable environment caused by environmental degradation. Significance statement Diet choice of a species may vary depending on fluctuations in the abundance of their food resource, but also within a population, there can be adaptations to use different food resources. The tawny owl exhibits a grey and a reddish-brown colour morph and is considered a generalist predator eating both mammal and bird prey. We find that the diet of the reddish-brown morph is more diverse than that of the grey. When the tawny owls' main prey, small mammals, are abundant both colour morphs prey on mammals, but in years with less small mammals, the reddish-brown morph is more prone of switching to small bird predation than the grey. The generalist strategy of the brown morph is likely to be more favourable than a stricter specialisation in small mammals of the grey under recently reoccurring irregularities in small mammal dynamics.

opencc-zeroAug 2021View details →

Greater Prairie-chicken data used in "Responses to land cover and grassland management vary across life-history stages for a grassland specialist"

Grassland birds have exhibited dramatic and widespread declines since the mid-20th century. Greater Prairie-Chickens (Tympanuchus cupido pinnatus) are considered an umbrella species for grassland conservation and are frequent targets of management, but their responses to land use and management can be quite variable. We used data collected during 2007-2009 and 2014-2015 to investigate effects of land use and grassland management practices on habitat selection and survival rates of Greater Prairie-Chickens in central Wisconsin, USA. We examined habitat, nest-site, and brood-rearing site selection by hens and modeled effects of land cover and management on survival rates of hens, nests, and broods. Prairie-chickens consistently selected grassland over other cover types, but selection or avoidance of management practices varied among life-history stages. Hen, nest, and brood survival rates were influenced by different land cover types and management practices. At the landscape scale, hens selected areas where brush and trees had been removed during the previous year, which increased hen survival. Hens selected nest sites in hay fields and brood-rearing sites in burned areas, but prescribed fire had a negative influence on hen survival. Brood survival rates were positively associated with grazing and were highest when home ranges contained ≈15-20% shrub/tree cover. The effects of landscape composition on nest survival were ambiguous. Collectively, our results highlight the importance of evaluating responses to management efforts across a range of life history stages, and suggest that a variety of management practices are likely necessary to provide structurally heterogeneous, high-quality habitat for Greater Prairie-Chickens. Brush and tree removal, grazing, hay cultivation, and prescribed fire may be especially beneficial for prairie-chickens in central Wisconsin, but trade-offs among life-history stages and the timing of management practices must be considered carefully.

opencc-zeroDec 2020View details →

Response of Avian communities to edges of tropical montane forests: Implications for the future of endemic habitat specialists

Tropical montane landscapes harbor diverse flora and fauna, and many species there are ecological specialists with narrow elevational distributions, limited geographic ranges, and small global populations. Along elevational gradients, environmental conditions and community composition change dramatically over small spatial scales. As forests are disturbed and edges formed with modified habitat, natural communities could be affected differently across elevations by the many physical and biotic changes at edges. We asked whether forest edges produced altered patterns of avian species composition along a cloud forest - dry forest gradient on the Pacific slope of the Tilarán mountains in Monteverde, Costa Rica. A strong moisture gradient produces cloud forests near the ridgetops, with a concentration of species endemic to the Costa Rica – Panama highlands that are habitat specialists. We conducted 552 point counts across 110 locations from 1100 to 1800 m elevation, yielding 6586 detections of 115 species in 10 km2 of montane forest. We analyzed differences in species composition and single-species abundances between interior and near-edge forest habitats for species grouped by geographic range size. Species composition changed markedly from forest edge to interior in cloud forest habitats, but not in drier forests downslope. Endemic species, especially in cloud forest, were detected less frequently in mature forest near edges than in mature forest interior, and this difference was more pronounced than for cosmopolitan species. On tropical mountainsides, we can expect habitat-specialist endemic species to be more sensitive to further habitat modification. This sensitivity could limit the resilience of tropical bird communities.

opencc-zeroJan 2023View details →

High capacity for a dietary specialist consumer population to cope with increasing cyanobacterial blooms

We present a common-garden experiment to study the feeding plasticity of a key deposit-feeder in the Baltic Sea, a low diversity system presenting a good model for studying local adaptations. Based on the latitudinal gradient in phytoplankton blooms, with a single diatom bloom (high nutritional quality) in the north and a diatom bloom followed by cyanobacteria bloom (low nutritional quality) in the south, we expected populations of the amphipod Monoporeia affinis to be dietary specialists in the north and generalists in the south. We tested this hypothesis using a combination of stable isotope tracers, trophic niche analyses, and various endpoints of growth and health status. We found that the toxin-producing cyanobacteria, when mixed with diatoms, were efficiently incorporated and used for growth by both populations. However, contrary to the expectations, the feeding plasticity was more pronounced in the northern population, indicating genetically-based divergence and suggesting that this population is capable of ecological adaptation to the climate-induced northward cyanobacteria expansion in this system. Results provide important understandings for adaptations to increasing cyanobacteria in a future warming world in both limnic and marine ecosystems by invertebrates, but are likely widely applicable to other consumers where questions on adaptations to altered food quality.

opencc-by-4.0Feb 2023View details →

Resistance but not recovery is related to the role of specialist taxa in river communities submitted to hydric stress

Data set of algal communities present in the paper "Resistance but not recovery is related to the role of specialist taxa in river communities submitted to hydric stress", by Laura Jiménez, Anna Freixa, Neus Besolí and Sergi Sabater. Published in The Science of the Total Environment DOI:10.1016/j.scitotenv.2023.161952

opencc-by-4.0Feb 2023View details →

A social niche breadth score reveals niche range strategies of generalists and specialists

Abstract Generalists can survive in many environments whereas specialists are restricted to a single environment. Although a classical concept in ecology, niche breadth has remained challenging to quantify for microbes because it depends on an objective definition of the environmental conditions. Here, by defining the environment of a microbe as the community it resides in, we integrated information from over 22 thousand environmental sequencing samples to derive a quantitative measure of the niche, which we call ‘social niche breadth’. At the level of genera, we explored niche range strategies throughout the prokaryotic tree of life. We found that social generalists include opportunists that stochastically dominate local communities, while social specialists are stable but low in abundance. Social generalists have a more diverse and open pan genome than social specialists, but we found no global correlation between social niche breadth and genome size. Instead, we observed two distinct evolutionary strategies, where specialists have relatively small genomes in habitats with low local diversity, but relatively large genomes in habitats with high local diversity. Together, our analysis shines data-driven light on microbial niche range strategies. Inside this repository This is the directory structure and code used to generate all data and figures in the paper "A social niche breadth score reveals niche range strategies of generalists and specialists" by F. A. Bastiaan von Meijenfeldt, Paulien Hogeweg, and Bas E. Dutilh. The code was made by F. A. Bastiaan von Meijenfeldt. <ul> <li>The code inside the ./MGnify directory was used to download the MGnify data.</li> <li>The code inside the ./niche_breadth directory was used to generate all other data and uses the MGnify data.</li> <li>The code inside the ./figures directory was used to generate all figures.  </li> <li>Each directory in ./MGnify and ./niche_breadth contains a commands.sh that if run, and if source files are present, will generate all content in that directory. No files are written outside the directory. For example running ./MGnify/commands.sh will generate all files within ./MGnify. The generated files are source files for some of the scripts in ./MGnify/2019-08-20_extra and ./MGnify/2019-08-20_extra/commands.sh can now be run to generate all files within. Source files for the ./niche_breadth subdirectories can be from the ./MGnify directory or from other subdirectories within ./niche_breadth.</li> <li>The ./figures directory and its subdirectories contain *.ipynb Jupyter Notebook files that if run, and source files are present, will generate the vector files that were used as raw input for the final figures.  </li> <li>The file ./figures/mappings.Figure_to_Notebook.txt contains the mapping of the figure to the notebook that was used to generate the figure. In some cases only part of the notebook output was used in the final figures.</li> </ul>

opencc-zeroFeb 2023View details →

Data from: Use of an exotic host plant shifts immunity, chemical defense, and viral burden in wild populations of a specialist insect herbivore

Defense against natural enemies constitutes an important driver of herbivore host range evolution in the wild. Populations of the Baltimore checkerspot butterfly, Euphydryas phaeton (Nymphalidae), have recently incorporated an exotic plant, Plantago lanceolata (Plantaginaceae), into their dietary range. To understand the tritrophic consequences of utilizing this exotic host plant, we examined immune performance, chemical defense, and interactions with a natural entomopathogen (Junonia coenia densovirus, Parvoviridae) across wild populations of this specialist herbivore. We measured three immune parameters, sequestration of defensive iridoid glycosides (IGs), and viral infection load in field-collected caterpillars using either P. lanceolata or a native plant, Chelone glabra (Plantaginaceae). We found that larvae using the exotic plant exhibited reduced immunocompetence, compositional differences in IG sequestration, and higher in situ viral burdens compared to those using the native plant. On both host plants, high IG sequestration was associated with reduced hemocyte concentration in the larval hemolymph, providing the first evidence of incompatibility between sequestered chemical defenses and the immune response (i.e., the "vulnerable host" hypothesis) from a field-based study. However, despite this negative relationship between IG sequestration and cellular immunity, caterpillars with greater sequestration harbored lower viral loads. While survival of virus-infected individuals decreased with increasing viral burden, it ultimately did not differ between the exotic and native plants. These results provide evidence that (1) phytochemical sequestration may contribute to defense against pathogens even when immunity is compromised, and (2) herbivore persistence on exotic plant species may be facilitated by sequestration and its role in defense against natural enemies.

opennotspecifiedMar 2023View details →

FIGURE 13. A in Unraveling Siren (Caudata: Sirenidae) systematics and description of a small seepage specialist

FIGURE 13. A comparison of larval and juvenile sirens. A Larval lineage B Siren intermedia from Escambia Co., Florida. B Larval S. lacertina from Jefferson Co., Florida (UF Herp 188601). C Larval lineage A S. intermedia from Liberty Co., Florida, that is slightly farther along in development than UF Herp 188601. D Larval Pseudobranchus striatus spheniscus from Jefferson Co., Florida (UF Herp 188600). E Juvenile S. sphagnicola (~3 cm TL) from Okaloosa Co., Florida, no voucher. F Juvenile S. lacertina from Walton Co., Florida (UF Herp 188739). G Juvenile lineage B S. intermedia from Washington Co., Florida (UF Herp 188735). H Head of a juvenile S. sphagnicola from Okaloosa Co., Florida (UF Herp 185068. I Juvenile lineage B S. intermedia from Escambia Co., Florida (UF Herp 185073 & UF Herp 185074).

opennotspecifiedMar 2023View details →

FIGURE 10 in Unraveling Siren (Caudata: Sirenidae) systematics and description of a small seepage specialist

FIGURE 10. Live Siren intermedia specimens belonging to mtDNA lineages B and C. A Lineage C from Berkeley Co., South Carolina (UF Herp 188612). B Lineage C from Berkeley Co., South Carolina (UF Herp 188613). C Lineage B from Holmes Co., Florida (UF Herp 188769). D Lineage B from Jackson Co., Florida (UF Herp 188901). E Head of lineage B specimen from Holmes Co., Florida (UF Herp 188769). F Head of lineage C specimen from Berkeley Co., South Carolina (UF Herp 188612) (lineage C). G Head of lineage C specimen from Berkeley Co., South Carolina (UF Herp 188613). The latter two specimens are from the same locality but differ dramatically in pattern and coloration.