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FIGURES 20–21. Rhyacophila evoluta McLachlan 1879, 5 in The larva of Rhyacophila albardana McLachlan 1879, including a discriminatory matrix to the Rhyacophila larvae with comb-shaped gills of Austria, Germany and Switzerland (Rhyacophilidae, Trichoptera)
FIGURES 20–21. Rhyacophila evoluta McLachlan 1879, 5th instar larva. 20, head, dorsal; 21, head, ventral. Scale bars: 0.5 mm.
Data from: Temporal stability versus community matrix measures of stability and the role of weak interactions
<p>Relationships between different measures of stability are not well understood in part because empiricists and theoreticians tend to measure different aspects and most studies only explore a single form of stability. Using time-series data from experimental plankton communities, we compared temporal stability typically measured by empiricists (coefficient of variation of biomass) to stability measures typically measured by theoreticians derived from the community matrix (asymptotic resilience, initial resilience, and intrinsic stochastic invariability) using first-order multivariate autoregressive models (MAR). Community matrices were also used to derive estimates of interaction strengths between plankton groups. We found no relationship between temporal stability and stability measures derived from the community matrix. Weaker interaction strengths were generally associated with higher stability for community matrix measures of stability but were not consistently associated with higher temporal stability. Temporal stability and stability measures derived from the community matrix stability appear to represent different aspects of stability reflecting the multi-dimensionality of stability.</p>
Data from: Multi-driver and multi-scale assessment of vine community structure and composition across a complex tropical environmental matrix
Ecological communities are structured by multiple processes operating at multiple scales yet understanding the scale-dependency of these processes remains an open challenge. This might be particularly true for parasites, for which biotic rather than abiotic processes may play a primary role in structuring communities. Focusing on vines, a group of structural parasites that gain access to the canopy using different climbing mechanisms, we examined the influence of abiotic factors in tandem with host-parasite and parasite-parasite interactions in the assembly of tropical vine communities. Two synthetic variables, namely Climate1 and landscape Variety, were consistently important in explaining variation in species richness and diversity, as well as species composition, but their importance varied with scale. Whereas Climate1 summarizes the largest variability among climatic variables, landscape Variety expresses landscape heterogeneity within a neighborhood. Significant patterns of species co-occurrences suggest that vine-vine interactions also contribute to vine community assembly. Our results may be critical to understand vine proliferation and help design management strategies for their control.
Data from: Matrix correspondence tests on the DNA phylogeny of the Tenerife lacertid elucidate both historical causes and morphological adaptation
Previous studies using partial regression Mantel tests of matrix correspondence on within-island geographic variation in the color pattern of the Tenerife (Canary Islands) lacertid lizard (Gallotia galloti) support natural selection for different north--south climatically determined biotopes but do not support any historical cause. However, tests on the DNA phylogeny based primarily on population data from 57 localities on Tenerife support the hypothesis that there were populations on two putative precursor islands that have come into secondary contact and introgressed after these islands were joined to form Tenerife by the eruption of the Canadas edifice. Subsequent partial Mantel tests continue to support the hypothesis that color pattern is adapted to the climatic biotopes even when this phylogenetic information is taken into account by (1) testing for color pattern adaptation separately within each lineage and (2) testing for color pattern adaptation across the entire island while considering the molecular phylogenetic relationships as representing an alternative explanation. Selection has largely expunged any trace of the geological history from current morphological variation, and the introgression of these island populations after an estimated 0.7 million years of separation gives an insight into the relationships between allopatric divergence and reproductive isolation.
Data from: Effect of the landscape matrix on gene flow in a coastal amphibian metapopulation
Functional connectivity is crucial for the persistence of a metapopulation, because migration among subpopulations enables recolonization and counteracts genetic drift, which is especially important in small subpopulations. We studied the degree and drivers of connectivity among occupied patches of a coastal dune metapopulation of the Natterjack Toad (Epidalea calamita Laurenti), on the basis of microsatellite variation. As spatial landscape heterogeneity is expected to influence dispersal and genetic structure, we analyzed which landscape features affect functional connectivity and to what extent. Sixty different landscape resistance scenarios as well as the isolation-by-distance model were compared using two landscape genetics approaches. We identified three subpopulations with unidirectional levels of gene flow among the two most geographically separated subpopulations, while inferred gene flow into the geographically intermediate subpopulation was limited. Urbanization and vegetation height negatively affected connectivity. Low estimates of genetic diversity and effective population size indicate that conservation measures in the smallest and most isolated subpopulation are required.
Generating fast sparse matrix vector multiplication from a high level generic functional IR
<p>Usage of high-level intermediate representations promises the generation of fast code from a high-level description, improving the productivity of developers while achieving the performance traditionally only reached with low-level programming approaches.</p> <p>High-level IRs come in two flavors:<br> 1) domain-specific IRs designed to express only for a specific application area; or<br> 2) generic high-level IRs that can be used to generate high-performance code across many domains.<br> Developing generic IRs is more challenging but offers the advantage of reusing a common compiler infrastructure various applications.</p> <p>In this paper, we extend a generic high-level IR to enable efficient computation with sparse data structures.<br> Crucially, we encode sparse representation using reusable dense building blocks already present in the high-level IR.<br> We use a form of dependent types to model sparse matrices in CSR format by expressing the relationship between multiple dense arrays explicitly separately storing the length of rows, the column indices, and the non-zero values of the matrix.</p> <p>We demonstrate that we achieve high-performance compared to spare low-level library code using our extended generic high-level code generator.<br> On an Nvidia GPU, we outperform the highly tuned Nvidia cuSparse implementation of SpMV multiplication across 28 sparse matrices of varying sparsity on average by $1.7\times$.</p>
Data from: Examining the full effects of landscape heterogeneity on spatial genetic variation: a multiple matrix regression approach for quantifying geographic and ecological isolation
Understanding the effects of landscape heterogeneity on spatial genetic variation is a primary goal of landscape genetics. Ecological and geographic variables can contribute to genetic structure through geographic isolation, in which geographic barriers and distances restrict gene flow, and ecological isolation, in which gene flow among populations inhabiting different environments is limited by selection against dispersers moving between them. Although methods have been developed to study geographic isolation in detail, ecological isolation has received much less attention, partly because disentangling the effects of these mechanisms is inherently difficult. Here, I describe a novel approach for quantifying the effects of geographic and ecological isolation using multiple matrix regression with randomization. I explored the parameter space over which this method is effective using a series of individual-based simulations and found that it accurately describes the effects of geographic and ecological isolation over a wide range of conditions. I also applied this method to a set of real-world datasets to show that ecological isolation is an often overlooked but important contributor to patterns of spatial genetic variation and to demonstrate how this analysis can provide new insights into how landscapes contribute to the evolution of genetic variation in nature.
Data from: MonotomidGen – A matrix-based interactive key to the New World genera of Monotomidae (Coleoptera, Cucujoidea)
A matrix-based Lucid key is presented for the twelve genera of Monotomidae (Coleoptera: Cucujoidea) represented in the New World. A general overview is given for the features and technical specifications of an original interactive key for the identification of these genera. The list of terminal taxa included with the key provides a current summary of monotomid generic diversity for the Nearctic and Neotropical regions.
Data from: Matrix type and landscape attributes modulate avian taxonomic and functional spillover across habitat boundaries in the Brazilian Atlantic Forest
Land use intensification drives biodiversity loss worldwide. In heterogeneous landscape mosaics, both overall forest area and anthropogenic matrix structure induce changes in biological communities in primary habitat remnants. However, community changes via cross-habitat spillover processes along forest-matrix interfaces remain poorly understood. Moreover, information on how landscape attributes affect spillover processes across habitat boundaries are embryonic. Here, we quantify avian and β-diversity (as proxies of spillover rates) across two dominant types of forest-matrix interfaces (forest-pasture and forest-eucalyptus plantation) within the Atlantic Forest biodiversity hotspot in southeast Brazil. We also assess the effects of anthropogenic matrix type and landscape attributes (forest cover, edge density and land-use diversity) on bird taxonomic and functional β-diversity across forest-matrix boundaries. Alpha taxonomic richness was higher in forest edges than within both matrix types, but between matrix types, it was higher in pastures than in eucalyptus plantations. Although significantly higher in forests edges than in the adjacent eucalyptus, bird functional richness did not differ between forest edges and adjacent pastures. Community changes (β-diversity) related to species and functional replacements (turnover component) were higher across forest-pasture boundaries, whereas changes related to species and functional loss (nested component) were higher across forest-eucalyptus boundaries. Forest edges adjacent to eucalyptus had significant higher species and functional replacements than forest edges adjacent to pastures. Forest cover negatively influenced functional β-diversity across both forest-pasture and forest-eucalyptus interfaces. We show the importance of matrix type and the structure of surrounding landscapes (mainly forest cover) on rates of bird assemblage spillover across forest-matrix boundaries, which has profound implications to biological fluxes, ecosystem functioning and land-use management in human-modified landscapes.
Data from: The role of species traits in mediating functional recovery during matrix restoration
Reversing anthropogenic impacts on habitat structure is frequently successful through restoration, but the mechanisms linking habitat change, community reassembly and recovery of ecosystem functioning remain unknown. We test for the influence of edge effects and matrix habitat restoration on the reassembly of dung beetle communities and consequent recovery of dung removal rates across tropical forest edges. Using path modelling, we disentangle the relative importance of community-weighted trait means and functional trait dispersion from total biomass effects on rates of dung removal. Community trait composition and biomass of dung beetle communities responded divergently to edge effects and matrix habitat restoration, yielding opposing effects on dung removal. However, functional dispersion—used in this study as a measure of niche complementarity—did not explain a significant amount of variation in dung removal rates across habitat edges. Instead, we demonstrate that the path to functional recovery of these altered ecosystems depends on the trait-mean composition of reassembling communities, over and above purely biomass-dependent processes that would be expected under neutral theory. These results suggest that any ability to manage functional recovery of ecosystems during habitat restoration will demand knowledge of species' roles in ecosystem processes.
Figures of Conductivity Transitions of La0.7Sr0.3MnO3±d andLa0.6Sr0.4Co0.2Fe0.8O3-d in Ce0.9Gd0.1O2-d Matrix for Dual-Phase Oxygen Transport Membranes
<p>Figures of the article "Conductivity Transitions of La0.7Sr0.3MnO3±d andLa0.6Sr0.4Co0.2Fe0.8O3-d in Ce0.9Gd0.1O2-d Matrix for Dual-Phase Oxygen Transport Membranes"</p>
Data from: Pollinator-mediated gene flow connects green roof populations across the urban matrix: a paternity analysis of the self-compatible forb Penstemon hirsutus
Gene flow between populations can help maintain genetic diversity and prevent inbreeding, which is especially important for small, fragmented habitats. Many plant species rely on pollinators to move pollen between populations. In urban areas, insufficient pollinator services may result in limited gene flow, which can have negative consequences such as genetic drift and inbreeding depression. Furthermore, restored populations that are established with few founders of low genetic diversity may have limited long-term population persistence. Here, we tested the hypotheses that populations of a self-compatible forb established on urban green roofs fromnursery stock are genetically depauperate and that limited gene (pollen) flow between populations will result in increased inbreeding. We compared the neutral genetic diversity of Penstemon hirsutus, using nine microsatellite loci, between three green roof populations established from nursery stock and three natural populations. We also established ten experimental populations on green roofs and measured rates of outcrossing and inbreeding and identified the movement of pollen within and between roofs using a paternity analysis. We found that neutral genetic diversity of populations established from nursery stock was lower than that of natural populations, although the level of inbreeding was also lower on the green roofs. In our experimental populations, we found that the rates of outcrossing and inbreeding varied between the roof populations. Our results suggest that inbreeding may be correlated with cover of co-flowering species but not with any of the other measured site properties. The location of likely pollen donors suggested that on average, 75% of pollen was derived from plants within the population (including self) and 25% came from plants on different roofs. Our results document realized pollen movement within and between green roofs, demonstrating that these habitats provide important connectivity in a fragmented environment.
Data from: Nest boxes increase reproductive output for Tree Swallows in a forest grassland matrix in central British Columbia
Secondary cavity-nesting birds depend on tree cavities for nesting and roosting, but many studies of these birds are conducted using nest boxes. Implementation of effective conservation strategies for cavity-nesting species such as nest-site supplementation requires careful comparisons of fecundity and other vital rates for birds using both natural and artificial nest site types. We compared breeding phenology, clutch and brood sizes, and fledging success of Tree Swallows (Tachycineta bicolor) nesting in tree cavities and nest boxes during 2001–2003 in British Columbia, Canada. Swallows using nest boxes initiated egg-laying and hatched young at approximately the same time as those in tree cavities (2 June, 23 June, respectively). Female Tree Swallows in boxes laid larger clutches (5.9 ± 0.9 eggs, N = 76) than those in tree cavities (4.2 ± 1.6 eggs, N = 67). The mean number of nestlings hatched was greater in nest boxes (5.2 ± 1.1 nestlings, N = 67) than in tree cavities (2.6 ± 2.0 nestlings, N = 58). Pairs in boxes were over twice as successful in producing fledglings (93.4%; 57 of 61 pairs fledged > 1 young) than those in tree cavities (35.8%; 19 of 53 pairs). Of those successful nests, pairs nesting in boxes fledged 5.1 ± 1.1 young (N = 57), whereas those in tree cavities fledged 3.5 ± 1.2 young (N = 18). Because cavities in nest boxes averaged 60% larger in volume and 1.8 cm wider internally than tree cavities, we suggest that increased reproductive output was correlated with boxes enabling a larger clutch size. In previous research, we found that Tree Swallows were a poor competitor with other cavity-nesting passerines for tree cavities. The addition of nest boxes may serve as an effective way to supplement local reproduction for secondary cavity-nesting bird populations by reducing competition for limited nest sites. This is especially true in regions where the availability of natural nesting sites is highly variable, and where species compete with many other cavity-nesting passerines using a similar ecological niche and nesting cavities.
Data from: Spectral diversity area relationships for assessing biodiversity in a wildland-agriculture matrix
Species-area relationships have long been used to assess patterns of species diversity across scales. Here this concept is extended to spectral diversity using hyperspectral data collected by NASA's Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) over western Michigan. This mixture of mesic forest and agricultural lands offers two end-points on the local-scale diversity continuum – one set of well mixed forest patches and one set of highly homogeneous agricultural patches. Using the sum of the first three principal component values and the principal components' convex hull volume, spectral diversity was compared within and among these plots and to null expectations for perfectly random and perfectly patchy landscapes. Overall the spectral diversity area relationship confirms the patterns that would be expected for this landscape, but this application suggests that this approach could be extended to less well understood landscapes and could reveal key insights about the relative importance of different drivers of community assembly, even in the absence of additional data about plant functional traits or species' identities.
Data from: The B-matrix harbours significant and sex-specific constraints on the evolution of multi-character sexual dimorphism
The extent to which sexual dimorphism can evolve within a population depends on an interaction between sexually divergent selection and constraints imposed by a genetic architecture that is shared between males and females. The degree of constraint within a population is normally inferred from the intersexual genetic correlation, rmf. However, such bivariate correlations ignore the potential constraining effect of genetic covariances between other sexually co-expressed traits. Using the fruit fly Drosophila serrata, a species that exhibits mutual mate preference for blends of homologous contact pheromones, we tested the impact of between-sex between-trait genetic covariances using an extended version of the genetic variance-covariance matrix, G, that includes Lande's (1980) between-sex covariance matrix, B. We find that including B greatly reduces the degree to which male and female traits are predicted to diverge in the face of divergent phenotypic selection. However, the degree to which B alters the response to selection differs between the sexes. The overall rate of male trait evolution is predicted to decline, but its direction remains relatively unchanged, whereas the opposite is found in females. We emphasise the importance of considering the B-matrix in microevolutionary studies of constraints on the evolution of sexual dimorphism.
Data from: Similarity in G matrix structure among natural populations of Arabidopsis lyrata
Understanding the stability of the G matrix in natural populations is fundamental for predicting evolutionary trajectories, yet, the extent of its spatial variation and how this impacts responses to selection remain open questions. With a nested paternal half-sib crossing design and plants grown in a field experiment, we examined differences in the genetic architecture of flowering time, floral display and plant size among four Scandinavian populations of Arabidopsis lyrata. Using a multivariate Bayesian framework, we compared the size, shape and orientation of G matrices and assessed their potential to facilitate or constrain trait evolution. Flowering time, floral display and rosette size varied among populations and significant additive genetic variation within populations indicated potential to evolve in response to selection. Yet, some characters, including flowering start and number of flowers, may not evolve independently because of genetic correlations. Using a multivariate framework, we found few differences in the genetic architecture of traits among populations. G matrices varied mostly in size rather than shape or orientation. Differences in multivariate responses to selection predicted from differences in G were small, suggesting overall matrix similarity and shared constraints to trait evolution among populations.
Development of a versatile source apportionment analysis based on positive matrix factorization: a case study of the seasonal variation of organic aerosol sources in Estonia
<p>This work presents an advanced source apportionment approach that estimates the uncertainties of the positive matrix factorization model. The selection of the environmentally meaningful solutions is challenging in such models and a systematic approach to identify and sort the factors is important. We applied this method to a novel data set covering one yearly cycle at three sites in Estonia. The main results showed that biomass burning dominates in winter, while biogenic sources prevail in summer.</p>
Pressure-induced amorphisation and a new high density amorphous metallic phase in matrix-free Ge nanoparticles: simulation data
<p>The folder contains:</p> <p>-Pseudopotential files for Ge and H in the .recpot format used in all calculations.</p> <p>-Input and output files for constant enthalpy geometry relaxations of hydrogenated Ge nanocrystals using the electronic enthalpy method within ONETEP (version 3.3).</p> <p>-Input and output files for the DFPT calculations performed with CASTEP (version 6.01).</p>
FIGURES 12–17. Figures 12–14. Plectrocnemia renetta Malicky 1975, 5 in The larva of Plectrocnemia renetta Malicky 1975 (Trichoptera, Polycentropodidae), including a discriminatory matrix to the larvae of Plectrocnemia Stephens 1836 species of Greece
FIGURES 12–17. Figures 12–14. Plectrocnemia renetta Malicky 1975, 5th instar larva: 12, abdominal segment IX, ventral (ip = innermost primary seta; op = outermost primary seta; p = intermediate primary setae); 13, abdominal segment IX, dorsal, posterolateral setal trio (is = inner secondary seta; os = outer secondary seta; p = primary seta); 14, left anal proleg, left lateral (sc = distal sclerotized section; so = proximal unsclerotized section; dotted lines = right angle superimposed on obtuse-angled anal claw). Figure 15. P. kingi McLachlan 1881, 5th instar larva, left foreleg, posterior (double arrow = projected half length of tibia). Figure 16. P. g. geniculata McLachlan 1871, 5th instar larva, abdominal segment IX, ventral (ip = innermost primary seta; op = outermost primary seta; p = intermediate primary setae). Figure 17. P. c. conspersa (Curtis 1834), 5th instar larva, abdominal segment IX, ventral (ip = innermost primary seta; op = outermost primary seta; p = intermediate primary setae). Scale bars: 0.5 mm.
FIGURES 22–24. Figures 22–23. Plectrocnemia g. geniculata McLachlan 1871, 5 in The larva of Plectrocnemia renetta Malicky 1975 (Trichoptera, Polycentropodidae), including a discriminatory matrix to the larvae of Plectrocnemia Stephens 1836 species of Greece
FIGURES 22–24. Figures 22–23. Plectrocnemia g. geniculata McLachlan 1871, 5th instar larva: 22, head, dorsal (dotted lines = half-trapezoidal pattern of spots on posterior frontoclypeus, about 100°); 23, labrum, dorsal. Figure 24. P. c. conspersa (Curtis 1834), 5th instar larva, labrum, dorsal (arrow = posterior mark). Scale bars: 0.5 mm.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.