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4,753 results for “SHAPE”
Chapter 3. Contrasting methane, sulfide, and nitrogen loading regimes in bioreactors shape microbial communities originating from methane-rich coastal sediment of the Stockholm Archipelago
<p>Supplementary Tables 1 to 7.</p> <p> </p>
Dataset for the project "The role of expansive and invasive plant species in shaping the activity of microbial communities and carbon sequestration in the soil of post-mining spoil heaps."
<p>Description of the project: Research on carbon sequestration in all types of ecosystems, including human-transformed oligotrophic ecosystems, has become more important today from a climate change perspective, as it can help mitigate its effects. Increasing the potential for C sequestration on brownfield sites can be achieved by improving biological processes and developing soil organic matter reservoirs. This may be particularly relevant for the functioning of oligotrophic ecosystems such as waste coal mine spoil heaps. In studies conducted to date on soil carbon dynamics, it has been found that carbon storage capacity is related to vegetation type, among other factors. This is mainly due to the fact that different plant species affect the physical and chemical properties of the soil, the chemical composition of the litter, detritus supply and rooting depth differently. Furthermore, plant species have been shown to influence the composition and biomass of soil microbial communities, and these microorganisms are responsible for the decomposition of organic compounds in the soil. There is little knowledge of soil microbial communities and their activities in the different plant communities of post-mining spoil heaps, especially with regard to the effects of specific microbial communities on soil carbon sequestration. The aim of the project was to compare the influence of a native expansive grass species (<em>Calamagrostis epigejos</em> (L.) ROTH) and an alien invasive species (<em>Solidago gigantea</em> AITION) on the activity and structure of soil microorganisms and carbon sequestration on post-mining spoil heaps spontaneously colonised by vegetation and subjected to reclamation. The study was carried out on a model post-mining heap, part of which has been reclaimed with overburdened soil, while the remaining part has not undergone any reclamation and is subject to spontaneous succession processes. An analysis of total organic carbon (TOC) in soil substrate samples was carried out to determine the effect of the plant species studied on carbon sequestration. TOC consists of organic compounds mainly derived from root exudates, microbial biomass and decomposition of plant litter and SOM by microorganisms. Therefore, the structure of soil microbial assemblages was also investigated by means of phospholipid fatty acid profiles and the activity of these microorganisms, by means of soil enzyme analysis and functional diversity of microorganisms using BIOLOG<sup>®</sup> Ecoplates. In addition, the in situ level of CO<sub>2</sub> release from the soil was also determined.</p>
Open ecosystems expansion, competition and predation shaped the evolution of Antilocapridae
Open the record for dataset details and reuse information.
DRAWING DIFFERENT SHAPES WITH PROGRAMS USING THE TURTLE MODULE
Open the record for dataset details and reuse information.
Figure 3 in Epiplastral and geographic variation in Echmatemys, a geoemydid turtle from the Eocene of North America: A multi-tiered analysis of epiplastral shape complexity
Figure 3. Maps at left showing the location of Utah (inset, Utah shaded red) and the Uinta Basin study site (rectangle). Google map at right showing the spatial relationships of identified Uintan Echmatemys callopyge and E. uintensis fossil specimens generated in ArcGIS. Symbols represent natural breaks in the data for each species, and are scaled proportional to their stratigraphic meter level. There is no significant difference in the geographic or stratigraphic distributions of these species.
Important role of intra-transform spreading centers in shaping thermal structure along the Blanco transform fault
<p> Input files for the seven models presented in the paper are shown in subdirectory models</p>
Secondary contacts and genetic admixture shape colonisation by an amphiatlantic epibenthic invertebrate
<p>Research on the genetics of invasive species often focuses on patterns of genetic diversity and population structure within the introduced range. However, a growing body of literature is demonstrating the need to study the native range, and how native genotypes affect both ecological and evolutionary mechanisms within the introduced range. Here we used genotyping-by-sequencing to study both native and introduced ranges [based on 1,653 single nucleotide polymorphisms (SNPs)] of the amphiatlantic marine invertebrate <i>Ciona intestinalis</i>. A previous study using microsatellites analysed samples collected along the Swedish west coast and showed the presence of genetically distinct lineages in deep and shallow waters. Using our SNP data from newly collected samples (285 individuals), we first confirmed the presence of this depth-defined genomic divergence along the Swedish coast. We then used Approximate Bayesian Computation to infer the historical relationship among sites from the North Sea, the English Channel and the northwest Atlantic and found evidence of ancestral divergence between individuals from deep waters off Sweden and individuals from the English Channel. This divergence was followed by a secondary contact that led to a genetic admixture between the ancestral populations (i.e. deep Sweden and English Channel), which originated the genotypes found in shallow Sweden. We then revealed that the colonisation of <i>C. intestinalis</i> in the northwest Atlantic was as a result of an admixture between shallow Sweden and the English Channel genotypes across the introduced range. Our results showed the presence of both past and recent genetic admixture events that together may have promoted the successful colonisations of <i>C. intestinalis</i>. Our study suggests that secondary contacts potentially reshape the evolutionary trajectories of invasive species through the promotion of intraspecific hybridisation and by altering both colonisation patterns and their ecological effects in the introduced range.</p>
Data from: On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity
A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, though these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analyzing the relationship among intraspecies diversity, interspecies divergence, and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centered on long non-coding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms.
Data from: Habitat connectivity and local conditions shape taxonomic and functional diversity of arthropods on green roofs
Summary 1. Increasing development of urban environments creates high pressure on green spaces with potential negative impacts on biodiversity and ecosystem services. There is growing evidence that green roofs – rooftops covered with vegetation – can contribute mitigate the loss of urban green spaces by providing new habitats for numerous arthropod species. 2. Whether green roofs can contribute to enhance taxonomic and functional diversity and increase connectivity across urbanized areas remains, however, largely unknown. Furthermore, only limited information is available on how environmental conditions shape green roof arthropod communities. 3. We investigated the community composition of arthropods (Apidae, Curculionidae, Araneae and Carabidae) on 40 green roofs and 40 green sites at ground level in the city of Zurich, Switzerland. We assessed how the site's environmental variables (such as area, height, vegetation, substrate and connectivity among sites) affect species richness and functional diversity using generalized linear models. We used an extension of co-inertia analysis (RLQ) and fourth-corner analysis to highlight the mechanism underlying community assemblages across taxonomic groups on green roof and ground communities. 4. Species richness was higher at ground-level sites, while no difference in functional diversity was found between green roofs and ground sites. Green roof arthropod diversity increased with higher connectivity and plant species richness, irrespective of substrate depth, height and area of green roofs. The species trait analysis reviewed the mechanisms related to the environmental predictors that shape the species assemblages of the different taxa at ground and roof sites. 5. Our study shows the important contribution of green roofs in maintaining high functional diversity of arthropod communities across different taxonomic groups, despite their lower species richness compared to ground sites. Species communities on green roofs revealed to be characterized by specific trait assemblages. The study also provides details on the environmental conditions that influence arthropod diversity and gives new perspectives on how the design of green roofs can be improved to increase their ecological value. Furthermore, the study highlights the importance of integrating green roofs in planning policies which aim to enhance urban habitat connectivity.
Figure 3 from: Zumstein P, Bruelheide H, Fichtner A, Schuldt A, Staab M, Härdtle W, Zhou H, Assmann T (2021) What shapes ground beetle assemblages in a tree species-rich subtropical forest? In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 907-927. https://doi.org/10.3897/zookeys.1044.63803
Figure 3 Relationships between ground beetle biomass and canopy cover (A) and herb cover (B). Black lines indicate significant relationships at p < 0.05 obtained from mixed-effects models (keeping other significant predictors fixed at their means) with grey areas indicating the 95% confidence intervals. Points (slightly jittered to improve visibility) represent observed values per trap. The fixed-effects explained 30% of the variation in ground beetle biomass.
Figure 4 from: Zumstein P, Bruelheide H, Fichtner A, Schuldt A, Staab M, Härdtle W, Zhou H, Assmann T (2021) What shapes ground beetle assemblages in a tree species-rich subtropical forest? In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 907-927. https://doi.org/10.3897/zookeys.1044.63803
Figure 4 Representatives of ground beetles from pitfall traps and flight interception traps in Gutianshan NP ACarabus kiukiangensisBCarabus davidisCLioptera erotyloidesDTricondyla macrodera.
Figure 2 from: Zumstein P, Bruelheide H, Fichtner A, Schuldt A, Staab M, Härdtle W, Zhou H, Assmann T (2021) What shapes ground beetle assemblages in a tree species-rich subtropical forest? In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 907-927. https://doi.org/10.3897/zookeys.1044.63803
Figure 2 Relationships between ground beetle species richness and canopy cover (A) and herb cover (B). Black lines indicate significant relationships at p < 0.05 obtained from mixed-effects models (keeping other significant predictors fixed at their means) with grey areas indicating the 95% confidence intervals. Points represent observed values per trap. Note that some traps had similar richness and predictor values. The fixed-effects explained 12% of the variation in ground beetle species richness.
Figure 1 from: Zumstein P, Bruelheide H, Fichtner A, Schuldt A, Staab M, Härdtle W, Zhou H, Assmann T (2021) What shapes ground beetle assemblages in a tree species-rich subtropical forest? In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 907-927. https://doi.org/10.3897/zookeys.1044.63803
Figure 1 Relationships between ground beetle abundance and canopy cover (A), herb cover (B) and pH-value of the soil (C). Black lines indicate significant relationships at p < 0.05 obtained from mixed-effects models (keeping other significant predictors fixed at their means) with grey areas indicating the 95% confidence intervals. Points represent observed values per trap. Note that some traps had similar abundance and predictor values. The fixed-effects explained 22% of the variation in ground beetle abundance.
Data from: Early and adult social environments shape sex-specific actuarial senescence patterns in a cooperative breeder
Sociality modulates life history traits through changes in resource allocation to fitness-related traits. However, how social factors at different stages of the life cycle modulate senescence remains poorly understood. To address this question, we assessed the influence of social environment in both early life and adulthood on actuarial senescence in the Alpine marmot, a cooperative breeder. The influence of helpers on actuarial senescence strongly differed depending on when help was provided, and on the sex of the dominant. Being helped when adult slowed down senescence in both sexes. However, the effect of the presence of helpers the year of birth of a dominant was sex-specific. Among dominants helped during adulthood, females born in the presence of helpers senesced slower, whereas males senesced faster. Among dominants without helpers during adulthood, females with helpers at birth senesced faster. Social environment modulates senescence, but acts differently between sexes and life stages.
Data from: Evolutionary shifts in mustelid (Mustelidae: Carnivora) cranial shape, body size, and body shape coincides with the Mid-Miocene Climate Transition
Environmental changes can lead to evolutionary shifts in phenotypic traits, which in turn facilitate exploitation of novel adaptive landscapes and lineage diversification. The global cooling, increased aridity, and expansion of open grasslands during the past 50 million years are prime examples of new adaptive landscapes that spurred lineage and ecomorphological diversity of several mammalian lineages such as rodents and large herbivorous megafauna. However, whether these environmental changes facilitated evolutionary shifts in small to mid-sized predator morphology is unknown. Here, I used a complete cranial and body morphological dataset to examine the timing of evolutionary shifts in cranial shape, body size, and body shape within extant mustelids (martens, otters, polecats, and weasels) during the climatic and environmental changes of the Cenozoic. I found that evolutionary shifts in all three traits occurred within extant mustelid subclades just after the onset of the Mid-Miocene Climate Transition. These mustelid subclades first shifted towards more elongate body plans followed by concurrent shifts towards smaller body sizes and more robust crania. I hypothesize that these cranial and body morphological shifts enabled mustelids to exploit novel adaptive zones associated with the climatic and environmental changes of the Mid to Late Miocene, which facilitated significant increases in clade carrying capacity.
Data from: The effect of leaf shape on the thermoregulation and frost tolerance of an annual vine, Ipomoea hederacea (Convolvulaceae)
Premise of study: Leaf shape is predicted to have important ecophysiological consequences; for example, theory predicts that lobed leaves should track air temperature more closely than their entire-margined counterparts. Hence, leaf-lobing may be advantageous during cold nights (∼0°C) when there is the risk of damage by radiation frost (a phenomenon whereby leaves fall below air temperature because of an imbalance between radiational heat loss and convective heat gain). Methods: Here, we test whether radiation frost can lead to differential damage between leaf shapes by examining a leaf-shape polymorphism in Ipomoea hederacea, where leaves are either lobed or heart-shaped depending on a single Mendelian locus. We logged leaf temperature during midautumn, and measured chlorophyll fluorescence and survival as proxies of performance. Furthermore, we tested if the leaf-shape locus confers freezing tolerance using freezing assays on leaf tissue from different leaf shapes. Key results: We found that lobed leaves consistently remain warmer than heart-shaped leaves during the night, but that no pattern emerged during the day, and that temperature differences between leaf shapes were typically small. Furthermore, we found that leaf types did not differ in frost tolerance, but that a 1°C decrease leads to a transition from moderate to complete damage. Conclusions: Our results demonstrate that Ipomoea hederacea leaf shapes do experience different nighttime temperatures, and that only minor temperature differences can lead to disparate levels of freezing damage, suggesting that the differential thermoregulation could result in different levels of frost damage.
Data from: A skull might lie: modelling ancestral ranges and diet from genes and shape of tree squirrels
Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they have diversified rapidly. Here, we compare signals from DNA sequences with morphological signals using pictures of skulls and computational simulations. Phylogenetic analyses reveal step-wise geographic divergence across the Northern Hemisphere. In Central and South America, tree squirrels form two separate clades, which split from a common ancestor. Simulations of ancestral distributions show western Amazonia as the epicenter of speciation in South America. This finding suggests that wet tropical forests on the foothills of Andes possibly served as refugia of squirrel diversification during Pleistocene climatic oscillations. Comparison of phylogeny and morphology reveals one major discrepancy: Microsciurus species are a single clade morphologically but are polyphyletic genetically. Modeling of morphology–diet relationships shows that the only group of species with a direct link between skull shape and diet are the bark-gleaning insectivorous species of Microsciurus. This finding suggests that the current designation of Microsciurus as a genus is based on convergent ecologically driven changes in morphology.
Data from: Mind the gap: genetic manipulation of basicranial growth within synchondroses modulates calvarial and facial shape in mice through epigenetic interactions
Phenotypic integration patterns in the mammalian skull have long been a focus of intense interest as a result of their suspected influence on the trajectory of hominid evolution. Here we test the hypothesis that perturbation of cartilage growth, which directly affects only the chondrocranium during development, will produce coordinated shape changes in the adult calvarium and face regardless of mechanism. Using two murine models of cartilage undergrowth that target two very different mechanisms, we show that strong reduction in cartilage growth produces a short, wide, and more flexed cranial base. This in turn produces a short, wide face in both models. Cranial base and face are already correlated early in ontogeny, and the relationship between these modules gains structure through postnatal growth and development. These results provide further evidence that there exist physical interactions between developing parts of the phenotype that produce variation at a distance from the actual locus upon which a particular selective pressure is acting. Phenotypic changes observed over the course of evolution may not all require adaptationist explanations; rather, it is likely that a substantial portion of observed phenotypic variation over the history of a clade is not directly adaptive but rather a secondary consequence of some local response to selection.
Species co-occurrence shapes spatial variability in plant diversity–biomass relationships in natural rangelands under different grazing intensities
<p>Grazing can alter plant species interactions in natural rangelands, which in turn might influence the productivity of the ecosystem but we do not fully understand how spatial variability in plant diversity-biomass relationships are modulated by grazing intensity. Here, we hypothesized that plant species co-occurrence in rangelands is mainly driven by niche segregation due to grazing and heterogeneity in local resources, and that grazing therefore modulates diversity–biomass relationships.<b> </b>We tested our hypothesis across 35 rangeland sites in Iran, using a species co-occurrence index to assess plant spatial aggregation within each site. At each site, we measured aboveground biomass, plant diversity, topography, soil nutrients and three levels of grazing intensity. High spatial segregation of plant communities (low species co-occurrence) was found at heavily grazed sites, whereas greater spatial aggregation (high species co-occurrence) was found on low and moderate grazed sites, showing varied associational patterns of species with grazing intensity. Soil nutrients increased with grazing intensity and spatial segregation of plant communities was greater at sites with high soil nutrient concentrations, indicating that grazing intensity influences the spatial heterogeneity of plant communities via nutrients deposited in urine and faeces. Declining plant biomass with grazing intensity was related to a strong decline in graminoid species diversity, which suggests that the diversity-biomass relationship is influenced by selective grazing of palatable species. The relationships between species co-occurrence and biomass or plant diversity suggest non-random patterns in species co-occurrences with grazing intensity, which could be the result of competition driven by high livestock grazing intensity. We therefore suggest that rangeland stocking rates should be managed properly to maintain rangeland production while promoting plant diversity.</p>
Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies
<p>Introgression is arguably one of the most important biological processes in the evolution of groups of related species, affecting at least 10% of the extant species in the animal kingdom. Introgression reduces genetic divergence between species, and in some cases can be highly beneficial, facilitating rapid adaptation to ever-changing environmental pressures. Introgression also significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically "intermediate" species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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.
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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
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