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831 results for “Partition”
Title: Partitioning plant spectral diversity into alpha and beta components
<p><span><span><span><span><span><span><span><span><span><span>Plant spectral diversity — how plants differentially interact with solar radiation — is an integrator of plant chemical, structural, and taxonomic diversity that can be remotely sensed. We propose to measure spectral diversity as spectral variance, which allows the partitioning of the spectral diversity of a region, called spectral <i>gamma</i> (<i>γ</i>) diversity, into additive alpha (<i>α</i>; within communities) and beta (<i>β</i>; among communities) components. Our method calculates the contributions of individual bands or spectral features to spectral <i>γ</i>-, <i>β</i>-, and <i>α</i>-diversity, as well as the contributions of individual plant communities to spectral diversity. We present two case studies illustrating how our approach can identify "hotspots" of spectral <i>α</i>-diversity within a region, and discover spectrally unique areas that contribute strongly to <i>β</i>-diversity. Partitioning spectral diversity and mapping its spatial components has many applications for conservation since high local diversity and distinctiveness in composition are two key criteria used to determine the ecological value of ecosystems.</span></span></span></span></span></span></span></span></span></span></p>
Nitrogen isotope composition of amino acids reveals trophic partitioning in two sympatric amphipods
<p>According to ecological theory two species cannot occupy the same niche. We tested the extent to which two sympatric deposit-feeding amphipods, Monoporeia affinis and Pontoporeia femorata, partition trophic resources by applying nitrogen isotope analyses (δ15N) of amino acids. We found that trophic position (TP), and resynthesis index (∑V; a proxy for degradation status of ingested material prior to assimilation by the consumer) differ between species. The surface-feeding M. affinis had higher TP and intermediate ∑V; both pointing to a large contribution of metazoans in its diet. P. femorata, which feeds in the sub-surface layers, had lower TP and a bimodal distribution of the ∑V values, supporting previous experimental evidence of a larger feeding niche. We also evaluated whether TP and ∑V values have consequences for amphipod fecundity and embryo viability and found that embryo viability in M. affinis was negatively linked to TP. Our results indicate that the amino acid-δ15N data paired with information about reproductive status are useful for detecting differences in the trophic ecology of sympatric amphipods. Key words: Compound-specific stable nitrogen isotope analyses, amino acids, trophic level, resynthesis index, reproductive status, Baltic Sea.</p>
Molecular Simulations of Lipid Membrane Partitioning and Translocation by Bacterial Quorum Sensing Modulators
<p>All simulation data and analysis tools for regenerating results from the journal paper:</p> <p>T. Jin, S. J. Patel, and R. C. Van Lehn. “Molecular simulations of lipid membrane partitioning and translocation by bacterial quorum sensing modulators.” <em>PLOS ONE</em>, <strong>accepted.</strong></p>
Manuscript data for "PASV: Automatic protein partitioning and validation using conserved residues"
<p>Manuscript data for "PASV: Automatic protein partitioning and validation using conserved residues"</p>
Data from: Limited trophic partitioning among sympatric delphinids off a tropical oceanic atoll
Understanding trophic relationships among marine predators in remote environments is challenging, but it is critical to understand community structure and dynamics. In this study, we used stable isotope analysis of skin biopsies to compare the isotopic, and thus, trophic niches of three sympatric delphinids in the waters surrounding Palmyra Atoll, in the Central Tropical Pacific: the melon-headed whale (Peponocephala electra), Gray's spinner dolphin (Stenella longirostris longirostris), and the common bottlenose dolphin (Tursiops truncatus). δ15N values suggested that T. truncatus occupied a significantly higher trophic position than the other two species. δ13C values did not significantly differ between the three delphinds, potentially indicating no spatial partitioning in depth or distance from shore in foraging among species. The dietary niche area—determined by isotopic variance among individuals—of T. truncatus was also over 30% smaller than those of the other species taken at the same place, indicating higher population specialization or lower interindividual variation. For P. electra only, there was some support for intraspecific variation in foraging ecology across years, highlighting the need for temporal information in studying dietary niche. Cumulatively, isotopic evidence revealed surprisingly little evidence for trophic niche partitioning in the delphinid community of Palmyra Atoll compared to other studies. However, resource partitioning may happen via other behavioral mechanisms, or prey abundance or availability may be adequate to allow these three species to coexist without any such partitioning. It is also possible that isotopic signatures are inadequate to detect trophic partitioning in this environment, possibly because isotopes of prey are highly variable or insufficiently resolved to allow for differentiation.
Data from: Life table invasion models: spatial progression and species-specific partitioning
Biological invasions are increasingly being considered important spatial processes that drive global changes, threatening biodiversity, regional economies, and ecosystem functions. A unifying conceptual model of the invasion dynamics could serve as a useful tool for comparison and classification of invasion processes involving different species across large geographic ranges. By dividing these geographic ranges that are subject to invasions into discrete spatial units we here conceptualize the invasion process as the transition from pristine to invaded spatial units. We use California cities as the spatial units and a long-term database of invasive tropical tephritids to characterize the invasion patterns. A new life-table method based on insect demography, including the progression model of invasion stage transition and the species-specific partitioning model of multispecies invasions, was developed to analyze the invasion patterns. The progression model allows us to estimate the probability and rate of transition, for individual cities, from pristine to infested stages and subsequently differentiate first year of detection from detection recurrences. Importantly, we show that the interval of invasive tephritid recurrence in a city declines with increasing invasion stages of the city. The species-specific partitioning model revealed profound difference in invasion outcome depending on which tephritid species was first detected (and then locally eradicated) in the early stage of invasion. Taken together, we discuss how these two life-table invasion models can cast new light on existing invasion concepts; in particular, on formulating invasion dynamics as the state transition of cities and partitioning species-specific role during multispecies invasions. These models provide a new set of tools for predicting the spatiotemporal progression of invasion and providing early warnings of recurrent invasions for efficient management.
Data from: Partitioning resources through the seasons: abundance and phenology of carrion beetles (Silphidae) in southeastern Ontario
<p>The coexistence of ecologically similar species is thought to require resource partitioning to minimize competition. Phenological, seasonal differences in activity may provide an important axis for resource partitioning. Here, we test for evidence of seasonal differences in activity within a diverse guild of carrion beetles (Silphidae) in a habitat preserve on the Frontenac Arch, southeastern Ontario, Canada using a large-scale survey during their active seasons (April to October). We then used generalized additive models to test for differences in seasonal abundance among eight co-occurring carrion beetle species, including five species of burying beetles (Nicrophorinae: <i>Nicrophorus </i>Fabricius, 1775) and three species from the Silphinae subfamily. Consistent with previous work, all species showed seasonal variation in abundance, with peak abundance of most species occurring between June and August. All but one species (<i>Nicrophorus sayi </i>Laporte, 1840) showed positive relationships between abundance and temperature. We find evidence consistent with seasonal partitioning of resources among <i>Nicrophorus </i>habitat generalists that could potentially reduce competition for limited carrion resources. In contrast, we find little evidence for seasonal differences in abundance among <i>Nicrophorus </i>habitat specialists, which instead may partition resources spatially. Overall, our results provide evidence consistent with an important role for seasonal resource partitioning among carrion beetle species that show higher levels of spatial (habitat) overlap within a temperate beetle guild.</p>
Data from: Genetic and genomic evidence of niche partitioning and adaptive radiation in mountain pine beetle fungal symbionts
Bark beetles form multipartite symbiotic associations with blue stain fungi (Ophiostomatales, Ascomycota). These fungal symbionts play an important role during the beetle's life cycle by providing nutritional supplementation, overcoming tree defences and modifying host tissues to favour brood development. The maintenance of stable multipartite symbioses with seemingly less competitive symbionts in similar habitats is of fundamental interest to ecology and evolution. We tested the hypothesis that the coexistence of three fungal species associated with the mountain pine beetle is the result of niche partitioning and adaptive radiation using SNP genotyping coupled with genotype–environment association analysis and phenotypic characterization of growth rate under different temperatures. We found that genetic variation and population structure within each species is best explained by distinct spatial and environmental variables. We observed both common (temperature seasonality and the host species) and distinct (drought, cold stress, precipitation) environmental and spatial factors that shaped the genomes of these fungi resulting in contrasting outcomes. Phenotypic intraspecific variations in Grosmannia clavigera and Leptographium longiclavatum, together with high heritability, suggest potential for adaptive selection in these species. By contrast, Ophiostoma montium displayed narrower intraspecific variation but greater tolerance to extreme high temperatures. Our study highlights unique phenotypic and genotypic characteristics in these symbionts that are consistent with our hypothesis. By maintaining this multipartite relationship, the bark beetles have a greater likelihood of obtaining the benefits afforded by the fungi and reduce the risk of being left aposymbiotic. Complementarity among species could facilitate colonization of new habitats and survival under adverse conditions.
Data from: Partitioning of genetic variation across the genome using multimarker methods in a wild bird population
The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high-density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex-, age- and environment-specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems.
Data from: Partitioning the effects of spatial isolation, nest habitat, and individual diet in causing assortative mating within a population of threespine stickleback
Assortative mating is measured as a phenotypic or genotypic correlation between mates. Although biologists typically view assortative mating in terms of mate preference for similar partners, correlations between mates can also arise from phenotypic spatial structure arising from spatial isolation or habitat preferences. Here, we test whether diet-assortative mating within an ecologically variable population of threespine stickleback results from small-scale geographic isolation or microhabitat preference. We find evidence for assortative mating in the form of a positive correlation between mated pairs' diets (measured using stable isotopes). Stable isotopes reveal diet differences between different nesting areas and among individuals using different nest habitat within a nesting area. This spatial segregation of diet types should generate some assortative mating, but is insufficient to explain the observed assortment strength. Significant male-female isotope correlations remain after controlling for spatial variables. We therefore conclude that sticklebacks' diet-assortative mating arises from additional behavioral preference. More generally, our results illustrate the point that spatial segregation can only drive appreciable levels of phenotypic assortative mating when environment-phenotype correlations are parallel and strong in both sexes. Consequently, intraspecific assortative mating may typically entail mating preferences rather than just spatial co-segregation of phenotypes.
Data from: Sex-specific winter distribution in a sexually dimorphic shorebird is explained by resource partitioning
Sexual size dimorphism (SSD) implies correlated differences in energetic requirements and feeding opportunities, such that sexes will face different trade-offs in habitat selection. In seasonal migrants, this could result in a differential spatial distribution across the wintering range. To identify the ecological causes of sexual spatial segregation, we studied a sexually dimorphic shorebird, the bar-tailed godwit Limosa lapponica, in which females have a larger body and a longer bill than males. With respect to the trade-offs that these migratory shorebirds experience in their choice of wintering area, northern and colder wintering sites have the benefit of being closer to the Arctic breeding grounds. According to Bergmann's rule, the larger females should incur lower energetic costs per unit of body mass over males, helping them to winter in the cold. However, as the sexes have rather different bill lengths, differences in sex-specific wintering sites could also be due to the vertical distribution of their buried prey, that is, resource partitioning. Here, in a comparison between six main intertidal wintering areas across the entire winter range of the lapponica subspecies in northwest Europe, we show that the percentage of females between sites was not correlated with the cost of wintering, but was positively correlated with the biomass in the bottom layer and negatively with the biomass in the top layer. We conclude that resource partitioning, rather than relative expenditure advantages, best explains the differential spatial distribution of male and female bar-tailed godwits across northwest Europe.
SAMPL7 Blind Challenge : Quantum-Mechanical Prediction of Partition Coefficients and Acid Dissociation Constants for Small Drug-like Molecules
<p>Global minima structures of <em>N</em>-acyl sulfonamides and sulfonamides derivatives (B3LYP-D3/6-311+G(d,p)) in gas phase.</p>
Data from: Partitioning drivers of spatial genetic variation for a continuously-distributed population of boreal caribou: implications for management unit delineation
Isolation-by-distance (IBD) is a natural pattern not readily incorporated into theoretical models nor traditional metrics for differentiating populations, although clinal genetic differentiation can be characteristic of many wildlife species. Landscape features can also drive population structure additive to baseline IBD resulting in differentiation through isolation-by-resistance (IBR). We assessed the population genetic structure of boreal caribou across western Canada using non-spatial (STRUCTURE) and spatial (MEMGENE) clustering methods and investigated the relative contribution of IBD and IBR on genetic variation of 1221 boreal caribou multilocus genotypes across western Canada. We further introduced a novel approach to compare the partitioning of individuals into management units (MU) and assessed levels of genetic connectivity under different MU scenarios. STRUCTURE delineated five genetic clusters while MEMGENE identified finer-scale differentiation across the study area. IBD was significant and did not differ for males and females both across and among detected genetic clusters. MEMGENE landscape analysis further quantified the proportion of genetic variation contributed by IBD and IBR patterns, allowing for the relative importance of spatial drivers, including roads, water bodies and wildfires, to be assessed and incorporated into the characterization of population structure for the delineation of MUs. Local population units, as currently delineated in the boreal caribou recovery strategy, do not capture the genetic variation and connectivity of the ecotype across the study area. Here, we provide the tools to assess fine-scale spatial patterns of genetic variation, partition drivers of genetic variation and evaluate the best management options for maintaining genetic connectivity. Our approach is highly relevant to vagile wildlife species that are of management and conservation concern and demonstrate varying degrees of IBD and IBR with clinal spatial genetic structure that challenges the delineation of discrete population boundaries.
Data from: Exotic flower visitors exploit large floral trait spaces resulting in asymmetric resource partitioning with native visitors
1.Exotic species often cause severe alterations in native communities due to their ability to rapidly and efficiently utilize a broad spectrum of resources. In flower-visitor interactions, the breadth of resource use by native and exotic animals as well as the partitioning of resources among them is often estimated based on the number of (shared) plant species used as resources. However, whether a flower visitor is able to exploit plant resources has been shown to be delimited by functional floral traits such as morphological barriers or attractive or repellent chemical cues. Each of the ecologically relevant traits can be viewed as a dimension of a Hutchinsonian n-dimensional hypervolume, which characterizes the range of phenotypes exploitable by a species. 2.In this study, we quantified the sizes and overlaps of n-dimensional hypervolumes defined by floral traits that are exploitable by native and exotic flower visitors (afterwards referred to as exploited space, ES). In the heavily invaded Hawai'i Volcanoes National Park, USA, we phenotyped 40 native and exotic plant species and recorded flower-visitor interactions. To quantify the size and overlap of ES, we applied dynamic range boxes (dynRB). 3.On average, exotic flower visitors were more generalized in resource use (larger ES) than natives ones, which is additionally indicated by the absence of native flower visitors on exotic flowering plant species. In particular, ES based on floral scent emission was larger for exotic flower visitors compared to native ones. The unevenly expanded ES of native and exotic animals led to an asymmetric overlap of floral ES where the exotic flower visitors shared only a small proportion of their ES with natives but occupied a large proportion of the ES of natives. 4.The asymmetry in resource use of native and exotic flower visitors suggests a potential advantage in resource exploitation of the latter, potentially explaining their success in Hawaiian ecosystems. Predicted range expansion of exotic plant and animal species may further increase the competition for and reduce the availability of resources for native animals. This may lead to further declines of native species and increasing threats for Hawaiian ecosystems.
Data from: Partitioning the effects of regional, spatial and local variables on beta diversity of salt marsh arthropods in Chile
Aim: We examined the influence of regional, spatial and local variables (edaphic characteristics and vegetation structure) on patterns of arthropod variation along the Chilean coast by partitioning beta diversity into its turnover and nestedness components. Location: 2000 km along the coast of Chile Methods: We collected ground-dwelling arthropod samples from 9 marshes during two seasons. A clustering method was used to examine patterns of arthropod similarity across salt marshes. We also calculated multiple site beta diversity and partitioned it into its turnover and nestedness components. Variation partitioning was then used to identify the major drivers of their variation (regional, spatial and local variables). We compared results for the whole arthropod community and for the most abundant, speciose and functionally different groups, Crustacea, Coleoptera and Araneae. Results: Salt marsh arthropod similarities did not depend on the geographic proximity of sites. Arthropod beta diversity was mainly determined by its turnover component. A significant fraction of community variation was structured according to regional (i.e. climate differences) or local (i.e. soil salinity) differences among marshes depending on the studied group. However, the exclusive contribution of spatial variables had also a role. Main conclusions: Each salt marsh on the Chilean coast has the capacity to accommodate unique invertebrate taxa. Niche sorting along the climatic gradient together with dispersal-based processes seem the key structuring force of the arthropods and Crustacean variation in the marshes we studied, while niche sorting alone might be more important for Coleoptera variation.
Data from: Towards a mechanistic understanding of thermal niche partitioning
We develop a theoretical framework to elucidate the mechanistic basis of thermal niche partitioning in ectotherms. Using a food web module of two consumers competing for a biotic resource, we investigate how temperature effects on species' attack and mortality rates scale up to population-level outcomes of coexistence and exclusion. We find that species' differences in competitive effects arise from asymmetries generated by the non-linear temperature response of mortality: cold-adapted species experience stronger intra-specific competition than warm-adapted species; they also exert weaker competition on, and experience stronger competition from, warm-adapted species. These asymmetries become greater as seasonal fluctuations increase, generating latitudinal variation in coexistence and priority effects. Characterizing species' thermal niches in terms of mechanistic descriptions of trait responses allows for testable predictions about population-level competitive outcomes based solely on three fundamental, and easily measurable, quantities: attack rate optima, response breadths and temperature sensitivity of mortality. We test our predictions with data from an insect host-parasitoid community. By quantifying the three basic quantities we predict that priority effects cannot occur, which is borne out by population-level experiments showing that the outcome of competition does not depend on initial conditions. More broadly, our framework can predict the conditions under which exotic invasive species can exclude, or coexist with, native biota, and the effects of climate warming on competitive communities across latitudinal gradients.
Data from: A new small captorhinid reptile from the lower Permian of Oklahoma and resource partitioning among small captorhinids in the Richards Spur fauna
Two partial reptile skulls and six dentigerous fragments from the lower Permian Richards Spur locality of Oklahoma represent a new genus and species of small captorhinid reptile. Labidosauriscus richardi gen. et sp. nov. is distinguished from other captorhinids in the reduction of the height of the ridges forming the characteristic net-like, ridge-and-pit cranial sculpturing of captorhinids, and the superimposition of a system of finer pits and furrows over the primary ridge-and-pit cranial ornamentation. Labidosauriscus richardi shares with C. laticeps a post-caniniform tooth morphology characterized by convex mesial and distal carinae that form a distinctly asymmetrical apex in labial aspect. The description of L. richardi brings to six the number of captorhinid species known from the productive Richards Spur fissure-fill locality. Each of these species exhibits a distinctive post-caniniform tooth morphology (or multiplication of these teeth), which is consonant with the hypothesis of resource partitioning among the small faunivorous and omnivorous captorhinids at Richards Spur. As an 'exhumed early Permian hill,' Richards Spur provides a unique window into early reptile diversification in a distinctive upland environment that is rarely preserved in the tetrapod fossil record.
Data from: When good neighbors don't need fences: Temporal landscape partitioning among baboon social groups
Intraspecific competition is a key factor shaping space-use strategies and movement decisions inmany species, yet how and when neighbors utilize shared areas while exhibiting active avoidance of one another is largely un- known. Here, we investigated temporal landscape partitioning in a population of wild baboons (Papio cynocephalus). We used global positioning system (GPS) collars to synchronously record the hourly locations of five baboon social groups for ∼900 days, and we used behavioral, demographic, and life history data to measure factors affecting use of overlap areas. Annual home ranges of neighboring groups overlapped substantially, as predicted (baboons are considered non-territorial), but home ranges overlapped less when space use was assessed over shorter time scales. Moreover, neighboring groups were in close spatial proximity to one another on fewer days than predicted by a null model, suggesting an avoidance-based spacing pattern. At all time scales examined (monthly, biweekly, and weekly), time spent in overlap areas was greater during time periods when groups fed on evenly dispersed, low-quality foods. The percent of fertile females in social groups was negatively correlated with time spent in overlap areas only during weekly time intervals. This suggests that broad temporal changes in ecological resources are a major predictor of how intensively overlap areas are used, and groups modify these ecologically driven spacing patterns at short time scales based on female reproductive status. Together, these findings offer insight into the economics of territoriality by highlighting the dynamics of spacing patterns at differing time scales.
Data from: Resource partitioning confirmed by isotopic signatures allows small mammals to share seasonally flooded meadows
Meadows in river deltas are characterized by a high diversity and abundance of small mammals. However, neither their spatial arrangement nor differences in their use of microhabitat can necessarily explain the dense co‐occurrence of sympatric species. We investigated how several small mammal species share a seasonally flooded meadow of limited size, testing predictions (P1) that herbivore, granivore, insectivore, and omnivore species are separated in time (dominant in different years), (P2) that sympatric species undergo isotopic partitioning, and (P3) that there are intraspecific differences in diet. Stable carbon and nitrogen isotope signatures in the hair of seven synantropic shrew, vole, and mice species were used as a proxy for their diet. We found that the three most abundant species in eight of the nine years were from different diet groups. However, based on the number of species in the functional groups, the state of small mammal community was considered unfavored in five out of the nine investigation years. In years with the greatest dominance of Apodemus agrarius, the small mammal community was characterized by decreased diversity and Micromys minutus was either in low abundance or absent. In 2014 and 2016, years of low abundance or absence of M. oeconomus, M. agrestis, and M. glareolus were both recorded in high numbers. Differences in the isotopic signatures of the three most abundant small mammal species in the community were clearly expressed and core areas in the isotopic space were separated, showing their dependence on different dietary resources. Intraspecific dietary separation between young and adult animals was observed only in M. oeconomus. Thus, the high species diversity of small mammals and the formation of their community in this investigated flooded meadow are maintained by isotopic partitioning (segregation in dietary space) and by changes in their number over time (shifting dominance).
Data from: Assessing feeding preferences of a consumer guild: partitioning variation among versus within species
Interspecific variation in resource use is critical to understanding species diversity, coexistence, and ecosystem functioning. A growing body of research describes analogous intraspecific variation and its potential importance for population dynamics and community outcomes. However, the magnitude of intraspecific variation relative to interspecific variation in key dimensions of consumer-resource interactions remains unknown, and is critical for understanding the importance of this variation for population and community processes. In this study, we examine feeding preference through repeated laboratory choice feeding assays of 444 wild-caught individuals of eight invertebrate grazer species on rocky reefs in northern California, USA. Between-species variation accounted for 25-33% of the total variation in preference for the preferred resource, while between-individual variation accounted for 4-5% of total variation. For two of the eight species, between-individual variation was significantly different from zero and contributed on-average 14% and 17% of the total diet variation, even after accounting for differences due to size and sex. Therefore, even with clearly distinguishable between-species differences in mean preference, diet variation between and within individuals can contribute to the dietary niche width of species and guilds, which may be overlooked by focusing solely on species' mean resource use patterns.
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