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Figure 10 from: Svantesson S, Larsson K-H, Kõljalg U, May TW, Cangren P, Nilsson RH, Larsson E (2019) Solving the taxonomic identity of Pseudotomentella tristis s.l. (Thelephorales, Basidiomycota) – a multi-gene phylogeny and taxonomic review, integrating ecological and geographical data. MycoKeys 50: 1-77. https://doi.org/10.3897/mycokeys.50.32432
Figure 10 Micromorphological features of P.atrofusca in KOH. Holotype: A, B basidiospores in frontal face C, D in lateral face.
Figure 1 from: Svantesson S, Larsson K-H, Kõljalg U, May TW, Cangren P, Nilsson RH, Larsson E (2019) Solving the taxonomic identity of Pseudotomentella tristis s.l. (Thelephorales, Basidiomycota) – a multi-gene phylogeny and taxonomic review, integrating ecological and geographical data. MycoKeys 50: 1-77. https://doi.org/10.3897/mycokeys.50.32432
Figure 1 Angle of spore faces. Dorsal side of spores, seen in a frontal face and b tilted frontal face.
Input data and Supplementary Results for "Community-level signatures of ecological succession in natural bacterial communities"
<p> </p> <p><strong>README<br> ======</strong></p> <p><br> This file describes the content of the different files included in this repository to<br> reproduce results from [1] and some of its supplementary results.</p> <p> </p> <p><strong>## Input files ##</strong></p> <p><strong>* 20151016_Functions_remainder.csv</strong></p> <p> Functions measured in [2]. The relevant quantities used in [1] are labelled with "7", and include:<br> <br> * Community: Id of the sample<br> * Replicate<br> * Plate<br> * mgCO2.7: CO2 measured along 7 days of experiment<br> * CPM7: Cell counts at the end of the experiment<br> * pgRPC.7: CO2 per cell<br> * ATP7: ATP measured (nM)<br> * mG7: beta glucosidase (mM)<br> * mN7: beta chitinase (mM)<br> * mX7: xylosidase (mM)<br> * mP7: phosphatase (mM)<br> <br> <strong>* samples_metadata_time0.tsv</strong></p> <p> * Samples: Id of the sample <br> * Part.dates: Date of sampling<br> * Part.GPS.PAM: Optimal sampling sites <br> * Part.SparCC.PAM.t0: Optimal partition using SparCC<br> * Part.SJD.PAM.t0: Optimal partition using Jensen-Shannon Divergence<br> * Part.Dir.t0: Optimal partition using Dirichlet mixtures<br> * Part.month: Month in which the community was sampled<br> <strong>* Dist_GPS-Haversine.dat</strong></p> <p> Haversine (spatial) distances between samples</p> <p><strong>* corMat-SparCC_20151016_OTU_remainder.clean.samples.txt</strong></p> <p> Matrix of correlations between samples computed with SparCC<br> <br> <strong>* distMat_ShannonJensen_Samples_Time0.clean.dat</strong></p> <p> Distance matrix computed with Jensen-Shannon divergence.</p> <p> </p> <p><br> <strong>## Supplementary results ##</strong></p> <p><strong>* SEMmodels.zip</strong></p> <p> Results for the Structural Equation Models analysed. The structure of the folders follows the one<br> available at the repository of the [project ](https://github.com/apascualgarcia/TreeHoles_descriptive).<br> <br> <strong>* TaxaSummaries.zip</strong></p> <p> The file contains one folder for each community-class, with matrices in different formats (biom and txt) computing the relative abundances of the OTUs at different taxonomic levels (labelled L2 being the proxy for Phylum to L6, the proxy of species). These matrices can be visualized interactively opening with a web browser the files area_charts.html.</p> <p><strong>#### References ####</strong></p> <blockquote> <p> [1] Pascual-García, A., & Bell, T. (2019). Community-level signatures of ecological succession in natural bacterial communities. Nature Communications (In press)</p> </blockquote> <blockquote> <p> [2] Rivett, Damian W., and Thomas Bell. Abundance determines the functional role of bacterial phylotypes in complex communities." Nature microbiology 3.7 (2018): 767.</p> </blockquote> <p> </p>
Fig. 6 Lunidia viridis n. gen. n in A new genus and species of African Phaneropterinae (Orthoptera: Tettigoniidae), with data on its ecology, bioacoustics and chromosomes
Fig. 6 Lunidia viridis n. gen. n. sp., male nymph, last instar
Fig. 4 Lunidia viridis n. gen. n in A new genus and species of African Phaneropterinae (Orthoptera: Tettigoniidae), with data on its ecology, bioacoustics and chromosomes
Fig. 4 Lunidia viridis n. gen. n. sp., female imitating a leaf
Figure 4 in Biodiversity, DNA barcoding data and ecological traits of caddisflies (Insecta, Trichoptera) in the catchment area of the Mediterranean karst River Cetina (Croatia)
Figure 4. Distribution of species Hydroptila vichtaspa according to Fauna Europaea (accessed on 12th May 2021) with location of the first finding in Croatia.
Data from: Positive feedback between ecological and reproductive character displacement in a young avian hybrid zone
Character displacement can reduce costly interspecific interactions between young species. We investigated the mechanisms behind divergence in three key traits - breeding habitat choice, timing of breeding and plumage coloration - in Ficedula flycatchers. We found that male pied flycatchers became expelled from the preferred deciduous habitat into mixed forest as the superior competitor, collared flycatchers, increased in numbers. The peak in food abundance differs between habitats, and the spatial segregation was paralleled by an increased divergence in timing of breeding between the two species. Male pied flycatchers vary from brown to black with brown coloration being more frequent in sympatry with collared flycatchers, a pattern often proposed to result from selection against hybridization, i.e. reinforcement. In contrast to this view, we show that brown male pied flycatchers more often hybridize than black males. Male pied flycatcher plumage coloration influenced the territory obtained in areas of co-occurrence with collared flycatchers, and brown male pied flycatchers experienced higher relative fitness than black males when faced with heterospecific competition. We suggest that allopatric divergence in resource defense ability causes a feedback loop at secondary contact where male pied flycatchers with the most divergent strategy compared to collared flycatchers are favored by selection.
Data from: Feeding ecology underlies the evolution of cichlid jaw mobility
The fish feeding apparatus is among the most diverse functional systems in vertebrates. While morphological and mechanical variation of feeding systems are well studied, we know far less about the diversity of the motions that they produce. We explored patterns of feeding movements in African cichlids from Lakes Malawi and Tanganyika, asking whether the degree of kinesis is associated with dietary habits of species. We used geometric morphometrics to measure feeding kinesis as trajectories of shape change, based on 326 high-speed videos in 56 species. Cranial morphology was significantly related to feeding movements, both of which were distributed along a dietary axis associated with prey evasiveness. Small-mouthed cichlids that feed by scraping algae and detritus from rocks had low kinesis strikes, while large-mouthed species that eat large, evasive prey (fishes and shrimps) generated the greatest kinesis. Despite having higher overall kinesis, comparisons of trajectory shape (linearity) revealed that cichlids that eat mobile prey also displayed more kinematically conserved, or efficient, feeding motions. Our work indicates that prey evasiveness is strongly related to the evolution of cichlid jaw mobility, suggesting that this same relationship may explain the origins and diversity of highly kinetic jaws that characterize the super-radiation of spiny-rayed fishes.
Data from: PaleoENM: applying ecological niche modeling to the fossil record
Ecological niche modeling (ENM) is a quantitative approach to predict species' abiotic requirements. It is a correlative technique, requiring geographically explicit information on species occurrences and the suites of environmental conditions experienced at each occurrence point. The output of these models is a set of environmental suitability rules that can be projected geographically and through time to test biogeographic, ecologic, and evolutionary hypotheses. Although developed by biologists and used extensively in the modern, ENM is in its early stages of application to the deep-time fossil record (hence PaleoENM). In part its limited use in the fossil record thus far reflects the methodological challenge of constructing paleoenvironmental layers needed for PaleoENM analysis, whereas in the modern these layers are available from large public databases (e.g., WorldClim). This paper provides a contextual and methodological framework for appropriately applying PaleoENM, including best practices for developing species occurrence and paleoenvironmental data sets for PaleoENM analyses.
Data from: Community functional trait composition at the continental scale: the effects of non-ecological processes
Ecological communities and their response to environmental gradients are increasingly being described by measures of trait composition at the community level – the trait-based approach. Whether ecological or non-ecological processes influence trait composition between communities has been debated. Understanding the processes that influence trait composition is important for reconstructing paleoenvironmental conditions from fossil deposits and for understanding changes in community functionality through time. Here, we assess the influence of ecological and non-ecological processes on the distribution of traits within North American mammals. We found that non-ecological processes including historical contingency, spatial autocorrelation, and evolutionary history do not influence trait composition; however, the variance in trait composition is highly explained by climate gradients. Our results suggest that habitat breadth, terrestriality, diet breadth, and reproductive traits are strong candidates as proxies for measuring functional aspects of environments in the past and present.
Data from: The ecological and genetic basis of convergent thick-lipped phenotypes in cichlid fishes
The evolution of convergent phenotypes is one of the most interesting outcomes of replicate adaptive radiations. Remarkable cases of convergence involve the thick-lipped phenotype found across cichlid species flocks in the East African Great Lakes. Unlike most other convergent forms in cichlids, which are restricted to East Africa, the thick-lipped phenotype also occurs elsewhere, e.g. in the Central American Midas Cichlid assemblage. Here we use an ecological genomic approach to study the function, the evolution and the genetic basis of this phenotype in two independent cichlid adaptive radiations on two continents. We applied phylogenetic, demographic, geometric morphometric and stomach-content analyses to an African (Lobochilotes labiatus) and a Central American (Amphilophus labiatus) thick-lipped species. We found that similar morphological adaptations occur in both thick-lipped species and that the 'fleshy' lips are associated with hard-shelled prey in the form of mollusks and invertebrates. We then used comparative Illumina RNA sequencing of thick versus normal lip tissue in East African cichlids and identified a set of 141 candidate genes that appear to be involved in the morphogenesis of this trait. A more detailed analysis of six of these genes led to three strong candidates: Actb, Cldn7 and Copb. The function of these genes can be linked to the loose connective tissue constituting the fleshy lips. Similar trends in gene expression between African and Central American thick-lipped species appear to indicate that an overlapping set of genes was independently recruited to build this particular phenotype in both lineages.
Data from: A novel integrative method for measuring body condition in ecological studies based on physiological dysregulation
1. The body condition of free-ranging animals affects their response to stress, decisions, ability to fulfil vital needs and, ultimately, fitness. However, this key attribute in ecology remains difficult to assess, and there is a clear need for more integrative measures than the common univariate proxies. 2. We propose a systems biology approach that positions individuals along a gradient from a 'normal/optimal' to 'abnormal/suboptimal' physiological state based on Mahalanobis distance computed from physiological biomarkers. We previously demonstrated the validity of this approach for studying ageing in humans; here, we illustrate its broad potential for ecological studies. 3. As an example, we used biomarker data on shorebirds and found that birds with an abnormal condition had a lower maximal thermogenic capacity and higher scores of inflammation, with important implications for their ecology and health. Moreover, Mahalanobis distance captured a signal of condition not detected by the individual biomarkers. 4. Overall, our results on birds and humans show that individuals with abnormal physiologies are indeed in worse condition. Moreover, our approach appears not to be particularly sensitive to which set of biomarkers is used to assess condition. Consequently, it could be applied easily to existing ecological data sets. 5. Our approach provides a general, powerful way to measure condition that helps resolve confusion as to how to deal with complex interactions and interdependence among multiple physiological and condition measures. It can be applied directly to topics such as the effect of environmental quality on body condition, risks of health outcomes, mechanisms of adaptive phenotypic plasticity, and mechanisms behind long-term processes such as senescence.
Data from: Ecological opportunity and ecomorphological convergence in Australasian robins (Petroicidae)
Ecological theories of adaptive radiation predict that ecological opportunity (EO) stimulates cladogenesis through entry into a novel environment and/or release of competition pressures. Due to its dynamic paleoclimatic and geological history, the Australo-Papuan region constitutes an opportune scenario to study patterns of diversification in relation to the colonization of new ecological niches. Here, we employ a comparative framework using the Australasian robins (Petroicidae) as a model system to test whether the diversification of this bird family fulfils a niche-filling process as predicted by the EO model, and to test whether the observed morphological similarity is described by a pattern of phylogenetic niche conservatism (PNC) or convergence. Although we detected an early-burst, we did not find a slowdown in speciation or morphological evolution as expected in a niche-filling scenario. Divergence in tarsus length and tail length (PC1) was consistent with a multi-peak model, in which PC1 represents a convergent trait among distantly related clades sharing the same foraging strategy. Our study thus shows that convergence rather than PNC seems to explain the existence of morphological similarity across independent lineages in the Petroicidae. We also found a low level of PNC regarding annual variations in temperature and precipitation, which is in agreement with the hypothesis that diversification within the Petroicidae involved repeated radiations. We suggest two non-mutually exclusive hypotheses to explain the overall lack of density-dependent cladogenesis. First, the extreme spatial and temporal heterogeneity of this region may have generated a pattern of repeated ecological opportunity over time and, second, this family may not yet have reached equilibrium diversity.
Data from: Sexual selection is positively associated with ecological generalism among agamid lizards
Natural and sexual selection shape the evolution of species, but the interplay between them is poorly understood. Two phylogenetic studies on birds have suggested that species with greater sexual dichromatism use more habitats. Here, we show that in Agamid lizards, species with more elaborate secondary sexual traits also are ecologically more opportunistic. Species with greater dimorphism in head size and ornamentation have greater altitudinal range and occupy more habitats, respectively, and species with greater sexual dichromatism have a wider microhabitat use. Body size was positively associated with sexual and ecological traits but associations between ecological and sexual traits remained after accounting for body size. The results are consistent with the earlier studies and we suggest that sexual and natural selection may be linked through sexual selection promotes generalism at the population level by favouring 'good genes', or higher population densities cause both stronger sexual selection and broader resource use.
Data from: Light sensing by opsins and fungal ecology: NOP-1 modulates entry into sexual reproduction in response to environmental cues
Understanding the genetic basis of the switch from asexual to sexual lifestyles in response to sometimes rapid environmental changes is one of the major challenges in fungal ecology. Light appears to play a critical role in the asexual–sexual switch—but fungal genomes harbour diverse light sensors. Fungal opsins are homologous to bacterial green-light-sensory rhodopsins, and their organismal functions in fungi have not been well understood. Three of these opsin-like proteins were widely distributed across fungal genomes, but homologs of the Fusarium opsin-like protein CarO were present only in plant-associated fungi. Key amino acids, including potential retinal binding sites, functionally diverged on the phylogeny of opsins. This diversification of opsin-like proteins could be correlated with life history-associated differences among fungi in their expression and function during morphological development. In Neurospora crassa and related species, knockout of the opsin NOP-1 led to a phenotype in the regulation of the asexual–sexual switch, modulating response to both light and oxygen conditions. Sexual development commenced early in ∆nop-1 strains cultured in unsealed plates under constant blue and white light. Furthermore, comparative transcriptomics showed that the expression of nop-1 is light-dependent and that the ∆nop-1 strain abundantly expresses genes involved in oxidative stress response, genes enriched in NAD/NADP binding sites, genes with functions in proton transmembrane movement and catalase activity, and genes involved in the homeostasis of protons. Based on these observations, we contend that light and oxidative stress regulate the switch via light-responsive and ROS pathways in model fungus N. crassa and other fungi.
Data from Hildesheim LS, Opedal ØH, Armbruster WS, Pélabon C. 2019. Quantitative and qualitative consequences of reduced pollen loads in a mixed-mating plant. Ecology and Evolution.
<p class="Normal1">Greater pollination intensity can enhance maternal plant fitness by increasing seed set and seed quality as a result of more intense pollen competition or enhanced genetic sampling. We tested experimentally these effects by varying the pollen load from a single pollen donor on stigmas of female flowers of <i>Dalechampia scandens </i>(Euphorbiaceae) and measuring the effects on seed number and seed mass.<b> </b>Seed set increased rapidly with pollen number at low to moderate pollen loads, and a maximum set of three seeds occurred with a mean pollen load of 19 pollen grains. We did not detect a trade-off between the number of seeds and seed mass within a fruit. Seed mass increased with increasing pollen load, supporting the hypothesis of enhanced seed quality via increased pollen-competition intensity or genetic sampling. These results suggest that maternal fitness increases with larger pollen loads, even when the fertilization success is already high. Our results further highlight the importance of high rates of pollen arrival onto stigmas, as mediated by reliable pollinators. Comparing the pollen-to-seed response curve obtained in this experiment with those observed in natural populations suggests that pollen limitation may be more severe in natural populations than detected in greenhouse studies. The results also indicate that declining pollinator abundance may decrease seed quality before an effect on seed set is detected.</p>
Data from: Using local ecological knowledge to build mutualistic networks in hyper-diverse and logistically challenging ecosystems
<p>1. Collecting interaction data to build frugivory or seed dispersal networks is logistically challenging in ecosystems that have very high plant and animal diversity and/or where fieldwork is difficult or dangerous. Consequently, the majority of available networks are from ecosystems with low species diversity or they represent a sub-set of the community. </p> <p>2. Here, we propose an approach using local ecological knowledge (LEK) of indigenous communities to build interaction databases and weighted networks that would otherwise be difficult to achieve with direct observations. Indigenous communities live and work in many hyper-diverse ecosystems and the people within these communities often have detailed knowledge of ecological processes. </p> <p>3. Working in a Sundaland biodiversity hotspot – Royal Belum State Park, Peninsular Malaysia – we used field data, visually-oriented interviews with indigenous people (Orang Asli, in the Jahai and Temiar ethnic subgroups), and published records to collate interactions, and their frequency of occurrence of animal fruit consumption and seed dispersal. </p> <p>4. We documented 2060 fruit consumption and 1330 seed dispersal interactions among 164 plant species and 34 animal taxa, the latter representing groups of closely related species or individual species. The majority of the interactions (97%) were identified by the LEK interviews, with the additional methods (field data and published records) used to support and marginally expand the interview data. The metrics for the networks we built reflect those of networks structured by biological mechanisms, supporting the validity of our novel method. </p> <p>5. Local ecological knowledge is highly relevant for building detailed databases for mutualistic interactions in hyper-diverse and/or challenging ecosystems. Such ecosystems are among the most vulnerable on earth, harbouring ecological interactions that are often poorly documented at a community-level. We show how LEK can broaden our knowledge of such sensitive ecosystems, but our approach is useful for any ecosystem where people retain rich local ecological knowledge.</p>
Data from: Insights into the ecology and evolution of polyploid plants through network analysis
Polyploidy is a widespread phenomenon throughout eukaryotes, with important ecological and evolutionary consequences. Although genes operate as components of complex pathways and networks, polyploid changes in genes and gene expression have typically been evaluated as either individual genes or as a part of broad-scale analyses. Network analysis has been fruitful in associating genomic and other 'omic'-based changes with phenotype for many systems. In polyploid species, network analysis has the potential not only to facilitate a better understanding of the complex 'omic' underpinnings of phenotypic and ecological traits common to polyploidy, but also to provide novel insight into the interaction among duplicated genes and genomes. This adds perspective to the global patterns of expression (and other 'omic') change that accompany polyploidy and to the patterns of recruitment and/or loss of genes following polyploidization. While network analysis in polyploid species faces challenges common to other analyses of duplicated genomes, present technologies combined with thoughtful experimental design provide a powerful system to explore polyploid evolution. Here, we demonstrate the utility and potential of network analysis to questions pertaining to polyploidy with an example involving evolution of the transgressively superior cotton fibres found in polyploid Gossypium hirsutum. By combining network analysis with prior knowledge, we provide further insights into the role of profilins in fibre domestication and exemplify the potential for network analysis in polyploid species.
FIGURE 7 in Rediscovery of the Earless Microteiid Lizard Anotosaura collaris Amaral, 1933 (Squamata: Gymnophthalmidae): A redescription complemented by osteological, hemipenial, molecular, karyological, physiological and ecological data
FIGURE 7. Karyotype of Anotosaura collaris after conventional staining, showing 2n=44 (20M + 22m).
Figs. 7-8 in Andrena (Suandrena) portosanctana COCKERELL, 1922 and A. (Suandrena) maderensis COCKERELL, 1922 - new taxonomical and ecological data for two closely related endemic bee species of the Madeira Archipelago, Portugal
Figs. 7-8: Syntype of Andrena portosanctana (female) deposited in the Department of Entomology, NMNH, Smithsonian Institution, Washington DC, USA (USNM 24656, barcode number 00533697); (7) head frontal view; (8) labels; photos: Department of Entomology, NMNH, Smithsonian Institution.
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.