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25 results for “Terrestrial environments”
Data from: Phylogenetic relatedness drives protists assembly in marine and terrestrial environments
<p>Aim: Assembly of protists communities is known to be driven mainly by environmental filtering, but the imprint of phylogenetic relatedness is unknown. In this study, we aim to test the degree at which co-occurrences and co-exclusions of protists in different phylogenetic relatedness classes are deviating from random expectation in two ecosystems in order to link them to ecological processes.</p> <p>Location: Global open-oceans and Neotropical rainforest soils</p> <p>Major taxa: Protists</p> <p>Time period: 2009-2013</p> <p>Methods: Protist metabarcoding data originated from two large scale studies. Co-occurrence and co-exclusion networks were constructed using a recent method combining a null distribution model with Spearman's rank correlation coefficients among pairs of OTU. Phylogenetic relatedness was estimated using either global pairwise sequence distance or phylogenetic distance inferred from best maximum-likelihood trees derived from multiple alignments of OTU representative sequences. Significance of observed patterns relating networks and phylogenies were evaluated by distance classes against two null models in which either the tips of the phylogenetic trees or the network edges were randomized.</p> <p>Results: Closely-related protists co-occurred more often than expected by chance in all datasets, but also co-excluded less often than expected by chance in the marine dataset only. Concurrent excess of co-occurrences and co-exclusions were observed at intermediate phylogenetic distances in the marine dataset.</p> <p>Main conclusions: This suggest that environmental filtering and dispersal limitation are the dominant forces driving protists co-occurrences in both environments, while signal of competitive exclusion was only detected in the marine environment. Co-exclusion differences are potentially linked to the individual environments: marine waters are more homogeneous, while the rainforest soils contain a myriad of nutrient rich micro-environment reducing the strength of mutual exclusion.</p>
Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments
For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways. <p></p> --
Data from: Phylogenetic relatedness drives protists assembly in marine and terrestrial environments
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Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments
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HIDRA simulations and post-processing scripts for JGR: SP manuscript: characterization of N+ abundances in the terrestrial polar wind using the multiscale atmosphere-geospace environment
<div> <div> <div> <p>The High-latitude Ionosphere Dynamics for Research Applications (HIDRA) model is part of the Multiscale Atmosphere-Geospace Environment (MAGE) model under development by the Center for Geospace Storms (CGS) NASA DRIVE Science Center. This study employs HIDRA to simulate upflows of H+, He+, O+, and N+ ions, with a particular focus on the relative N+ concentrations, production and loss mechanisms, and thermal upflow drivers as functions of season, solar activity, and magnetospheric convection. The simulation results demonstrate that N+ densities typically exceed He+ densities, N+ densities are typically ∼ 10% O+ densities, and N+ concentrations at quiet-time are approximately 50-100% of N+ concentrations during storm-time. Furthermore, the N+ and O+ upflow fluxes show similar trends with variations in magnetospheric driving. The inclusion of ion-neutral chemical reactions involving metastable atoms is shown to have significant effects on N+ production rates. With this metastable chemistry included, the simulated ion density profiles compare favorably with satellite measurements from Atmosphere Explorer C (AE-C) and Orbiting Geophysical Observatory 6 (OGO-6).</p> </div> </div> </div>
The influence of history, geography and environment on patterns of diversification in the western terrestrial garter snake
<p><b>Aim:</b> A central aim of biogeography is to understand how biodiversity is generated and maintained across landscapes. Here, we establish phylogenetic and population genetic patterns in a widespread reptile to quantify the influence of historical biogeography and current environmental variation on patterns of genetic diversity.</p> <p><b>Location: </b>Western North America.</p> <p><b>Taxon: </b>Western terrestrial garter snake, <i>Thamnophis elegans</i>.</p> <p><b>Methods: </b>We used double-digest RADseq to estimate phylogenetic relationships and characterize population genetic structure across the three widespread subspecies of <em>T. elegans</em>: <em>T. e. vagrans</em> (wandering garter snake), <em>T. e. elegans </em>(mountain garter snake) and <em>T. e. terrestris</em> (coast garter snake). We assessed patterns of dispersal and vicariance across biogeographic regions using ancestral area reconstruction (AAR) and deviations from isolation-by-distance across the landscape using estimated effective migration surfaces (EEMS). We identified environmental variables potentially shaping local adaptation in regional lineages using genetic-environment association (GEA) analyses.</p> <p><b>Results:</b> We recovered three well-differentiated genetic groups that correspond to the three subspecies. AAR analyses inferred the eastern Cascade Range as the ancestral area, with dispersal to both the east and west across western North America. Populations of <em>T. e. elegans</em> displayed a latitudinal gradient in genetic variation across the Sierra Nevada and northern California, while populations of <em>T. e. terrestris</em> show discrete genetic breaks consistent with well-known biogeographic barriers. Lastly, GEA analyses identified allele frequency shifts at loci associated with a common set of environmental variables in both <em>T. e. elegans</em> and <em>T. e. terrestris</em>.</p> <p><b>Main Conclusion: </b><em>T. elegans </em>is composed of distinct evolutionary lineages, each with its own geographic range and history of diversification. <em>T. e. elegans</em> and <em>T. e. terrestris</em> show unique patterns of diversification as populations dispersed from east to west and while adapting to the new environments they colonized. Historical events, landscape features and environmental variation have all contributed to patterns of differentiation in <em>T. elegans</em>.</p> <p> </p>
Risks for overwintering eggs of the dragonfly Sympetrum vicinum in aquatic and terrestrial environments
<p>Risk-spreading behaviour is often exhibited by animals as a response to unpredictably variable environments. Using field and laboratory studies, we tested the hypothesis that Sympetrum vicinum dragonflies spread the risks of winter environments by laying eggs across a terrestrial–aquatic gradient. Sympetrum vicinum eggs that overwintered in terrestrial and benthic-limnetic habitats had significantly higher hatching success compared with eggs that overwintered in littoral sites. Low success may have been caused by hypoxia due to excess sediment in the littoral samples in the lab. While hypoxia experienced under winter conditions (4°C) had no negative effect on hatching success, hatching in hypoxic and anoxic water significantly decreased hatching success. Opportunistic egg predation by a winter-active caddisfly significantly decreased egg hatching success. Because S. vicinum eggs have a relatively low supercooling point (− 26.25°C), freezing may not be a significant source of mortality in terrestrial or aquatic sites. By ovipositing in both terrestrial and aquatic environments, female dragonflies may be balancing the unpredictable risks of both the failure to inundate the eggs and egg predation. Our research highlights the potential for biotic interactions during winter to shape the behaviour and life-history of aquatic invertebrates.</p>
Combined data file for Jokinen et al. "Terrestrial organic matter input drives sedimentary trace metal sequestration in a human-impacted boreal estuary", Science of the Total Environment 717, 2020
<p>The datafile contains all the new raw data presented in the figures in the publication.</p>
HIDRA simulations and post-processing scripts for JGR: SP manuscript: characterization of N+ abundances in the terrestrial polar wind using the multiscale atmosphere-geospace environment
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Effects of consumer surface sterilization on diet DNA metabarcoding data of terrestrial invertebrates in natural environments and feeding trials
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The influence of history, geography and environment on patterns of diversification in the western terrestrial garter snake
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Risks for overwintering eggs of the dragonfly Sympetrum vicinum in aquatic and terrestrial environments
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Data from: Mosquito derived ingested DNA as a tool for monitoring terrestrial vertebrates within a peri-urban environment
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Lophuromys medicaudatus, L. woosnami, and L. luteogaster are in subgenus Kivumys and woosnami species group. Monotypic. Distribution. Endemic to the Albertine Rift, occurring around Lake Kivu in E DR Congo and Rwanda and SW Uganda (Bwindi). Descriptive notes. Head—body 92-112 mm, tail 73-95 mm, ear 15-19 mm, hindfoot 18-23 mm; weight 29-43 g. Similar to other species in subgenus Kivumys, the Western Rift Brush-furred Rat has unspeckled pelage, and tail ¢.85% of head-body length. Dorsum is uniform dark brown-olive, and venter is orange. Females have three pairs of mammae. Habitat. Mountain swamps and mountain forests at elevations of 1850-2500 m. Food and Feeding. The Western Rift Brush-furred Rat is omnivorous; diets contain 30-100% arthropods, mollusks, seeds, and fruits. Breeding. Female Western Rift Brush-furred Rats can have 1-2 embryos. Pregnant females were observed in February, April, and July. Activity patterns. The Western Rift Brush-furred Rat is terrestrial. Movements, Home range and Social organization. No information. Status and Conservation. Classified as Vulnerable on The IUCN Red List. The Western Rift Brush-furred Rat has never been found in modified secondary environment and is quite rare. Bibliography. Dieterlen (1976b, 1987 2013g), Kasangaki et al. (2003), Verheyen et al. (1996). in Muridae
Lophuromys medicaudatus, L. woosnami, and L. luteogaster are in subgenus Kivumys and woosnami species group. Monotypic. Distribution. Endemic to the Albertine Rift, occurring around Lake Kivu in E DR Congo and Rwanda and SW Uganda (Bwindi). Descriptive notes. Head—body 92-112 mm, tail 73-95 mm, ear 15-19 mm, hindfoot 18-23 mm; weight 29-43 g. Similar to other species in subgenus Kivumys, the Western Rift Brush-furred Rat has unspeckled pelage, and tail ¢.85% of head-body length. Dorsum is uniform dark brown-olive, and venter is orange. Females have three pairs of mammae. Habitat. Mountain swamps and mountain forests at elevations of 1850-2500 m. Food and Feeding. The Western Rift Brush-furred Rat is omnivorous; diets contain 30-100% arthropods, mollusks, seeds, and fruits. Breeding. Female Western Rift Brush-furred Rats can have 1-2 embryos. Pregnant females were observed in February, April, and July. Activity patterns. The Western Rift Brush-furred Rat is terrestrial. Movements, Home range and Social organization. No information. Status and Conservation. Classified as Vulnerable on The IUCN Red List. The Western Rift Brush-furred Rat has never been found in modified secondary environment and is quite rare. Bibliography. Dieterlen (1976b, 1987 2013g), Kasangaki et al. (2003), Verheyen et al. (1996).
Phenotypic Plasticity Structure of Metasequoia glyptostroboides (Taxodiaceae) Fine Adventitious Roots Adapt to Aquatic and Terrestrial Environments
<p>Supplement 1. Phellogen close to the remnant exodermis and under lysigenous primary phloem. Match to Fig. 2C, D, secondary xylem, vascular cambium (below arrowhead), phellogen (arrows), lysigenous primary phloem (black arrow), phloem aerenchyma, dilated parenchyma (*), phloem fibers, remnant exodermis (ex), staining: TBO; scale bars = 50 μm;</p> <p> </p> <p>Supplement 2. Phellogen under lysigenous primary phloem. Match to Fig. 2C, D, secondary xylem, vascular cambium (below arrow), phellogen (arrows), lysigenous primary phloem (black arrow), cortical aerenchyma, dilated parenchyma (*), phloem fibers, remnant exodermis (ex), staining: TBO; scale bars = 50 μm;</p>
Supplementary material 2 from: Szlavecz K, Vilisics F, Tóth Z, Hornung E (2018) Terrestrial isopods in urban environments: an overview. In: Hornung E, Taiti S, Szlavecz K (Eds) Isopods in a Changing World. ZooKeys 801: 97-126. https://doi.org/10.3897/zookeys.801.29580
List of terrestrial isopod species records in urban areas : Explanation note: Species name have been cross-checked with the world catalog by Schmalfuss (2003). Synonyms have been changed to valid species names. In some cases the species was not listed in the catalog. Notes regarding uncertainties are also from Schmalfuss (2003).
Supplementary material 1 from: Szlavecz K, Vilisics F, Tóth Z, Hornung E (2018) Terrestrial isopods in urban environments: an overview. In: Hornung E, Taiti S, Szlavecz K (Eds) Isopods in a Changing World. ZooKeys 801: 97-126. https://doi.org/10.3897/zookeys.801.29580
List of cities with terrestrial isopod records : Explanation note: Publications older than 70 years are not included. Localities listed here are mapped on Fig. 2 in the text. Source of geographical coordinates and population data: https://latitude.to
3D printed models are an accurate, cost-effective, and reproducible tool for quantifying terrestrial thermal environments
<p>Dataset used in Alujević et al. 2023. 3D printed models are an accurate, cost-effective, and reproducible tool for quantifying terrestrial thermal environments. </p>
Data from: Artificial agri-environment scheme ponds do not replicate natural environments despite higher aquatic and terrestrial invertebrate richness and abundance
<p class="MsoNoSpacing">1. Farmland ponds are a highly threatened freshwater habitat which has undergone dramatic losses during the last 200 years due to land drainage schemes and agricultural intensification. Agri-environment schemes (AES) incentivise farmers to adopt farming methods to benefit biodiversity, yet there are a paucity of data evaluating the success of artificially created AES ponds as analogues of natural ponds in an attempt to recreate lost environments.</p> <p class="MsoNoSpacing">2. We examined variation in environmental parameters and aquatic and terrestrial invertebrate communities between 38 natural ponds and 91 artificial ponds that were created in south-west Ireland (<i>n</i>=129).</p> <p class="MsoNoSpacing">3. Artificial ponds in agricultural grassland did not replicate natural ponds in adjacent semi-natural habitats differing significantly in size, pH, conductivity, productivity (indicated by submerged and emergent plant cover including algae) and surrounding vegetation structure i.e. sward height. These differences significantly influenced aquatic and terrestrial invertebrate community structure with a suite of indicator taxa in both natural and artificial ponds.</p> <p class="MsoNoSpacing">4. The conservation value of artificial ponds in agricultural grasslands should not be underestimated as they had 43% higher aquatic species richness and 33% higher aquatic species abundance than natural ponds in adjacent semi-natural habitats.</p> <p class="MsoNoSpacing"><i>5. Synthesis and applications</i>. We demonstrate that artificial agri-environment scheme ponds created in agricultural grasslands, whilst not direct analogues of natural ponds in adjacent semi-natural habitats, do fulfil a role in preserving high local biodiversity albeit representing a different community of species. Creation of ponds in farmland as well as in adjacent natural habitats could provide a wider range of environmental conditions and richer associated macroinvertebrate communities, increasing landscape connectivity and further enhancing regional biodiversity.</p>
Figure 3 from: Szlavecz K, Vilisics F, Tóth Z, Hornung E (2018) Terrestrial isopods in urban environments: an overview. In: Hornung E, Taiti S, Szlavecz K (Eds) Isopods in a Changing World. ZooKeys 801: 97-126. https://doi.org/10.3897/zookeys.801.29580
Figure 3 Responses of three synanthropic isopod species to urbanization gradient. Each data point is percentage of total number of individuals (N) of a given species caught in pitfall traps. Philosciamuscorum: N = 7473, Porcellioscaber: N = 12314, Armadillidiumvulgare: N = 816. The study was carried out in urban, suburban, and rural forest patches and parks in Sorø, Denmark. Data from Vilisics et al. (2007); original figure.
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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)
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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.