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opencc-zeroDec 2016View details →

Data from: Different genetic structures revealed resident populations of a specialist parasitoid wasp in contrast to its migratory host

Genetic comparisons of parasitoids and their hosts are expected to reflect ecological and evolutionary processes that influence the interactions between species. The parasitoid wasp, Cotesia vestalis, and its host diamondback moth (DBM), Plutella xylostella, provide opportunities to test whether the specialist natural enemy migrates seasonally with its host or occurs as resident population. We genotyped 17 microsatellite loci and two mitochondrial genes for 158 female adults of C. vestalis collected from 12 geographical populations, as well as nine microsatellite loci for 127 DBM larvae from six separate sites. The samplings covered both the likely source (southern) and immigrant (northern) areas of DBM from China. Populations of C. vestalis fell into three groups, pointing to isolation in northwestern and southwestern China and strong genetic differentiation of these populations from others in central and eastern China. In contrast, DBM showed much weaker genetic differentiation and high rates of gene flow. TESS analysis identified the immigrant populations of DBM as showing admixture in northern China. Genetic disconnect between C. vestalis and its host suggests that the parasitoid did not migrate yearly with its host but likely consisted of resident populations in places where its host could not survive in winter.

opencc-by-4.0Oct 2023View details →

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>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><h3>Data</h3>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.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.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.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>).The data on species composition and environmental variables are provided in two formats: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.Three CSV files with columns separated by commas: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).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).Klinkovska_et_al_semi_dry_grasslands_S_Moravia_head.csv contains header data for the vegetation plots.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>).<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>

opencc-zeroJan 2024View details →

Data for: Specialist carabids in mixed montane forests are positively associated with biodiversity-oriented forestry and abundance of roe deer

The ongoing transition within forest management towards more biodiversity-oriented practices, such as close-to-nature forestry and retention forestry, may benefit forest fauna such as forest-specialized ground beetles (Coleoptera: Carabidae). However, it remains unclear how forest carabids are jointly affected by these practices in Central European montane forests, which host particularly sensitive, range-restricted carabid species, and where biodiversity-oriented forestry is widely applied. Moreover, roe deer (Capreolus capreolus), the most common large herbivore in these forests, is intensively managed to reduce browsing pressure, but it is yet unknown how this may affect carabids, alongside the effect of silviculture. On 66 1-ha plots in the Black Forest region of Germany, we sampled carabids with pitfall traps, measured roe deer abundances using camera trapping, and measured several structural variables directly related to close-to-nature and retention practices, as well as variables describing microclimate and landscape-level forest cover. We found that the carabid assemblage was dominated by forest specialists, with little influence from fragmentation of the surrounding forest. Higher broadleaf share (and canopy cover for montane specialists) was correlated with higher carabid activity-density. Increasing stand maturity (and lying deadwood volume for montane specialists), was correlated with higher species richness. Plots with higher roe deer abundances showed higher carabid richness and activity-density. Assemblage composition changed along the altitudinal gradient, and both richness and activity-density increased with elevation. Thus, carabid communities, including montane specialists and several species of conservation interest, stand to benefit from close-to-nature and retention practices, if applied throughout the altitude range of montane forests. Forest carabids may additionally profit from maintaining higher roe deer abundances, but further research is needed to understand this causal link, as well as to weigh the costs and benefits of deer culling for forest biodiversity.

opencc-zeroMar 2024View details →

Data from: The spotted parrotfish genome provides evolutionary insight into the ecological adaptation of a keystone dietary specialist

With over 600 valid species, the wrasses (family Labridae) are among the largest and most successful of the marine teleosts. They feature prominently on coral reefs where they are known not only for their impressive diversity in colouration and form, but also in their functional specialization and ability to occupy a wide variety of trophic guilds. Among the wrasses, the parrotfishes (tribe Scarini) display some one of the most dramatic examples of trophic specialization. Using abrasion-resistant biomineralized teeth, parrotfishes are able to mechanically extract protein-rich micro-photoautotrophs growing in and amongst reef carbonate material, a dietary niche that is inaccessible to most other teleost fishes. This ability to exploit an otherwise untapped trophic resource is thought to have played a role in the diversification and evolutionary success of the parrotfishes. In order to better understand the key evolutionary innovations leading to the success of these dietary specialists, we sequenced and analysed the genome of a representative species, the spotted parrotfish (Cetoscarus ocellatus). We find significant expansion, selection, and duplication within several detoxification gene families and a novel poly-glutamine expansion in the enamel protein ameloblastin, and we consider their evolutionary implications. Our genome provides a useful resource for comparative genomic studies investigating the evolutionary history of this highly specialized teleostean radiation.

opencc-zeroMar 2024View details →

Contrasting effects of host or local specialization: widespread haemosporidians are host generalist whereas local specialists are locally abundant

Aim: Despite the wide distribution of many parasites around the globe, the range of individual species varies significantly even among phylogenetically related taxa. Since parasites need suitable hosts to complete their development, parasite geographical and environmental ranges should be limited to communities where their hosts are found. Parasites may also suffer from a trade-off between being locally abundant or widely dispersed. We hypothesize that the geographical and environmental ranges of parasites are negatively associated to their host specificity and their local abundance. Location: Worldwide Time period: 2009 to 2021 Major taxa studied: Avian haemosporidian parasites Methods: We tested these hypotheses using a global database which comprises data on avian haemosporidian parasites from across the world. For each parasite lineage, we computed five metrics: phylogenetic host-range, environmental range, geographical range, and their mean local and total number of observations in the database. Phylogenetic generalized least squares models were ran to evaluate the influence of phylogenetic host-range and total and local abundances on geographical and environmental range. In addition, we analysed separately the two regions with the largest amount of available data: Europe and South America. Results: We evaluated 401 lineages from 757 localities and observed that generalism (i.e. phylogenetic host range) associates positively to both the parasites' geographical and environmental ranges at global and Europe scales. For South America, generalism only associates with geographical range. Finally, mean local abundance (mean local number of parasite occurrences) was negatively related to geographical and environmental range. This pattern was detected worldwide and in South America, but not in Europe. Main Conclusions: We demonstrate that parasite specificity is linked to both their geographical and environmental ranges. The fact that locally abundant parasites present restricted ranges, indicates a trade-off between these two traits. This trade-off, however, only becomes evident when sufficient heterogeneous host communities are considered.

opencc-by-4.0Apr 2024View details →

From Generalist to Specialist: Incorporating Domain-Knowledge into Flamingo for Chest X-Ray Report Generation

This subset of the MIMIC-CXR split file contains the study identifiers and paths to the chest X-ray images used for training, validation and testing of all models presented in the paper: "From Generalist to Specialist: Incorporating Domain-Knowledge into Flamingo for Chest X-Ray Report Generation".

opencc-zeroMar 2022View details →

Native generalist natural enemies and an introduced specialist parasitoid together control an invasive forest insect

Specialized natural enemies have long been considered a major force driving the population dynamics of outbreaking forest insects. While research has traditionally focused on the role of specialist parasitoids, recent studies and reviews reflect an appreciation of complex interactions among many regulatory factors. The sources suggest that specialist parasitoids and generalist predators can each inflict strong top‐down effects and that specialists and generalists can interact to regulate insect herbivore populations. Here we use the model study organism winter moth (Operophtera brumata) in its invasive range in the northeast United States to investigate interactions between the introduced, host-specific tachinid parasitoid Cyzenis albicans and native, generalist pupal predators. Prior research in Canada showed that predation of winter moth pupae increased after C. albicans establishment. To explain this phenomenon, the following hypotheses have been suggested: (1) parasitoids suppress the winter moth population to a density that can be maintained by generalist predators, (2) unparasitized pupae are preferred by predators and thus experience higher mortality rates, or (3) C. albicans sustain higher predator populations throughout the year more effectively than winter moth alone. We tested these hypotheses by deploying winter moth pupae over six years spanning 2005 to 2017 and by modeling pupal predation rates as a function of winter moth density and C. albicans establishment. We also compared predation rates of unparasitized and parasitized pupae and considered additional mortality by a native pupal parasitoid. We found support for the first hypothesis; we detected both temporal and spatial density dependence, but only in the latter years of the study when winter moth densities were lower. We found no evidence for the latter two hypotheses. Our findings suggest that pupal predators have a regulatory effect on winter moth populations only after populations have been reduced, presumably by the introduction of the host-specific parasitoid C. albicans.

opencc-by-4.0Sep 2022View details →

Complex plant quality - microbiota - population interactions modulate the response of a specialist herbivore to the defense of its host plant.

1. Many specialist herbivores have evolved strategies to cope with plant defenses, with gut microbiota potentially participating to such adaptations. 2. In this study we assessed whether the history of plant use (population origin) and microbiota may interact with plant defense adaptation. 3. We tested whether microbiota enhance the performance of Melitaea cinxia larvae on their host plant, Plantago lanceolata and increase their ability to cope the defensive compounds, iridoid glycosides (IGs). 3. The gut microbiota was significantly affected by both larval population origin and host plant IG level. Contrary to our prediction, impoverishing the microbiota with antibiotic treatment did not reduce larval performance. 5. As expected for this specialized insect herbivore, sequestration of one of IGs was higher in larvae fed with plants producing higher concentration of IGs. These larvae also showed metabolic signature of intoxication (i.e. decrease in Lysine levels). However, intoxication on highly defended plants was only observed when larvae with history of poorly defended plants were simultaneously treated with antibiotics. 6. Our results suggest that both adaptation and microbiota contribute to the metabolic response of herbivores to plant defense though complex interactions.

opencc-zeroSep 2022View details →

Environmental stochasticity increases extinction risk to a greater degree in pollination specialists than in generalists

Pollination sustains terrestrial food webs and agricultural systems and links the dynamics of interacting plant and pollinator species. Although environmental stochasticity is ubiquitous and can propagate through communities via species interactions in a way that increases extinction risk, it is unknown whether stochasticity affects species uniformly across pollination networks. In this paper, we introduce a stochastic dynamic model that makes novel use of the birth function and apply it to pollination networks of increasing size. We start with two- and four-species networks, in order to first illustrate the effects of stochasticity per se and then how those effects combine with specialization. We then describe the relationship between partner number and stochastic extinction risk in empirical networks with >20 species. In the 2-species network, increasing the variance of the stochastic term of the model increased the size of the region in parameter space where extinctions occur. In networks with 4 or more species, specialists were more vulnerable to extinction than generalists over a broad range of variances. Extinction risk in networks with >20 species declined nonlinearly with increasing mutualist partner number. Our results demonstrate the importance of including species interactions and stochasticity when using population-dynamic models to compare species' extinction risk. While models that omit either of these factors are likely to underestimate extinction risk, they disproportionately underestimate the vulnerability of specialists.

FIGURE 6 in Evaluating the ecology of Spinosaurus: Shoreline generalist or aquatic pursuit specialist?

FIGURE 6. Suggested head positions of Spinosaurus relative to water. A) when dipping the snout in the water to forage while leaving the naris above the waterline as per the wading model. Head angle of 45 degrees based on Schade et al. (2020) for Irritator. B) while lying submerged, keep the naris and orbit clear of the water while minimising the amount of head that is exposed as per Arden et al. (2019), C) fully submerged as if coming up for air and trying to expose only the nares to breathe. Scale bar equals 1 m.

FIGURE 9 in Evaluating the ecology of Spinosaurus: Shoreline generalist or aquatic pursuit specialist?

FIGURE 9. Line drawings of mid caudal vertebrae and chevrons of assorted reptiles (all in left lateral view) compared to A) Spinosaurus (Ibrahim et al., 2020a). Taxa with known or inferred signaling structures linked to their elongate neural spines (top row), B) Bagaceratops (Tereschenko and Singer, 2013), the sail-finned lizards C) Hydrosaurus* and D) Basiliscus* (courtesy of Jeroen Costeseque), E) the drepanosaur Drepanosaurus (redrawn from Sues, 2019), F) the chameleon Trioceros (courtesy of Steven Huskey), and those which show adaptations for aquatic locomotion (bottom row), G) a juvenile specimen of the crocodylian Tomistoma* (courtesy of Mathew Wedel), H) the phytosaur Mystriosuchus (Renesto and Lombardo, 1999) I) the mosasaur Mosasaurus (modified from Lindgren et al., 2011), J) the sea snake Pelamis (modified from Lindgren et al., 2011), and K) diapsid Hovasaurus* (redrawn from Sues, 2019). Scale bars are A) 200 mm, B) 20 mm, C) 10 mm, D) 10 mm, E) 20 mm, F) 10 mm, G), 20 mm, H) 20 mm, I) 100 mm, J) 2 mm K) 20 mm.

FIGURE 8 in Evaluating the ecology of Spinosaurus: Shoreline generalist or aquatic pursuit specialist?

FIGURE 8. Depth of water required for Spinosaurus to avoid the considerable effects of wave drag. Even with the hind limbs lifted up, the animal is nearly 3 m in dorsoventral height so to avoid wave drag (fully submerged by over 3.5 m) the water would need to be close to 6 m in depth for Spinosaurus to swim efficiently. This is a minimum and the real value is likely to be higher (see text for details). Outline modified from Ibrahim et al. (2020a) and scale bar equals 1 m.

FIGURE 4 in Evaluating the ecology of Spinosaurus: Shoreline generalist or aquatic pursuit specialist?

FIGURE 4. Graph of theropod ungual curvature vs ungual length. The inset shows how the curvature of the unguals was measured. In lateral view a line AB is drawn between the ungual tip and the base. This is bisected by a perpendicular line until it contacts the ungual at point C. Lines are drawn from A to C and A to B and the internal angle measured. Unguals of Spinosaurus are in red, a further specimen attributed to a spinosaur is in yellow, and individual specimens are abbreviated as follows: Ab, abelisaurid; Ac, Acrocanthosaurus; Ai, Alioramus; Al, Allosaurus; Ca, Caudipteryx; Ce, ceratosaur; Co, Compsognathus; Di, Dilophosaurus; Ga, Gaulicho; Gg, Gigantoraptor; Gl, Gallimimus; Gu, Guanlong; Ha, Halszkaraptor; Ju, Juravenator; Ki, Kileskus; Li, Limusaurus; Mj, Majungasaurus; Sc, Spectrovenator; Sd, spinosaurid; Sn, Sinraptor; Sp, Spinosaurus; SB, Spinosaurus B; Tt, Tyrannotitan; Ty, Tyrannosaurus.