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1,271 results for “Data Flow”
Data from: Genetic architecture and genomic patterns of gene flow between hybridizing species of Picea
Hybrid zones provide an opportunity to study the effects of selection and gene flow in natural settings. We employed nuclear microsatellites (single sequence repeat (SSR)) and candidate gene single-nucleotide polymorphism markers (SNPs) to characterize the genetic architecture and patterns of interspecific gene flow in the Picea glauca × P. engelmannii hybrid zone across a broad latitudinal (40–60 degrees) and elevational (350–3500 m) range in western North America. Our results revealed a wide and complex hybrid zone with broad ancestry levels and low interspecific heterozygosity, shaped by asymmetric advanced-generation introgression, and low reproductive barriers between parental species. The clinal variation based on geographic variables, lack of concordance in clines among loci and the width of the hybrid zone points towards the maintenance of species integrity through environmental selection. Congruency between geographic and genomic clines suggests that loci with narrow clines are under strong selection, favoring either one parental species (directional selection) or their hybrids (overdominance) as a result of strong associations with climatic variables such as precipitation as snow and mean annual temperature. Cline movement due to past demographic events (evidenced by allelic richness and heterozygosity shifts from the average cline center) may explain the asymmetry in introgression and predominance of P. engelmannii found in this study. These results provide insights into the genetic architecture and fine-scale patterns of admixture, and identify loci that may be involved in reproductive barriers between the species.
Data from: Cryptic speciation and gene flow in a migratory songbird species complex: insights from the red-eyed vireo (Vireo olivaceus)
Migratory species that alternate between sympatry and allopatry over the course of an annual cycle are promising subjects for studies seeking to understand the process of speciation in the absence of strict geographic isolation. Here we sought to identify cryptic species and assess rates of gene flow in a clade of neotropical migrant songbirds in which geography and taxonomy are currently out of sync: the Red-Eyed Vireo (V. olivaceus) Species Complex. Phylogenetic, clustering, and statistical species delimitation analyses found that V. olivaceus includes two non-sister lineages migrating in opposite directions across the equator. Analyses of gene flow identified low levels of introgression between two species pairs, but none between northern and southern olivaceus. We also identified substantial well-supported conflicts between nuclear and mitochondrial topologies. Although the geographic distribution of mito-nuclear discordance is suggestive of hybridization and mitochondrial capture, we found no evidence of introgression in the nuclear genome of populations with discordant mitochondrial gene trees. Our study finds that species boundaries match breeding range and migratory phenology rather than the existing taxonomy in this group, and demonstrates the utility of genomic data in inferring species boundaries in recently diverged clades.
Data from: Asymmetric hybridization and gene flow between Joshua trees (Agavaceae: Yucca) reflects differences in pollinator host specificity.
The angiosperms are by far the largest group of terrestrial plants. Their spectacular diversity is often attributed to specialized pollination. Obligate pollination mutualisms where both a plant and its pollinator are dependent upon one another for reproduction are thought to be prone to rapid diversification through co-evolution and pollinator isolation. However, few studies have evaluated the degree to which pollinators actually mediate reproductive isolation in these systems. Here, we examine evidence for hybridization and gene flow between two subspecies of Joshua tree (Yucca brevifolia brevifolia and Yucca brevifolia jaegeriana) pollinated by two sister species of yucca moth. Previous work indicated that the pollinators differ in host specificity, and DNA sequence data suggested asymmetric introgression between the tree subspecies. Through intensive sampling in a zone of sympatry, a large number of morphologically intermediate trees were identified. These included trees with floral characters typical of Y. b. jaegeriana, but vegetative features typical of Y. b. brevifolia. The opposite combination—Y. b. brevifolia flowers with Y. b. jaegeriana vegetative morphology—never occurred. Microsatellite genotyping revealed a high frequency of genetically admixed, hybrid trees. Coalescent-based estimates of migration indicated significant gene flow between the subspecies and that the direction of gene flow matches differences in pollinator host fidelity. The data suggest that pollinator behaviour determines the magnitude and direction of gene flow between the two subspecies, but that specialized pollination alone is not sufficient to maintain species boundaries. Natural selection may be required to maintain phenotypic differences in the face of ongoing gene flow.
Data from: Scope for genetic rescue of an endangered subspecies though re-establishing natural gene flow with another subspecies
Genetic diversity is positively linked to the viability and evolutionary potential of species but is often compromised in threatened taxa. Genetic rescue by gene flow from a more diverse or differentiated source population of the same species can be an effective strategy for alleviating inbreeding depression and boosting evolutionary potential. The helmeted honeyeater Lichenostomus melanops cassidix is a critically endangered subspecies of the common yellow-tufted honeyeater. Cassidix has declined to a single wild population of ~130 birds, despite being subject to intensive population management over recent decades. We assessed changes in microsatellite diversity in cassidix over the last four decades and used population viability analysis to explore whether genetic rescue through hybridization with the neighbouring Lichenostomus melanops gippslandicus subspecies constitutes a viable conservation strategy. The contemporary cassidix population is characterized by low genetic diversity and effective population size (Ne < 50), suggesting it is vulnerable to inbreeding depression and will have limited capacity to evolve to changing environments. We find that gene flow from gippslandicus to cassidix has declined substantially relative to pre-1990 levels and argue that natural levels of gene flow between the two subspecies should be restored. Allowing gene flow (~4 migrants per generation) from gippslandicus into cassidix (i.e. genetic rescue), in combination with continued annual release of captive-bred cassidix (i.e. demographic rescue), should lead to positive demographic and genetic outcomes. Although we consider the risk of outbreeding depression to be low, we recommend that genetic rescue be managed within the context of the captive breeding programme, with monitoring of outcomes.
Data from: Breaking out of the comfort zone: El Niño-Southern Oscillation as a driver of trophic flows in a benthic consumer of the Humboldt Current ecosystem
The trophic flow of a species is considered a characteristic trait reflecting its trophic position and function in the ecosystem and its interaction with the environment. However, climate patterns are changing and we ignore how patterns of trophic flow are being affected. In the Humboldt Current ecosystem, arguably one of the most productive marine systems, El Niño-Southern Oscillation is the main source of interannual and longer-term variability. To assess the effect of this variability on trophic flow we built a 16-year series of mass-specific somatic production rate (P/B) of the Peruvian scallop (Argopecten purpuratus), a species belonging to a former tropical fauna that thrived in this cold ecosystem. A strong increase of the P/B ratio of this species was observed during nutrient-poor, warmer water conditions typical of El Niño, owing to the massive recruitment of fast-growing juvenile scallops. Trophic ecology theory predicts that when primary production is nutrient limited, the trophic flow of organisms occupying low trophic levels should be constrained (bottom-up control). For former tropical fauna thriving in cold, productive upwelling coastal zones, a short time of low food conditions but warm waters during El Niño could be sufficient to waken their ancestral biological features and display massive proliferations.
Data from: Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae)
Background and Aims: Disentangling the relative roles of past fragmentation (vicariance), colonization (dispersal) and post-divergence gene flow in the genetic divergence of continental island organisms remains a formidable challenge. Amplified fragment length polymorphisms (AFLPs) were used to (1) gain further insights into the biogeographical processes underlying the Pleistocene diversification of the Aegean Nigella arvensis complex; (2) evaluate the role of potential key factors driving patterns of population genetic variability (mating system, geographical isolation and historical contingencies); and (3) test the robustness of conclusions previously drawn from chloroplast (cp) DNA. Methods: Genetic diversity was analysed for 235 AFLP markers from 48 populations (497 individuals) representing 11 taxa of the complex using population genetic methods and Bayesian assignment tests. Key Results: Most designated taxa are identifiable as genetically distinct units. Both fragmentation and dispersal-driven diversification processes occurred at different geological time scales, from Early to Late Pleistocene, specifically (1) sea barrier-induced vicariant speciation in the Cyclades, the Western Cretan Strait and Ikaria; and (2) bi-regional colonizations of the 'Southern Aegean Island Arc' from the Western vs. Eastern Aegean mainland, followed by allopatric divergences in Crete vs. Rhodos and Karpathos/Kasos. Outcrossing island taxa experienced drift-related demographic processes that are magnified in the two insular selfing species. Population genetic differentiation on the mainland seems largely driven by dispersal limitation, while in the Central Aegean it may still be influenced by historical events (island fragmentation and sporadic long-distance colonization). Conclusions: The biogeographical history of Aegean Nigella is more complex than expected for a strictly allopatric vicariant model of divergence. Nonetheless, the major phylogeographical boundaries of this radiation are largely congruent with the geography and history of islands, with little evidence for ongoing gene exchange between divergent taxa. The present results emphasize the need to investigate further biological and landscape features and contemporary vs. historical processes in driving population divergence and taxon diversification in Aegean plant radiations.
Data from: Postpartum family planning integration with maternal, newborn, and child health services: a cross-sectional analysis of client flow patterns in India and Kenya
Objectives: Maternal, newborn, and child health (MNCH) services represent opportunities to integrate postpartum family planning (PPFP). Objectives were to determine levels of MNCH-family planning (FP) integration and associations between integration, client characteristics, and service delivery factors in facilities that received programmatic PPFP support. Design and setting: Cross-sectional client flow assessment conducted May–July 2014, over 5 days at 10 purposively selected public sector facilities in India (four hospitals) and Kenya (two hospitals, four health centers). Participants: 2,158 client visits tracked (1,294 India; 864 Kenya). Women aged 18 or older accessing services while pregnant and/or with a child under 2 years. Interventions: PPFP/postpartum intrauterine device—Bihar, India (2012–2013); Jharkhand, India (2010–2014); Embu, Kenya (2008–2012). Maternal, infant, and young child nutrition/FP integration—Bondo, Kenya (2011–2013). Primary outcome measures: Proportion of visits where clients received integrated MNCH-FP services, client characteristics as predictors of MNCH-FP integration, and MNCH-FP integration as predictor of length of time spent at facility. Results: Levels of MNCH-FP integration varied widely across facilities (5.3% to 63.0%), as did proportion of clients receiving MNCH-FP integrated services by service area. Clients traveling 30–59 minutes were half as likely to receive integrated services versus those traveling under 30 minutes (odds ratio [OR] 0.5, 95% confidence interval [CI] 0.4–0.7, p<.001). Clients receiving MNCH-FP services (versus MNCH services only) spent an average of 10.5 minutes longer at the facility (95% CI −0.1–21.9, not statistically significant). Conclusions: Findings suggest importance of focused programmatic support for integration by MNCH service area. FP integration was highest in areas receiving specific support. Integration does not seem to impose an undue burden on clients in terms of time spent at the facility. Clients living furthest from facilities are least likely to receive integrated services.
Data from: Speciation in sympatry with ongoing secondary gene flow and an olfactory trigger in a radiation of Cameroon cichlids
The process of sympatric speciation in nature remains a fundamental unsolved problem. Cameroon crater lake cichlid radiations were long regarded as one of the most compelling examples; however, recent work showed that their origins were more complex than a single colonization event followed by isolation. Here, we performed a detailed investigation of the speciation history of a radiation of Coptodon cichlids from Lake Ejagham using whole-genome sequencing data. The existence of this radiation is remarkable since this 0.5 km2 lake offers limited scope for divergence across a shallow depth gradient, disruptive selection is weak, and the species are sexually monochromatic. We infer that Lake Ejagham was colonized by riverine cichlids soon after its formation 9,000 years ago, yet speciation occurred only in the last 1,000-2,000 years. We show that secondary gene flow from riverine species has been ongoing, into ancestral and extant Lake Ejagham lineages, and identify and date river-to-lake admixture blocks. One of these contains a cluster of olfactory receptor genes that introgressed close to the time of the first speciation event and coincides with a higher overall rate of admixture into the recipient lineages. Olfactory signaling is a key component of mate choice and species recognition in cichlids. A functional role for this introgression event is consistent with previous findings that assortative mating appears much stronger than ecological divergence in Ejagham Coptodon. We conclude that speciation in this radiation took place in sympatry, yet may have benefited from ongoing riverine gene flow.
Data from: Investigation of turbulent flow in a Schwarz Diamond monolith using MRI and CFD
<p>MRI data from article: Clarke, Coe, Galvosas, and Holland. Investigation of turbulent flow in a Schwarz Diamond monolith using MRI and CFD (2025) Chemical Engineering Journal, 524, 168921</p> <p>Note that the data.zip file decompresses to about 7.5 GB.</p> <p>Version 2:</p> <p>- Fixed critical bugs in data processing scripts pertaining to how spiread.m was called (lines 37, 50 of spiVelProc3D_CS_5step.m, line 30 of turbDiffProc.m). </p> <ul> <li>Added spiread.m to the turbulentDiffusivity directory to fix issue where TopSpin data was read with a custom function not included in this dataset.</li> </ul> <p>Edited description on 2025.10.10 to include journal details.</p>
Data from: Comparison of priority rules, machine allocation, and stage allocation strategies for hybrid flow shop instances using combinatorial logic and a standard trace format
<p>datsets.zip contains benchmark data by Ruiz et al. (2008), Naderi et al.(2010), and Wittwock (1988). The according publications are listed in the related works section. The instances are publicly available under unclear license.</p><p>results.zip contains computational results for the aforementioned benchmarks using the algorithms described in "Comparison of priority rules, machine allocation, and stage allocation strategies for hybrid flow shop instances using combinatorial logic and a standard trace format". The data is licensed under Creative Commons Attribution 4.0 International license.</p>
Fitacf data for "Ionospheric Flow Vortex Induced by the Sudden Decrease in the Solar Wind Dynamic Pressure"
<p>This is the SuperDARN dataset in fitacf format (2.5) from the Hankasalmi radar. The data is used in the publication: Jin, Y., Moen, J. I., Spicher, A., Liu, J., Clausen, L. B. N., & Miloch, W. J. (2023). Ionospheric flow vortex induced by the sudden decrease in the solar wind dynamic pressure. Journal of Geophysical Research: Space Physics, 128, e2023JA031690. https://doi.org/10.1029/2023JA031690</p>
Data for publication "On the flow behaviour of unconfined dual porosity aquifers with sloping base"
<p>Data used in the paper </p> <p>"On the flow behaviour of unconfined dual porosity aquifers with sloping base", </p> <p>by Konstantinos N. Moutsopoulos, John N. E. Papaspyros, Antonis D. Koussis, Frédérick Delay, and Marwan Fahs, </p> <p>submitted to Advances in Water Research.</p>
Fig. 3 in Data from: Climate niche differentiation between two passerines despite ongoing gene flow
Fig. 3 Sexual dimorphism oc the CF and FM duration oc echolocation pulses emitted bv hanging Hipposideros pratti. A-1, B-1, C-1 ss. A-2, B-2, C-2: the distribution oc CF and FM duration oc echolocation pulses recorded crom male and cemale bats. A-3, B-3, C-3: statistical comparison oc these two temporal parameters oc echolocation pulses recorded crom male and cemale bats (see Fig. 2 cor legends)
Fig. 2 in Data from: Climate niche differentiation between two passerines despite ongoing gene flow
Fig. 2 Sexual dimorphism oc the CF, FM bandwidth, and PRR oc echolocation pulses emitted bv hanging Hipposideros pratti. A-1, B-1, C-1 ss. A-2, B-2, C-2: the distribution oc CF, FM bandwidth, and PRR oc echolocation pulses recorded crom male and cemale bats. A-3, B-3, C-3: statistical comparison oc these three pulse parameters recorded crom male and cemale bats. The number within each parenthesis indicates the sample size. Student's t test: *p <0.05; **p <0.01
Fig. 1 in Data from: Climate niche differentiation between two passerines despite ongoing gene flow
Fig. 1 The sonogram (a) and power spectrum (b) oc a representatise echolocation pulse emitted bv a hanging Hipposideros pratti. The CF (kHz), FM bandwidth (kHz), CF duration (ms), and FM duration (ms) oc this echolocation pulse were 60.0, 12.8, 7.5, and 2.7. Clearlv, the second harmonic is the predominant one that contains the highest energv
Data from: The ORFIUS complex regulates ORC2 localization at replication origins (Flow cytometry)
<p>In this work, we use bromodeoxyuridine (BrdU)/propidium iodide cell cycle flow cytometry profiling to demonstrate that treatment of ovarian cancer cell lines with gene specific siRNAs, shRNAs, or drugs leads to minimal or no cell cycle arrest which might otherwise influence observed phenotypes. All raw FCS files for flow cytometry data presented in Figures 4E, 6G, S3A, S4C, S5B, S5F, S8C, S8D, S8E, S9C, S10C, and S12B are available here.</p>
Data from: Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex
<p>Mitochondrial genome assembly of populations of three clownfish species (<em>Amphiprion </em><em>akallopisos</em>, <em>A. sandaracinos</em> and <em>A. akallopisos</em>), presented in "Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex".</p>
Data for paper "Information flow between motor cortex and striatum reverses during skill learning"
<p>Simultaneous spiking activity and local field potential (LFP) recordings from motor cortex (M1) and dorsolateral striatum (DLS) during learning of a reach-to grasp task.<br>Deposited data include spiking activity and LFP recordings, reaching trajectories, andi single-trial success data for the 8 animals included in the paper "Information flow between motor cortex and striatum reverses during skill learning".</p>
Multi-scale soil moisture data and process-based modeling reveal the importance of lateral groundwater flow in a subarctic catchment
<p>Hydrological data measured in Lompolonjängänoja (LJO) catchment and used in Nousu et al.</p> <p> </p> <p>ET_fluxes.csv<br>- Eddy-covariance based, daily evapotranspiration (ET) fluxes [mm/d] at Kenttärova (NFOR) and Lompolojänkkä (NWET) stations</p> <p>GW_levels.csv<br>- Observed groundwater levels [m] relative to the ground surface measured around the LJO catchment</p> <p>Q_runoff.csv<br>- Observed specific discharge [mm/d] at the LJO catchment outlet</p> <p>THETA_kenttarova.csv<br>- Automatically measured soil moisture (i.e. volumetric water content [m3/m3]) around Kenttärova stations</p> <p>THETA_spatial.csv<br>- Manually measured soil moisture (i.e. volumetric water content [m3/m3]) around the LJO catchment</p>
Data from: Plane wave Doppler determination of blood flow in retinopathy of prematurity
<p>Retinopathy of prematurity (ROP) is a disorder affecting low birthweight, preterm neonates. In the preterm eye, the retina is not fully developed and neovascularization may occur at the margin between the developed vascular retina and undeveloped avascular retina. Without timely treatment by laser or intravitreal anti-vascular endothelial growth factor (VEGF) therapy, this can lead to tractional retinal detachment and blindness. Visualization of the retina in regular examinations by indirect ophthalmoscopy is hence the current standard of care, but the exams are stressful and interpretation of images is subjective.</p> <p>The upregulation of VEGF in ROP would suggest an increase in ocular blood flow. In this report, we evaluate the potential of ultrafast plane-wave Doppler ultrasound (PWU) to detect increased flow velocities in the orbital vessels supplying the eye in a gentle exam with objective findings.</p> <p>We imaged both eyes of 50 low-birthweight preterm neonates using 18 MHz PWU. Flow velocity in the central retinal artery (CRA) and vein (CRV), and the short posterior ciliary arteries were determined and values at each ROP Stage compared.</p> <p>We found significantly increased velocities in the CRA and CRV in Stage 3 ROP eyes, where intervention would be considered. We compared multivariate models for identifying Stage 3 eyes comprised solely of clinical factors, solely of Doppler parameters, and clinical plus Doppler parameters. The respective models provided areas under their respective ROC curves of 0.760, 0.812, and 0.904. </p> <p>PWU Doppler represents a gentle, objective means for identifying neonates at risk for ROP that could complement ophthalmoscopy.</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)
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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.