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Figure 1 in Acoustic ecology of an anuran assemblage in the arid Caatinga of northeastern Brazil
Figure 1. Phylogeny of anurans used in canonical phylogenetic ordination for microhabitat and diet data. Phylogenetic tree based in phylogenies of Nascimento et al. (2005), Ponssa (2008), Pyron and Wiens (2011).
Figure 1 in Influence of riparian quality on macroinvertebrate assemblages in subtropical mountain streams
Figure 1. Localization of the study area and distribution of reaches of good (white dots, 1–5), poor (grey dots, 6–8) and bad (black dots, 9–11) quality of their riparian zone.
Figure 7 from: Pujana RR, Wilf P, Gandolfo MA (2020) Conifer wood assemblage dominated by Podocarpaceae, early Eocene of Laguna del Hunco, central Argentinean Patagonia. PhytoKeys 156: 81-102. https://doi.org/10.3897/phytokeys.156.54175
Figure 7 Galleries in two indeterminate conifer woods: A gallery filled with apparently spherical coprolites (TS), MPEF-Pb 10736 B gallery filled with compact frass (RLS), MPEF-Pb 10725 C detail of the frass (RLS), MPEF-Pb 10725. Scale bars: 500 μm (A, B); 200 μm (C).
Figure 6 from: Pujana RR, Wilf P, Gandolfo MA (2020) Conifer wood assemblage dominated by Podocarpaceae, early Eocene of Laguna del Hunco, central Argentinean Patagonia. PhytoKeys 156: 81-102. https://doi.org/10.3897/phytokeys.156.54175
Figure 6 Schematic drawing of the cross-fields: AProtophyllocladoxylon francisiaeB cf. Cupressinoxylon sp. 1 CPhyllocladoxylon antarcticumD cf. Cupressinoxylon sp. 2. Scale bar: 50 μm.
Figure 5 from: Pujana RR, Wilf P, Gandolfo MA (2020) Conifer wood assemblage dominated by Podocarpaceae, early Eocene of Laguna del Hunco, central Argentinean Patagonia. PhytoKeys 156: 81-102. https://doi.org/10.3897/phytokeys.156.54175
Figure 5 cf. Cupressinoxylon sp. 2, MPEF-Pb 10778: A Growth rings of type B (TS) B detail of a growth ring of type B boundary (TS) C uniseriate non contiguous intertracheary radial pits D uni- and biseriate intertracheary radial pits, opposite when biseriate (arrowheads) E uniseriate non contiguous intertracheary radial pits F cross-fields with bordered pits (RLS) G and H cross-fields with bordered pits (SEM) I uniseriate rays (TLS). Scale bars: 5 mm (A); 200 μm (B, I); 50 μm (C, D, E); 20 μm (F, G, H).
Figure 4 from: Pujana RR, Wilf P, Gandolfo MA (2020) Conifer wood assemblage dominated by Podocarpaceae, early Eocene of Laguna del Hunco, central Argentinean Patagonia. PhytoKeys 156: 81-102. https://doi.org/10.3897/phytokeys.156.54175
Figure 4 cf. Cupressinoxylon sp. 1, MPEF-Pb 10733: A Growth rings (TS) B detail of a growth ring boundary (TS) C Detail of roundish tracheids and axial parenchyma (arrowheads) (TS) D uniseriate non contiguous intertracheary radial pits and cross-field pit (arrowhead) (SEM) E and F cross-fields with bordered pits (SEM) G axial parenchyma (arrowhead) and cross-fields with bordered pits (RLS) H uniseriate rays (TLS) I uniseriate rays (TLS). Scale bars: 5 mm (A); 500 μm (B); 100 μm (C, I); 20 μm (D, E, F, G); 200 μm (H).
Figure 3 from: Pujana RR, Wilf P, Gandolfo MA (2020) Conifer wood assemblage dominated by Podocarpaceae, early Eocene of Laguna del Hunco, central Argentinean Patagonia. PhytoKeys 156: 81-102. https://doi.org/10.3897/phytokeys.156.54175
Figure 3 Phyllocladoxylon antarcticum: A Growth rings of type D (TS), MPEF-Pb 10747 B detail of a growth ring of type D boundary (TS), MPEF-Pb 10776 C detail of roundish tracheids (TS), MPEF-Pb 10765 D opposite contiguous biseriate intertracheary radial pits (arrowheads) (RLS), MPEF-Pb 10767 E uniseriate non contiguous intertracheary radial pits (scanning electron microscope, SEM), MPEF-Pb 10776 F uniseriate contiguous (arrowheads) and non contiguous intertracheary radial pits (SEM), MPEF-Pb 10776 G cross-fields with large simple pits (RLS), MPEF-Pb 10707 H cross-fields with large pointed and narrow-bordered pits (RLS), MPEF-Pb 10765 I cross-fields with large simple pits (SEM), MPEF-Pb 10710 J wall alteration of the secondary walls of tracheids (RLS), MPEF-Pb 10767 K uniseriate rays (TLS), MPEF-Pb 10767 L uniseriate rays (TLS), MPEF-Pb 10747. Scale bars: 5 mm (A); 200 μm (B, K); 100 μm (C, L); 50 μm (D, F, G, H, I, J); 20 μm (E).
Figure 2 from: Pujana RR, Wilf P, Gandolfo MA (2020) Conifer wood assemblage dominated by Podocarpaceae, early Eocene of Laguna del Hunco, central Argentinean Patagonia. PhytoKeys 156: 81-102. https://doi.org/10.3897/phytokeys.156.54175
Figure 2 Protophyllocladoxylon francisiae, MPEF-Pb 10694: A Growth rings of type D (transverse section, TS) B detail of a growth ring of type D boundary (TS) C opposite (arrowheads) intertracheary radial pits (radial longitudinal section, RLS) D alternate (arrowheads) intertracheary radial pits (RLS) E and F cross-fields (RLS) G wall alteration of the secondary walls of tracheids (tangential longitudinal section, TLS) H uniseriate rays (TLS) I uniseriate rays (TLS). Scale bars: 5 mm (A); 500 μm (B); 50 μm (C, D, E, F, G); 100 μm (H); 200 μm (I).
Figure 1 from: Pujana RR, Wilf P, Gandolfo MA (2020) Conifer wood assemblage dominated by Podocarpaceae, early Eocene of Laguna del Hunco, central Argentinean Patagonia. PhytoKeys 156: 81-102. https://doi.org/10.3897/phytokeys.156.54175
Figure 1 Location map and satellite images (Instituto Geográfico Nacional de la República Argentina, upper, and Google, CNES / Airbus, below) showing the Laguna del Hunco section and sampling locations. Scale in the satellite image below (tilted) varies across the map.
Links between prey assemblages and poison frog toxins: a landscape ecology approach to assess how biotic interactions affect species phenotypes
<p>Ecological studies of species pairs showed that biotic interactions promote phenotypic change and eco-evolutionary feedbacks. However, it is unclear how phenotypes respond to synergistic interactions with multiple taxa. We investigate whether interactions with multiple prey species explain spatially structured variation in the skin toxins of the Neotropical poison frog <i>Oophaga pumilio</i>. Specifically, we assess how dissimilarity (i.e., beta diversity) of alkaloid-bearing arthropod prey assemblages (68 ant species) and evolutionary divergence between frog populations (from a neutral genetic marker) contribute to frog poison dissimilarity (toxin profiles composed of 230 different lipophilic alkaloids sampled from 934 frogs at 46 sites). We find that models that incorporate spatial turnover in the composition of ant assemblages explain part of the frog alkaloid variation, and we infer unique alkaloid combinations across the range of <i>O. pumilio</i>. Moreover, we find that alkaloid variation increases weakly with the evolutionary divergence between frog populations. The analytical framework proposed here can be extended to other multi-trophic systems, coevolutionary mosaics, microbial assemblages, and ecosystem services.</p>
Cold-water coral assemblages on vertical walls: distribution patterns from the Northeast Atlantic
<p><b>Aim</b>: In this study, we assess patterns of cold-water coral assemblages observed on deep-sea vertical walls. Similar to their shallow-water counterparts, vertical and overhanging walls in the deep sea can host highly diverse communities, but because of their geometry, these habitats are generally overlooked and remain poorly known. These vertical habitats are however of particular interest, because they can protect vulnerable coral ecosystems from trawling activities. As such, it is important to understand their ecology and assess their global importance. </p> <p><b>Location</b>: Vertical walls on complex geomorphic features, in particular walls of the Rockall Bank Slope Failure Escarpment, Whittard and Explorer Canyons, Northeast Atlantic.</p> <p><b>Methods</b>: Video analysis of ROV transects carried out at five sites is used to investigate differences in species composition and diversity across walls and to compare those to nearby cold-water coral sites on flat terrain. A high-resolution photogrammetric reconstruction is further employed to examine whether wall complexity plays a role in promoting niche differentiation at very fine spatial scales. </p> <p><b>Results</b>: The investigated walls showed differences in species assemblage both across walls as well as in comparison to flat sites, with the fine-scale heterogeneity engendered by walls allowing niche differentiation between closely-related taxa. </p> <p><b>Main Conclusions</b>: Vertical walls represent an important cold-water coral habitat with differences in species composition across walls within a region, illustrating their role in driving diversity patterns. Based on publicly available bathymetric datasets and a catalogue of broad-scale terrain features, globally over 8,000 features are likely to have vertical walls and cold-water corals, which highlights the need to consider deep-sea vertical habitats in current conservation efforts.</p>
Data from: Temperature-driven colour lightness and body size variation scale to local assemblages of European Odonata but are modified by propensity for dispersal
<p>1. Previous macrophysiological studies suggested that temperature-driven colour lightness and body size variations strongly influence biogeographical patterns in ectotherms. However, these trait-environment relationships scale to local assemblages and the extent to which they can be modified by dispersal remains largely unexplored. We test whether the predictions of the thermal melanism hypothesis and the Bergmann's rule hold for local assemblages. We also assess whether these trait-environment relationships are more important for species adapted to less stable (lentic) habitats, due to their greater dispersal propensity compared to those adapted to stable (lotic) habitats.</p> <p>2. We quantified the colour lightness and body volume of 99 European dragon- and damselflies (Odonata) and combined these trait information with survey data for 518 local assemblages across Europe. Based on this continent-wide yet spatially explicit dataset, we tested for effects temperature and precipitation on the colour lightness and body volume of local assemblages and assessed differences in their relative importance and strength between lentic and lotic assemblages, while accounting for spatial and phylogenetic autocorrelation.</p> <p>3. The colour lightness of assemblages of odonates increased and body size decreased with increasing temperature. Trait-environment relationships in the average and phylogenetic predicted component were equally important for assemblages of both habitat types but were stronger in lentic assemblages when accounting for phylogenetic autocorrelation.</p> <p>4. Our results show that the mechanism underlying colour lightness and body size variations scale to local assemblages, indicating their general importance. These mechanisms were of equal evolutionary significance for lentic and lotic species, but higher dispersal ability seems to enable lentic species to cope better with historical climatic changes. The documented differences between lentic and lotic assemblages also highlight the importance of integrating interactions of thermal adaptations with proxies of the dispersal ability of species into trait-based models, for improving our understanding of climate-driven biological responses.</p>
FIG. 4 in Early Miocene squamate assemblage from the Mokrá-Western Quarry (Czech Republic) and its palaeobiogeographical and palaeoenvironmental implications
FIG. 4. — Lacertoidea indet. (A, B) and? Scincoidea indet. (C, D) from the early Miocene (MN 4) of MWQ. Left dentary Pal. 1571 (2/2003 Reptile Joint) in (A) lateral and (B) medial aspects with detail of teeth. Left maxilla Pal. 1573 (2/2003 Reptile Joint) in (C) lateral and (D) medial aspects with detail of teeth. Abbreviations: dc, dental crest; cm, carina maxillaris; lf, labial foramina; Mg, Meckel`s groove; np, nasal process; sbs, subdental shelf; srs, supradental shelf; st, striations. Scale bars: A-D, 1 mm; B', D', 100 µm.
Flightlessness in insects enhances diversification and determines assemblage structure across whole communities
<p><span><span><span>Dispersal limitation has been recurrently suggested to shape both macroecological patterns and microevolutionary processes within invertebrates. However, because of potential interactions among biological, environmental, temporal, and spatial variables, causal links among flight-related traits, diversification and spatial patterns of community assembly remain elusive. Integrating genetic variation within species across whole insect assemblages, within a simplified spatial and environmental framework, can be used to reduce the impact of these potentially confounding variables. Here we used standardised sampling and mtDNA sequencing for a whole-community characterisation of the beetle fauna inhabiting a singular forested-habitat (laurel forest) within an oceanic archipelago setting (Canary Islands). The spatial structure of species assemblages together with species-level genetic diversity was compared at the archipelago and island scales for 104 winged and 110 wingless beetle lineages. We found that wingless beetle lineages have (i) smaller range sizes at the archipelago scale, (ii) lower representation in younger island communities, (iii) stronger population genetic structure, and (iv) greater spatial structuring of species assemblages between and within islands. Our results reveal that dispersal limitation is a fundamental trait driving diversity patterns at multiple hierarchical levels by promoting spatial diversification and affecting the spatial configuration of entire assemblages at both island and archipelago scales.</span></span></span></p>
Data from: Shining light on benthic macroalgae: mechanisms of complementarity in layered macroalgal assemblages
Phototrophs underpin most ecosystem processes, but to do this they need sufficient light. This critical resource, however, is compromised along many marine shores by increased loads of sediments and nutrients from degraded inland habitats. Increased attenuation of total irradiance within coastal water columns due to turbidity is known to reduce species' depth limits and affect the taxonomic structure and architecture of algal-dominated assemblages, but virtually no attention has been paid to the potential for changes in spectral quality of light energy to impact production dynamics. Pioneering studies over 70 years ago showed how different pigmentation of red, green and brown algae affected absorption spectra, action spectra, and photosynthetic efficiency across the PAR (photosynthetically active radiation) spectrum. Little of this, however, has found its way into ecological syntheses of the impacts of optically active contaminants on coastal macroalgal communities. Here we test the ability of macroalgal assemblages composed of multiple functional groups (including representatives from the chlorophyta, rhodophyta and phaeophyta) to use the total light resource, including different light wavelengths and examine the effects of suspended sediments on the penetration and spectral quality of light in coastal waters. We show that assemblages composed of multiple functional groups are better able to use light throughout the PAR spectrum. Macroalgal assemblages with four sub-canopy species were between 50–75% more productive than assemblages with only one or two sub-canopy species. Furthermore, attenuation of the PAR spectrum showed both a loss of quanta and a shift in spectral distribution with depth across coastal waters of different clarity, with consequences to productivity dynamics of diverse layered assemblages. The processes of light complementarity may help provide a mechanistic understanding of how altered turbidity affects macroalgal assemblages in coastal waters, which are increasingly threatened by diminishing light quantity and altered spectral distributions through sedimentation and eutrophication.
Data from: Interactive effects of pasture management intensity, release from grazing and prescribed fire on forty subtropical wetland plant assemblages
Pasture management intensity, livestock grazing and prescribed fire are three widespread agricultural practices that affect small, isolated wetlands, but few studies have investigated their individual and interactive effects. Pasture management intensity refers to the degree of human alteration of grassland, ranging from intensively managed pastures planted with introduced forage, fertilizer/lime additions and artificial drainage to semi-natural pastures with mixed native and non-native vegetation, no fertilizer/lime additions and little or no artificial drainage. We examined individual and interactive effects of these three agricultural practices on individual, isolated wetlands using a replicated, full-factorial experiment on 40 entire wetlands in south Florida, USA. Wetlands were embedded in two pasture management intensities: intensively managed and semi-natural. After three years of treatment initiation, vegetation of wetlands released from grazing and unburned embedded in semi-natural pastures had significantly lower evenness and coefficient of conservatism scores compared to wetlands released from grazing and burned, grazed unburned wetlands and grazed burned wetlands in the same pasture management intensity. For wetlands embedded in intensively managed pastures, evenness and coefficient of conservatism scores did not differ among treatments. Release from grazing increased abundance of the native, weedy herb, Eupatorium capillifolium. Grazing interacted with prescribed fire to affect shrub abundance and non-native richness; relative abundance of shrubs and non-native richness were greater in wetlands released from grazing and burned and did not differ among burn treatments in grazed wetlands. Interactive effects, especially three-way interactions, were uncommon and not as important as differences between the two pasture management intensities. Synthesis and applications. Vegetation diversity and floristic quality of wetlands embedded in intensively managed pastures resisted common restoration management techniques such as release from grazing and prescribed fire, at least in the short term. In contrast, removing all top-down disturbances from wetlands embedded in semi-natural grasslands can negatively affect vegetation species diversity and floristic quality. Future studies should examine how intensity and seasonality of grazing and prescribed fire affect wetland vegetation, and track long-term responses to evaluate lag effects.
Data from: Grazer effects on soil carbon storage vary by herbivore assemblage in a semi-arid grassland
1. Accounting for 10-30% of global soil organic carbon, grassland soils potentially present a large reservoir for storing atmospheric CO2. Livestock grazing management can substantially affect grassland soil carbon (C) storage, but few controlled experiments have explored how herbivore assemblages (different herbivore species and combinations) affect soil C storage. 2. We examined effects of moderate grazing by different herbivore assemblages (no grazing; sheep grazing; cattle grazing; mixed grazing by sheep and cattle) on soil organic carbon storage in two types of grassland communities (high forbs/high diversity and low forbs/low diversity), within a semi-arid grassland with a five-year grazing history. 3. We found that herbivore assemblage generated varying effects on soil C storage and the effects were subject to grassland community types. In the low diversity community, none of three herbivore assemblages studied had obvious effects on soil C storage. In the high diversity community, however, sheep grazing significantly decreased soil C storage due to high selectivity for high quality forbs, and cattle grazing had no effects on soil C storage, while mixed grazing by sheep and cattle significantly increased soil C storage. Overall, soil C storage was highest in mixed-grazed grassland sites with high diversity. 4. Synthesis and applications. Our study suggests that explicitly incorporating grazer species and the combination of grazing livestock into grassland grazing management may help mitigate greenhouse gas emissions. Caution should be exercised when using grazer species with high food selectivity when grazing management is also aimed at climate mitigation, especially in grasslands with abundant high quality forbs and high plant diversity, as sheep grazing may reduce soil carbon (C) storage. Moreover, mixed grazing, including multiple herbivore species, may contribute to a reduction in foraging selectivity for a plant community by means of complementary foraging. It could therefore be considered as an optimal grazing management strategy to maintain and improve soil C storage.
Data from: Bacterial microbiota assemblage in Aedes albopictus mosquitoes and its impacts on larval development
Interactions between bacterial microbiota and mosquitoes play an important role in mosquitoes' capacity to transmit pathogens. However, microbiota assemblages within mosquitoes and the impact of microbiota in environments on mosquito development and survival remain unclear. This study examined microbiota assemblages and the effects of aquatic environment microbiota on the larval development of the Aedes albopictus mosquito, an important dengue virus vector. Life table studies have found that reducing bacterial load in natural aquatic habitats through water filtering and treatment with antibiotics significantly reduced the larva-to-adult emergence rate. This finding was consistent in two types of larval habitats examined—discarded tires and flowerpots, suggesting that bacteria play a crucial role in larval development. Pyrosequencing of the bacterial 16S rRNA gene was used to determine the diversity of bacterial communities in larval habitats and the resulting numbers of mosquitoes under both laboratory and field conditions. The microbiota profiling identified common shared bacteria among samples from different years; further studies are needed to determine whether these bacteria represent a core microbiota. The highest microbiota diversity was found in aquatic habitats, followed by mosquito larvae, and the lowest in adult mosquitoes. Mosquito larvae ingested their bacterial microbiota and nutrients from aquatic habitats of high microbiota diversity. Taken together, the results support the observation that Ae. albopictus larvae are able to utilize diverse bacteria from aquatic habitats, and that live bacteria from aquatic habitats play an important role in larval mosquito development and survival. These findings provide new insights into bacteria's role in mosquito larval ecology.
Data from: Nitrogen loads influence trophic organization of estuarine fish assemblages
Nutrient (N and P) loading may affect functioning in aquatic ecosystems by restructuring producer assemblages with flow-on effects to consumers. Trophic niche occupancy and trophic organization of consumers are key components of ecosystem function that have been increasingly investigated using quantitative isotopic niche indices. These indices are based on the premise that the isotopic values of consumer tissues indicate their assimilated diet. Typically, isotopic niche indices are calculated using only consumer isotope data, which limit their application for spatial and temporal comparisons because consumer isotopic niches depend on isotopic variability of available autotrophs. We used measures of isotopic variability of autotrophs to standardize isotopic niche indices, which enabled us to compare trophic organization of fish assemblages in nine estuaries spanning a broad range of nutrient loading. We related standardized isotopic niche indices of fish assemblages to nitrogen and phosphorous loads and hydrological flushing of the estuaries in autumn and spring. The estuarine fish assemblages studied here showed greater trophic diversity and less redundancy given moderate to high inorganic nitrogen loading. Taxonomic richness partly influenced three isotopic niche indices measuring trophic diversity, but not measures of redundancy. Similar patterns may occur in other systems in which nitrogen loads have increased but the diversity of primary producers has not been reduced to a single dominant source. Our results demonstrate bottom-up controls of estuarine food webs. Effects of inorganic nitrogen loading were transmitted upwards through the food web to affect the trophic organization of higher trophic levels, demonstrating the crucial role of nitrogen for estuarine trophic dynamics.
Data from: A new framework for investigating biotic homogenization and exploring future trajectories: oceanic island plant and bird assemblages as a case study
Studies of biotic homogenization have focused primarily on characterizing changes that have occurred between some past baseline and the present day. In order to understand how homogenization may change in the future, it is important to contextualize the processes driving these changes. Here, we examine empirical patterns of change in taxonomic similarity among oceanic island plant and bird assemblages. We use these empirical cases to unpack dynamic properties of biotic homogenization, thereby elucidating two important factors that have received little attention: 1) initial similarity and 2) the influence of six classes of introduction and extinction events. We use Jaccard's Index to explore the interplay among these factors in determining the changes in similarity that have occurred between human settlement and the present. Specifically, we develop general formulas for changes in similarity resulting from each of the six types of introductions and extinctions, so that the effect of each event type is formulated in terms of initial similarity and species richness. We then apply these insights to project how similarity levels would change in the future if the present patterns of introductions and extinctions continue. We show that the six event types, along with initial similarity, can show dramatically different behavior in different systems, leading to widely variable influences on similarity. Plant and bird biotas have homogenized only slightly to date, but their trajectories of change are highly divergent. Although existing patterns of colonization and extinction might not continue unchanged, if they were to do so then plant assemblages would show little additional change, whereas bird assemblages would become much more strongly homogenized. Our results suggest that moderate changes in similarity observed to date mask the potential for more dramatic changes in the future, and that the interaction among initial similarity and differential introduction and extinction regimes drives these dynamics.
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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)
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.