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169 results for “morphological models”
Data from: Morphological, phylogenetic, and ecological diversity of the new model species Setaria viridis (Poaceae: Paniceae) and its close relatives
Premise of the study: Species limits of the emerging model organism Setaria viridis (tribe Paniceae, subtribe Cenchrinae) are not well defined. It is thought to be related to S. adhaerens, S. faberi, S. verticillata, and S. verticilliformis and in North America occurs with the morphologically similar S. pumila. An integrated approach was taken to evaluate its variation and relationships with the other taxa. Methods: Statistical morphology, flow cytometry, molecular phylogenetics, and growth experiments were employed to examine the group's physical variation, polyploidy, evolutionary relationships, and drought ecology, respectively. Key results: Setaria viridis contributed one genome to the tetraploids S. faberi, S. verticillata, and S. verticilliformis; the other genome of the latter two was contributed by S. adhaerens. Setaria pumila is unrelated. Morphologically, S. viridis is most similar to S. faberi, but all tested accessions of S. viridis were diploid, whereas those of S. faberi were all tetraploid. Principal component analysis of 70 morphological characters consistently separated S. viridis from S. faberi, largely by spikelet characters. The diagnostic morphological characters are not affected by watering. Setaria faberi is far more sensitive to drought, in terms of mortality and morphological stunting, than S. viridis or S. pumila. Conclusions: Setaria viridis is a diploid species and has contributed to several polyploid derivatives. The most morphologically similar of the polyploids is S. faberi, which differs in spikelet features, phylogenetics, genome size, and ecological response to drought. Researchers using field-collected S. viridis as a model organism will benefit from the clear delimitation provided in this study.
Data from: Complementary responses of morphology and physiology enhance the stand-scale production of a model invasive species under elevated CO2 and nitrogen
1. Elevated atmospheric carbon dioxide (eCO2) concentrations and nitrogen (N) enrichment are known to enhance plant productivity and invasion. However, the implications of their interactive effects for plant productivity are not well understood, especially at the stand scale, presumably because morphological and physiological responses to these global change factors are rarely studied together in the field or assessed at the stand-level. 2. We first determined how leaf-level morphological and physiological traits responded to factorial combinations of ambient and elevated CO2 and N. We collected trait data from the model invasive species Phragmites australis (common reed) that were measured over three years in a long-term global change field experiment. We then combined the trait data and additional descriptions of P. australis canopies in a simulation model of carbon assimilation to determine how morphology and physiology contribute to P. australis' stand scale productivity. 3. At the leaf level, we found that light-saturated rates of photosynthesis were strongly stimulated by eCO2 (37%) and that this effect was enhanced by increasing salinity. N had a smaller effect (17% stimulation) on physiological responses than eCO2, but leaf morphological traits responded primarily to N; plant height increased by 27% and leaf area increased by 47%. 4. Stand scale simulations demonstrated that that morphological and physiological adjustments induced approximately additive responses when P. australis experienced both eCO2 and N enrichment. The simulations also indicated that morphological changes (which were primarily associated with canopy size) influenced stand scale carbon assimilation more than physiological changes. Moreover, 97% of the N response was due to changes in morphology, whereas 62% of the eCO2 response was caused by physiological shifts. 5. Our analysis indicates that morphological and physiological trait responses to elevated CO2 and nitrogen are likely to enhance the productivity of P. australis in complementary ways, potentially accelerating its invasion in North America. Furthermore, our data suggest that changes in morphological traits may have a greater influence on carbon gain than leaf-level physiology under near-future environmental conditions. Our study also highlights the importance of accounting for both morphological and physiological responses when attempting to infer global change responses from leaf-level data.
Bed morphology adjustment under the impact of a near-bank emergent model vegetation patch: implications for urban channel restoration
<p>The dataset (including videos) are uploaded to support the research study <strong>Bed morphology adjustment under the impact of a near-bank emergent model vegetation patch: implications for urban channel restoration</strong> </p>
Data from: Quantifying the effect of gape and morphology on bite force: biomechanical modeling and in vivo measurements in bats
Maximum bite force is an important metric of feeding performance that defines the dietary ecology of many vertebrates. In mammals, theoretical analyses and empirical studies suggest a trade-off between maximum bite force and gape at behavioural and evolutionary scales; in vivo bite force is expected to decrease at wide gapes, and cranial morphologies that enable high mechanical advantage are thought to have a lower ability to generate high bite forces at wide gapes, and vice versa. However, very few studies have confirmed these relationships in free-ranging mammals. This study uses an ecologically diverse sample of bats to document the variation in bite force with respect to gape angle, and applies three-dimensional models of the feeding apparatus to identify the major morphological and biomechanical predictors of the gape-bite force relationship. In vivo and model data corroborated that bite force decreases significantly at wide gapes across species, but there is substantial intraspecific variation in the data obtained from live bats. Results from biomechanical models, analysed within a phylogenetic framework, revealed that species with larger temporalis muscles, higher temporalis stretch factors and high mechanical advantages experience a steeper reduction in bite force with increasing gape. These trends are illustrated by short-faced durophagous frugivores. The results from this study suggest that gape-mediated changes in bite force can be explained both by behavioural effects and cranial morphology, and that these links are relevant for functional analyses of mammal dietary ecology.
Data from: A test of the "flexible stem" model of evolution: ancestral plasticity, genetic accommodation, and morphological divergence in the threespine stickleback radiation
If an ancestral stem group repeatedly colonizes similar environments, developmental plasticity specific to that group should consistently give rise to similar phenotypes. Parallel selection on those similar phenotypes could lead to the repeated evolution of characteristic ecotypes, a property common to many adaptive radiations. A key prediction of this "flexible stem" model of adaptive radiation is that patterns of phenotypic divergence in derived groups should mirror patterns of developmental plasticity in their common ancestor. The threespine stickleback radiation provides an excellent opportunity to test this prediction because the marine form is representative of the ancestral stem group, which has repeatedly given rise to several characteristic ecotypes. We examined plasticity of several aspects of shape and trophic morphology in response to diets characteristic of either the derived benthic or limnetic ecotypes. When marine fish were reared on alternative diets, plasticity of head and mouth shape paralleled phenotypic divergence between the derived ecotypes, supporting the flexible stem model. Benthic and limnetic fish exhibited patterns of plasticity similar to the marine population; however, some differences in population means were present, as well as subtle differences in shape plasticity in the benthic population, indicating a role for genetic accommodation in this system.
Data from: Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
Systematics at the species level is still marked by theoretical and empirical tensions amongst the desires to identify geographical lineages, delimit species, and estimate their relationships. These goals are often confounded because each relies, at least to some extent, on the others being known. However, recently developed methods can simultaneously address all three. Furthermore, next-generation genomic sequencing allows us to generate large-scale molecular data sets to examine variation within species at a fine scale. Finally, a renaissance in morphological species validation allows us to integrate historical species definitions with coalescent models for species delimitation. Here, we investigate the applicability of these methods in an empirical case, in the Nearctic snake genus Storeria. Integrating trait data into species delimitation reduces the number of species delimited from molecular data alone. Whereas molecular data support eight distinct species-level lineages, including morphological data reduces this to four. The taxa Storeria dekayi, Storeria occipitomaculata, Storeria storerioides, and Storeria victa are considered distinct, monotypic species, with no subspecies recognized. We highlight the need for careful assessment of species delimitation, combining both computational genetic methods as well as traditional character-based descriptions. It is now possible to identify phylogeographical lineages, delimit species using molecular and morphological data, and estimate their relationships in a single coherent set of analyses. Moving forward, this will allow for more rapid and objective assessments of cryptic diversity at the species level.
Morphological parameters of microglia in the CDS-based microglia depletion model
<p>The data set includes morphological parameters (cell soma size, process length, branching points, and Sholl analysis) of microglial cells after treatment with clodronate disodium salt (CDS), phosphate buffered saline (PBS) or sham in mice.</p>
Figure 2 in Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
Figure 2. Map of Storeria ranges and sampling locations, showing geographical extent of populations, and range of former species with respect to re-delimited taxa. A, previous geographical extent of Storeria occipitomaculata is shown in red; circles indicate sampling localities. The asterisk indicates the sample of Storeria 'hidalgoensis' examined for morphology, with the range of this subpopulation, now considered part of S. occipitomaculata, indicated in pink. The range of Storeria storerioides is indicated in blue, with the sampling locality indicated by a square. B, previous geographical extent of Storeria dekayi is shown in yellow, with pentagons indicating sampling localities of S. dekayi, triangles indicating Storeria victa, and a line drawn to approximate the range boundary. The asterisk in the Central American population indicates the collection location of the specimen of Storeria 'tropica' examined for morphology, which is now considered part of S. dekayi.
Fig. 8 in On the southernmost high Andean scorpion species, with the identification of a cryptic new species of Brachistosternus (Bothriuridae) through morphology, molecular data and species distribution models
Fig. 8. Map of central western Argentina showing the known distribution of Brachistosternus diaguita n. sp. (black circles), Brachistosternus montanus (black stars), and Brachistosternus intermedius (black triangles). The "Diaguita" district of the "Altoandina" biogeographical region is depicted in red, the "Cuyano" district of this region is depicted in blue, the "Puna" biogeographical region is depicted in orange, the "Prepuna" district of the "Monte" biogeographical region is depicted in green, and the Septentrional district of this region is depicted in turquoise.
Fig. 7. Brachistosternus diaguita n in On the southernmost high Andean scorpion species, with the identification of a cryptic new species of Brachistosternus (Bothriuridae) through morphology, molecular data and species distribution models
Fig. 7. Brachistosternus diaguita n. sp., A‒C. Telson. a. male, dorsoexternal aspect; B. male, lateral aspect; C. female, lateral aspect; D‒F. Hemipermatophore. D. left hemispermatophore, external aspect; E. left hemispermatophore, internal aspect; F. right hemispermatophore, internal aspect. Scale bars: 1 mm.
Fig. 5. A in On the southernmost high Andean scorpion species, with the identification of a cryptic new species of Brachistosternus (Bothriuridae) through morphology, molecular data and species distribution models
Fig. 5. A. Brachistosternus intermedius, pedipalp chela, male, internal aspect. B–H. Brachistosternus diaguita n. sp. B‒E. Pedipalp chela, male. B. internal aspect, C. dorsal aspect, D. external aspect, E. ventral aspect; F. Pedipalp chela, female, ventro-internal aspect. G. pedipalp patela, male, external aspect; H. pedipalp femur, male, dorsal aspect. Scale bars: 1 mm.
Fig. 6. A‒F. Metasomal segment V. A‒C. Brachistosternus diaguita n in On the southernmost high Andean scorpion species, with the identification of a cryptic new species of Brachistosternus (Bothriuridae) through morphology, molecular data and species distribution models
Fig. 6. A‒F. Metasomal segment V. A‒C. Brachistosternus diaguita n. sp., male. A. ventral aspect; B. dorso-external aspect, C. dorsal aspect; D. Brachistostenus intermedius, male, ventral aspect; E‒F. Brachistosternus montanus, male, E. dorsoexternal aspect, F. dorsal aspect. Scale bars: 1 mm.
Fig. 3 in On the southernmost high Andean scorpion species, with the identification of a cryptic new species of Brachistosternus (Bothriuridae) through morphology, molecular data and species distribution models
Fig. 3. Potential distribution of Brachistosternus species studied in this contributions A. Brachistosternus diaguita n. sp. B. Brachistosternus montanus. C. Brachistosternus intermedius. Warmer colors show areas with better predicted conditions. Black dots show the presence locations.
Fig. 2. A in On the southernmost high Andean scorpion species, with the identification of a cryptic new species of Brachistosternus (Bothriuridae) through morphology, molecular data and species distribution models
Fig. 2. A. Bayesian phylogeny of selected Brachistosternus species inferred using MrBayes. The values at the nodes are Bayesian posterior probabilities. The scale bar represents the branch lengths in substitutions per site. B. Bayesian species tree with nodeage estimates inferred using *BEAST. The values at the nodes are Bayesian posterior probabilities and the node bars represent the 95% highest posterior densities of the node age estimates. The scale axis is set to show Million years before present.
Morphology of the excited hydroxyl in the Martian atmosphere: A model study. Where to search for airglow on Mars?
<p>The data for Remote Sensing article figures.</p>
Fig. 8 in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data
Fig. 8. Myosotis antarctica subsp. traillii photographs and distribution map. (a) Habit. (b, d) Rosette leaf tips: (b) adaxial and (d) abaxial sides. (c) Flower. (e) Nutlets. (f) Map of georeferenced herbarium specimens observed by J. M. Prebble (35). Whie scale bars: 2 mm; black scale bars: 1 mm. Photo credits: a, e by J. M. Prebble (a: WELT SP100487, Tiwai Point, Southland, South Island; e: WELT SP104518, cultivated ex Mason Bay, Stewart Island). b, c © Te Papa by H. M. Meudt (b: WELT SP090544, Manihi Rd, Taranaki, North Island; c: WELT SP090629, Hukanui, Gisborne, North Island; d: WELT SP090631, Waipuna, Gisborne, North Island).
Fig. 2 in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data
Fig. 2. Maps of MaxEnt niche models for pygmy Myosotis in New Zealand and southern South America. (a) Myosotis glauca (light blue circles). (b) M. pygmaea (green circles). (c, h) M. "Volcanic Plateau" (grey triangles). (d) M. brevis (yellow cir-cles). (e) M. drucei (dark blue circles; excluding individuals identified as M. "Volcanic Plateau"). (f) M. drucei (dark blue circles) + M. pygmaea (green circles) + M. "Volcanic Plateau" (grey triangles) (g) M. antarctica (pink circles; Chilean locations), note scale is the same as for maps of New Zealand. a–f use models based on the nine-layer model (see Table 1), whereas g and h are based on the sevenlayer model.
Fig. 5 in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data
Fig. 5. Myosotis glauca photographs and distribution map. (a) Habit. (b) Rosette leaves, adaxial and abaxial sides. (c) Calyces, left to right most to least mature. (d) Nutlets. (e) Map of georeferenced herbarium specimens observed by J. M. Prebble (16). White scale bars: 2 mm; black scale bar: 1 mm. Photo credits: all by J. M. Prebble (WELT SP093285, Nevis Valley, Otago).
Fig. 4 in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data
Fig. 4. Myosotis brevis photographs and distribution map. (a) Habit. (b) Inflorescence showing cauline leaf abaxial side. (c) Inflorescence showing cauline leaf adaxial side, calyces, and flower. (d) Rosette leaf adaxial side showing colour morphs. (e) Flower. (f) Nutlet. (g) Map of georeferenced herbarium specimens observed by J. M. Prebble (25). White scale bars: 2 mm; black scale bar: 1 mm. Photo credits: a–e © Te Papa by H. M. Meudt (a: WELT SP090549, Te Ikaamaru Bay, Wellington; b, c: WELT SP090545, Ngawi, Wairarapa; d: WELT SP090543, Stent Road, Taranaki; e: WELT SP090550, Ohau Bay, Wellington); f by J. M. Prebble (WELT SP090543, cultivated ex Stent Road, Taranaki).
Fig. 7. Myosotis antarctica subsp. antarctica. Illustration reproduced from Bot. Antarct. Voy. I in Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data
Fig. 7. Myosotis antarctica subsp. antarctica. Illustration reproduced from Bot. Antarct. Voy. I. (Fl. Antarct.) Part I, plate 38 (Hooker 1844). Illustration by W. H. Fitch. This image is in the public domain, downloaded from the Biodiversity Heritage Library (https:// www.biodiversitylibrary.org/page/13448452#page/81/ mode/1up, accessed 8 June 2021). Draft pencil drawings for this figure are attached to the type specimen of M. antarctica (K0007878799; visible online at http:// apps.kew.org/herbcat/getImage.do?imageBarcode= K000787899, accessed 8 June 2021), which was collected by J. D. Hooker from Campbell Island.
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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.