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2,721 results for “Connectivity”
Highland forest's environmental complexity drives landscape genomics and connectivity of the rodent Peromyscus melanotis
<p>We evaluate how the environmental complexity of La Malinche volcano influences patterns of genomic variation in <em>Peromyscus melanotis</em>, across two mountain slopes and global and regional geographic scales.Using reduced representation genomic sequencing we estimated population genetic diversity, subdivisions and migration rates. Remote sensing data and drone image processing were used to characterize landscape variables. We evaluated their effect on connectivity, based on a landscape analyses framework, using resistance surfaces, circuit theory and omnidirectional connectivity. Our findings showed how the forest environmental complexity across different geographic scales drives dispersal, genomic structure and connectivity patterns in this rodent, where dirt roads and disturbed areas limit its connectivity, while exhibiting higher connectivity at the highest elevations where the forest is less disturbed. Notably, that our 3D variable of tree height was significant demonstrates the utility in incorporating 3D vegetation structure variables into landscape genetic analyses.</p>
Area, connectivity and plant life strategy diversity and abundance in temporary ponds of Southeastern Carpathians (Romania, Europe)
<p><span>We used this dataset to determine whether area and connectivity of temporary ponds can predict plant species diversity, and the diversity and abundance of different plant life histories within the ponds. The studied system is located in the Ciuc Basin of the </span>Southeastern Carpathian Mountains, Romania. We collected data on the macrophyte species diversity of 28 temporary ponds between 2006-2009. Plant species identified in the ponds were assigned into one of the social behaviour types proposed by Borhidi (1995), which describe plant-habitat interactions within a framework extended from Grime's evolutionary life strategies (Grime 1988), as follows: competitors, stress tolerants (generalists or specialists) and ruderals (natural pioneers i.e., plants of habitats disturbed by natural factors, and plants of habitats disturbed by human factors, classified as either: disturbance tolerants, native weeds, naturalised crops, adventitious weeds, ruderal competitors, alien competitors). We expressed species diversity as observed species richness (total number of species) and Shannon diversity index, and abundance as cumulative vegetation cover, calculated for each pond and for each social behaviour type separately. We calculated pond area using the short and long axis of the ellipse that best approximated the pond shape. Pond connectivity with the Olt river was defined as the pond present and respectively past (preceding river regulation) geographic distance from the Olt river, measured between the pond GPS coordinate and the nearest point of the river.</p>
Data from: Forest connectivity boosts pollen flow among populations of the oil-producing Nierembergia linariifolia
<p>Context</p> <p>The process of forest fragmentation determines landscapes with isolated forest patches immersed in a distinct matrix. This process may hinder pollinator movement throughout the landscape, which may negatively impact on pollen flow among native plant populations.</p> <p>Objectives</p> <p>We evaluated the effect of the loss of forest connectivity on pollen dispersal by specialized native bees in the oil-producing and self-incompatible <em>Nierembergia linariifolia</em>.</p> <p>Methods</p> <p>We estimated pollen flow between plants of <em>N. linariifolia</em> at an agroecosystem with remnant forest of central Argentina. Six plant populations (source populations) were treated with fluorescent dyes as pollen analogues, and stigmata of recipient plants were collected to seek for dye particles. Dye deposition rate was assessed for plants that were connected through remnant forest to a source population or unconnected by a crop matrix, and at increasing distances to a source population.</p> <p>Results</p> <p>Deposition rate per plant was higher in connected than in unconnected plants, and decreased with increasing distances to a source population in an exponential fashion. Most of the dispersal events between connected plants occurred at the vicinity of a source population. Long dispersal events (up to 1259 m) were recorded between plants located at neighbouring forest patches separated by an agricultural matrix.</p> <p>Conclusions</p> <p>Landscape connectivity through forest remnants is key to enhance pollen flow between self-incompatible plants such as <em>N. linariifolia</em>. Besides, the evidence of pollen dispersal through the agricultural matrix pinpoints the essential role of native pollinators in maintaining pollen flow among unconnected plant populations in fragmented landscapes.</p>
High-density electrode recordings reveal strong and specific connections between retinal ganglion cells and midbrain neurons.
<p>This is the source file to be use for debugging problems on your own set-up. This files is a good example to both the repository provided for visual processing on the Kremow GitHub:</p> <p>https://github.com/KremkowLab/Axon-on-Neuropixels-in-Kilosort</p> <p>https://github.com/KremkowLab/tangential_recording</p>
Phylogeographical break and limited connectivity between multiple refugia in panantarctic moss species
<p><span><strong>Aim</strong>:</span><span> Historical biogeography of the Antarctic terrestrial biota remains poorly studied and understood. We aim to advance this through a range-wide, multilocus analysis of a pan-Antarctic moss species, in the context of its age, range dynamics, phylogeographical structure, and location of possible long-term refugia. </span></p> <p><span><strong>Location</strong>:</span><span> Continental and maritime Antarctic, South America (Patagonia), Australasia.</span></p> <p><span><strong>Taxon</strong>:</span><span> <em>Syntrichia sarconeurum</em> Ochyra & R.H. Zander (Pottiaceae).</span></p> <p><span><strong>Methods</strong>:</span><span> We used a comprehensive, range-wide and taxonomically-informed sampling, and multilocus sequencing of nuclear and plastid DNA regions. Temporal evolutionary framework, regional genetic diversification and diversity were assessed with phylogenetic and phylogeographic reconstructions, molecular dating, haplotype networks, mismatch analysis, and S-DIVA reconstruction of past events and ancestral areas.</span></p> <p><span><strong>Results</strong>:</span><span> Intercontinental disjunction between Australia and Antarctica/S. America was dated to 3.77 Ma, while diversification of extant <em>Syntrichia sarconeurum</em> lineages had taken place since roughly 1.36 Ma. Antarctic populations contained two high-frequency, allopatric cpDNA haplotypes, which highlighted separation of the continental populations. <em>ITS</em> data showed higher diversification and revealed three main lineages with a main genetic break mostly concordant with plastid data. <em>ITS</em> also showed contrasting diversity between the Antarctic continent and maritime Antarctic/Patagonia.</span></p> <p><span><strong>Main conclusions</strong>:</span><span> Age of the Antarctic range of <em>Syntrichia sarconeurum</em> potentially reaches back to mid-Pliocene, while diversification of extant genetic lineages was linked with recurrent macroenvironmental changes of the Pleistocene. Significant phylogeographical structure displays a major genetic break, which coincides with a known boundary in the terrestrial biota and suggests constrained population connectivity. <em>S. sarconeurum</em> persisted <em>in situ</em> over several glacial periods in refugia both in the peripheral maritime Antarctic and within the Antarctic continent. Disparity in genetic diversity among these areas hypothetically reflects asymmetric changes of reproduction mode in the past. Finally, nested topology of Patagonian subclades and ancestry analysis indicates that South American populations were secondary and originated through multiple dispersal from the Antarctic region.</span></p>
Microbiome network connectivity and composition linked to disease resistance in strawberry plants
<p>The two R data files correspond phyloseq objects used in the study. The file phyloseq_nochim_silva.RData and phyloseq_nochim_unite.RData correspond to bacterial and fungal phyloseq objects, respectively. Both objects include count table, taxonomy table and metadata information. </p>
Connectivity among thermal habitats buffers the effects of warm climate on life-history traits and population dynamics
<p>1. Contemporary climate change affects population dynamics, but its influence varies with landscape structure. It is still unclear whether landscape fragmentation buffers or enhances the effects of climate on population size and on the age and body size of individuals composing these populations.</p> <p>2. This study aims to investigate the impacts of warm climates on lizard life-history traits and population dynamics in habitats varying in their connectivity.</p> <p>3. We monitored common lizard (<em>Zootoca vivipara</em>) populations for three years in an experimental system in which both climatic conditions and connectivity among habitats were simultaneously manipulated. We considered two climatic treatments (i.e., present-day climate and warm climate (+1.4°C than present-day climate)) and two connectivity treatments (i.e., a connected treatment in which individuals could move from one climate to the other and an isolated treatment in which movement between climates was not possible). We monitored survival, reproduction, growth, dispersal, age and body size of each individual in the system as well as population density through time.</p> <p>4. We found that the influence of warm climates on the life-history traits and population dynamics depended on the connectivity among thermal habitats. Populations in warm climates were i) composed of younger individuals only when isolated; ii) larger in population size only in connected habitats; and iii) composed of larger age-specific individuals independently of the landscape configuration. The connectivity among habitats altered population responses to climate warming likely through asymmetries in the flow and phenotype of dispersers between thermal habitats.</p> <p>5. Our results demonstrate that landscape fragmentation can drastically change the dynamics and persistence of populations facing climate change.</p>
Data for: Connecting voice profiling to genomics
<p>This dataset contains a graph-based path-finding algorithm to detect chainlink genes for voice chains that connect the genes in chromosomal microdeletion regions to the FOXP2 gene. Instructions are within multiple README files included with the package. The code is set up to be used on Linux platforms.</p>
Analyses, data and figures related to: "Connecting ships: Using dendrochronological network analysis to determine the wood provenance of Roman-period river barges found in the Lower Rhine region and visualise wood use patterns"
<p>Analyses, data and figures related to: "Connecting ships: using dendrochronological network analysis to determine the wood provenance of Roman-period river barges found in the Lower Rhine region and to visualise patterns of wood use" by Ronald M. Visser (Saxion University of Applied Sciences, Deventer, the Netherlands) and Yardeni Vorst (Vorst wood research, Zaandam, the Netherlands) submitted to the International Journal of Wood Culture</p>
Supplementary data for "Upward leaders from instrumented lightning rods competing to connect a downward leader during a lightning attachment process"
<p>High-speed videos of the lightning attachment to lightning rods observed by the Vision Reserch Phantom V12 and V711 cameras. See Instructions file to play the videos.</p>
Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma
<p>This repository contains signalling to metabolic pathways interconnecting (S-M) protein-protein interaction (PPI) paths. The repository consists of two file:</p> <p><a href="https://zenodo.org/api/files/61dbb365-104e-4c41-ad0a-79f4c657bbee/S-M_paths_z-score_greater_equal_1.txt">S-M_paths_z-score_greater_equal_1.txt </a>: It contains all the S-M paths having z-score >= 1.</p> <p><a href="https://zenodo.org/api/files/61dbb365-104e-4c41-ad0a-79f4c657bbee/S-M_paths_z-score_greater_equal_3.txt">S-M_paths_z-score_greater_equal_3.txt </a>: It contains all the S-M paths having z-score >=3</p>
Data from: Dispersal and connectivity in increasingly extreme climatic conditions
<p>While climate change has been shown to impact several life-history traits of wild-living animal populations, little is known about its effects on dispersal and connectivity.</p> <p>Here, we capitalize on the highly variable flooding regime of the Okavango Delta to investigate impacts of changing environmental conditions on dispersal and connectivity of the endangered African wild dog (Lycaon pictus). Based on remote sensed flood extents observed over 20 years, we derive two extreme flood scenarios: a minimum and a maximum flood extent; representative of very dry and very wet environmental periods. These conditions are akin to those anticipated under increased climatic variability, as it is expected under climate change. Using a movement model parametrized with GPS data from dispersing individuals, we simulate 12,000 individual dispersal trajectories across the ecosystem under both scenarios and investigate patterns of connectivity.</p> <p>Across the entire ecosystem, surface water coverage during maximum flood extent reduces dispersal success (i.e., the propensity of individuals to disperse between adjacent subpopulations) by 12% and increases dispersal durations by 17%. Locally, however, dispersal success diminishes by as much as 78%. Depending on the flood extent, alternative dispersal corridors emerge, some of which in the immediate vicinity of human-dominated landscapes. Notably, under maximum flood extent, the number of dispersing trajectories moving into human-dominated landscapes decreases by 41% at the Okavango Delta's inflow, but increases by 126% at the Delta's distal end. This may drive the amplification of human-wildlife conflict.</p> <p>Whilst predicting the impacts of climate change on environmental conditions on-the-ground remains challenging, our results highlight that environmental change may have significant consequences for dispersal patterns and connectivity, and ultimately, population viability. Acknowledging and anticipating such impacts will be key to effective conservation strategies and to preserve vital dispersal corridors in light of climate change and other human-related landscape alterations.</p>
VCF for neutral data set and potential connectivity matrices of Harpagifer antarcticus, along the Western Antarctic Peninsula
<p>Connectivity is a fundamental process of population dynamics in marine ecosystems. In the last decade, with the emergence of new methods, combining different approaches to understand the patterns of connectivity among populations and their regulation has become increasingly feasible. The Western Antarctic Peninsula (WAP) is characterized by complex oceanographic dynamics, where local conditions could act as barriers to population connectivity. Here, the notothenioid fish <em>Harpagifer antarcticus</em>, a demersal species with a complex life cycle (adults with poor swim capabilities and pelagic larvae), was used to assess connectivity along the WAP by combining biophysical modeling and population genomics methods. Both approaches showed congruent patterns. Areas of larvae retention and low potential connectivity, observed in the biophysical model output, coincide with four genetic groups within the WAP: (1) South Shetland Islands, (2) Bransfield Strait, (3) the central, and (4) the southern area of WAP (Marguerite Bay). These genetic groups exhibited limited gene flow between them, consistent with local oceanographic conditions, which would represent barriers to larval dispersal. The joint effect of geographic distance and larval dispersal by ocean currents, had a greater influence on the observed population structure, than each variable evaluated separately. The combined effect of geographic distance and a complex oceanographic dynamic would be generating limited levels of population connectivity in the fish <em>H. antarcticus</em>along the WAP. Based on this population connectivity estimations, priority areas for conservation were discussed, considering the Marine Protected Area proposed for this threatened region of the Southern Ocean.</p>
Moving in the landscape: omnidirectional connectivity dynamics in China from 1985 to 2020
<p><span>Global changes in human land use have profoundly transformed natural landscapes, leading to significant habitat fragmentation and threatening key ecosystem functions. To address this issue, we employed morphological methods and circuit theory to evaluate the dynamics of ecological corridors and their connectivity in China from 1985 to 2020.</span></p>
Data from: Small but connected islands can maintain populations and genetic diversity under climate change
<p>In response to the striking effects of environmental change, conservation strategies often include the identification of conservation areas that can effectively maintain vulnerable species. Consequently, identifying system-specific conditions that maintain the demographic and genetic viability of species of conservation concern is essential. Connectivity plays a critical role in the persistence of populations. Islands have been model systems to understand connectivity and metapopulation processes and have emerged as particularly favorable targets for conservation. While islands can be isolated from mainland disturbances, it is unknown what degree of isolation is necessary to avoid unfavorable changes but remain sufficiently connected to maintain population viability. To test this question, we explored connectivity within the Apostle Islands, an archipelago of 22 islands within Lake Superior, by comparing historical and contemporary trends in ice bridge connectivity and by simulating the effect of reduced connectivity within this system. We developed a demographically informed individual-based model to explicitly test the role of connectivity to influence the persistence and genetic diversity of American marten (<em>Martes americana</em>), a forest carnivore at risk across its southern range boundary. We found that genetic diversity was resilient to moderate changes in ice cover, but a complete loss of connectivity resulted in rapid genetic erosion. Despite genetic erosion, populations persisted as long as nominal connectivity occurred between islands. Our work suggests that connectivity will decline, but martens would be resilient to moderate changes, and, in the short term, the Apostle Islands can act as a refuge along this species' southern range boundary. Identifying thresholds in connectivity that maintain populations but allow for isolation from disturbance will be necessary to identify suitable areas for species conservation across space and time.</p>
Occurrence of equatorial plasma bubbles (EPBs) over the Indian region on 15 January 2022 and their plausible connection to the Tonga volcano eruption
<p><span>This study focuses on the causes for the generation of equatorial plasma bubbles (EPBs) over the Indian subcontinent and their correlation with atmospheric-ionospheric disturbances resulting from the eruption of the Tonga volcano on 15 January 2022. Concurrent ionosonde observations obtained from Tirunelveli (8.67<sup>o</sup>N, 77.81<sup>o</sup>E) and Prayagraj (25.41<sup>o</sup>N, 81.93<sup>o</sup>E) show the presence of spread-F traces in ionograms. Notably, the EPBs are also accompanied by plasma blobs (PBs), with their pronounced occurrence during midnight at Prayagraj and Tirunelveli. Analysis of in situ electron density observations obtained from the Swarm B and C satellites reveals substantial plasma density depletions associated with EPBs. An intriguing observation is the intensification of Pre-Reversal Enhancement (PRE) immediately preceding the onset of spread-F at Tirunelveli due to enhanced eastward F region zonal winds by Tonga Volcano, as seen in the satellite observations. Furthermore, the isofrequency analysis from Tirunelveli shows the presence of gravity wave-like oscillations in the equatorial F-region over India. The investigation of Total Electron Content (TEC) obtained from a Pseudo Random Number (PRN)-14 over Indian longitudes suggests the presence of two dominant modes of Traveling Ionospheric Disturbances (TIDs) with speeds ~452 m/s and ~406 m/s having periods in the range of ~65–75 minutes. These observations reaffirm that volcano triggered atmospheric/ionospheric disturbances can propagate long</span><span> distances for several hours</span><span> and can provide necessary seeding conditions for the generation of EPBs.</span></p>
Data from: Earthworms promote crop growth by enhancing the connections among soil microbial communities
<p>Earthworms benefit plant growth and play a vital role in shaping soil microbial communities. However, how earthworms modify the soil microorganisms and thus affect plant growth is still unclear. Although fertilizers alter the assembly of microbial communities, further investigations are required to test the effect of fertilizer type on the relationship between earthworms, soil microbial communities, and plants. We evaluated the role of earthworms in soil microorganisms and maize plant growth characteristics under organic or chemical fertilizers in field and greenhouse experiments. We explored the relationships between earthworms, soil microbial community, and plant growth under different fertilizer types. We found that the presence of earthworms promoted plant growth, increased the amount of plant root exudates, and enhanced the connections between rhizosphere bacterial, fungal, and protist communities. Both earthworms and fertilizer application significantly changed the structure of soil bacterial, fungal, and protist communities. The complexity of the soil microbial community network increased under organic, compared to chemical fertilizer application. The greenhouse experiment showed that the effect of earthworms on plant growth was weakened when maize plants were grown in sterilized soil under organic or chemical fertilizers.</p> <p><em>Synthesis and applications:</em> Our study provides solid evidence that earthworms largely depend on soil microorganisms for their effects on plants under the application of different fertilizer conditions. This may provide new insights into reducing the amounts of fertilizer used by enhancing the role of earthworms and soil microorganisms.</p>
Ionospheric Connection Explorer (ICON) EUV Lunar Calibration Data
<p>This dataset provides the processed lunar calibraton data for the Ionospheric Connection Explorer Extreme Ultraviolet Spectrometer (ICON EUV) that were used in the study by Sirk et al. (2024, submitted).</p>
Data from: Environmental and anthropogenic factors mediating the functional connectivity of the mesquite lizard along the eastern Trans-Mexican Volcanic Belt
<p>Functional connectivity, the extent to which a landscape facilitates or impedes the dispersal of individuals across the landscape, is a key factor for the survival of species. Anthropogenic activities such as urbanization, agriculture, and roads, negatively impact functional connectivity of most species, particularly low-vagility species like lizards. Here, we examine how a landscape modified by anthropogenic activities affects the functional connectivity, at both broad and fine scales, of a widely distributed generalist lizard <em>Sceloporus grammicus</em> in the eastern Trans-Mexican Volcanic Belt, Mexico. We estimated for the first time the species genetic structure, gene flow, and functional connectivity in agricultural and forest zones using genomic data, a comprehensive landscape characterization, and novel methods including gravity models. Our results showed marked genetic differentiation across the study region but also that functional connectivity is maintained for tens of kilometers despite <em>S. grammicus</em> low vagility. Specifically, we found that substrate and air temperature facilitated connectivity over broad and fine scales, respectively, while agricultural cover, relative humidity, and slope were important for connectivity and gene flow. Contrastingly, forest cover and roads favored (broad-scale) and limited (fine-scale) connectivity, likely associated with movement facilitated by small forest patches and with thermoregulation. Altogether, these results support that <em>S. grammicus</em> alternates its thermoregulatory behavior depending on the distance traveled and the habitat environmental conditions, and that it can disperse through relatively modified landscapes, mainly using agricultural zones. The information obtained is crucial to understanding the response of lizards to current anthropogenic pressures and their potential to adapt.</p>
Using explainable artificial intelligence as a diagnostic tool for exploration of hydrologic connectivity at watershed scale
<p><strong><span>Using explainable artificial intelligence as a diagnostic tool for exploration of hydrologic connectivity at watershed scale</span></strong></p>
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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.