Partitioning the variation among spatial,temporal and environmental components in a multivariate data set

Abstract We propose a method of partitioning the variation in a multivariate set of data according to (i) environmental variables, (ii) variables describing the spatial structure in the data and (iii) temporal variables. This method is an extension of an existing method for partialling out the spatial component of environmental variation, using canonical analysis. Our proposed method extends this approach by including temporal variables in the analysis. Thus, the partitioning of variation for a data matrix of species’abundances or biomass can include, by our methodology, the following components: (1) pure environmental, (2) pure spatial, (3) pure temporal, (4) pure spatial component of environmental, (5) pure temporal component of environmental, (6) pure combined spatial/temporal component, (7) combined spatial/temporal component of environmental and (8) unexplained. In addition, permutation testing accompanying the analyses allows tests of significance for the relationship between the different components and the species data. We illustrate the method with a set of survey data of penaeid species (prawns) obtained on the far northern Great Barrier Reef, Australia. This extension is a useful tool for multivariate analysis of ecological data from surveys, where space, time and environment commonly overlap and are important influences on observed variation.     

Craniometric variation in the Americas

Craniofacial variation is investigated in Latin America and the Caribbean. The samples included in this study are two historic and one prehistoric sample from Ecuador; prehistoric and modern Cuban samples; a prehistoric Peruvian sample; two prehistoric Mexican samples and one contemporary admixed Mexican sample; a 16th/17th-century Spanish sample; and Terry blacks. Biological distance is investigated using traditional craniometrics by computing size and shape variables according to Mosimann and colleagues. This study shows that there is much biological variation within the Americas.     

Craniometric variation in the Eurasian badger, Meles meles

A multivariate examination of cranial variation within and between European populations of Meles meles (L.) revealed that populations from Ireland, Great Britain, Norway, and the Slovak Republic could be differentiated both by cranial form and by the degree of sexual dimorphism exhibited. Irish material was characterized by low sexual dimorphism, particularly when compared to Slovak specimens. Badgers from the British Isles had larger skulls than other samples and were more similar to each other than they were to badgers from mainland Europe. Size played a greater role in differentiating samples of female badgers than it did in males. Significant variation occurred within the British Isles, with individual samples being highly differentiable. There was, however, little relationship between morphological similarity and geographic proximity. We contend that macrogeographical (between-country) variation in the species is primarily determined by historical factors and adaptation to current conditions, while microgeographic (within-country) variation is a result of selectively neutral processes.     

The Phlesirtes complex (Orthoptera,Tettigoniidae, Conocephalinae,Conocephalini) reviewed: integrating morphological,molecular, chromosomal and bioacoustic data

The tettigoniid genus Phlesirtes Bolivar and its allies are reviewed. Morphological, ecological and molecular data prompt the erection of the new genus Chortoscirtes gen.n. with type species Xiphidion meruense Sjöstedt. The genera Phlesirtes, Chortoscirtes, Karniella and Naskreckiella are characterized by morphological characters supported by molecular, acoustic, ecological and chromosomal data. Four species, Chortoscirtes pseudomeruensis sp.n. , C. masaicus sp.n. , C. puguensis sp.n. and C. serengeti sp.n. , are described from localities in northern and coastal Tanzania and one Karniella, K. crassicerca sp.n. , is described from Uganda. The following comb n. are proposed: Phlesirtes kibonotensis (Sjöstedt) and Phlesirtes kilimandjaricus (Sjöstedt). Subtribal status is proposed for the four investigated African genera. A key to the Chortoscirtes species is provided.     

A new genus of African Karniellina (Orthoptera,Tettigoniidae, Conocephalinae,Conocephalini): integrating morphological,molecular and bioacoustical data

Melanoscirtes gen.n. is established within Karniellina. The members of this subtribe are small conocephaline bush crickets, confined to Africa. Melanoscirtes is erected on Phlesirtes kibonotensis, a species restricted to forest clearings and forest edge in the submontane and montane zones of Mt. Kilimanjaro. A subspecies, M. kibonotensis uguenoensis, is described from the North Pare mountains, a mountain range of the Eastern Arc adjacent to Mt. Kilimanjaro. Further species of Melanoscirtes occur on other mountain ranges of the northern branch of the Eastern Arc mountains of northern Tanzania and southern Kenya. The South Pare mountains harbour M. shengenae; the West Usambaras, M. usambarensis, and the Taita Hills, M. taitensis. All species and subspecies of Melanoscirtes exhibit a similar morphology and occupy analogous habitats on the respective mountains. The song patterns for all species found within this genus are very similar, and this, together with evidence from molecular data, suggests that allopatric speciation is the reason for the biogeographic pattern found in this genus. A key for the subspecies and species of Melanoscirtes is provided.     

Probability distributed time delays: integrating spatial effects into temporal models

Background  

In order to provide insights into the complex biochemical processes inside a cell, modelling approaches must find a balance between achieving an adequate representation of the physical phenomena and keeping the associated computational cost within reasonable limits. This issue is particularly stressed when spatial inhomogeneities have a significant effect on system's behaviour. In such cases, a spatially-resolved stochastic method can better portray the biological reality, but the corresponding computer simulations can in turn be prohibitively expensive.     

Community structure in north temperate ants: temporal and spatial variation

Summary Ant communities in Vermont and New York woods were sampled in four time periods to determine species composition, relative abundances, and nest locations in space. The Vermont community was richer, containing more species and higher nest densities than New York. Both communities followed the geometric distribution of species abundances, suggesting that a single resource was mediating competition. The resource most clearly implicated was suitable nest sites, principally pre-formed plant cavities. Nonrandom species associations, underdispersion in every season, and the occurrence of incipient nests overwintering aboveground all implicated shortage of such cavities. Furthermore, microhabitat differences which produce suitable nest sites occur over a very small scale in these communities.     

Characterizing the spatial and temporal variation of malaria incidence in Bangladesh, 2007

ABSTRACT: BACKGROUND: Malaria remains a significant health problem in Bangladesh affecting 13 of 64 districts. The risk of malaria is variable across the endemic areas and throughout the year. A better understanding of the spatial and temporal patterns in malaria risk and the determinants driving the variation are crucial for the appropriate targeting of interventions under the National Malaria Control and Prevention Programme. METHODS: Numbers of Plasmodium falciparum and Plasmodium vivax malaria cases reported by month in 2007, across the 70 endemic thanas (sub-districts) in Bangladesh, were assembled from health centre surveillance reports. Bayesian Poisson regression models of incidence were constructed, with fixed effects for monthly rainfall, maximum temperature and elevation, and random effects for thanas, with a conditional autoregressive prior spatial structure. RESULTS: The annual incidence of reported cases was 34.0 and 9.6 cases/10,000 population for P. falciparum and P. vivax respectively and the population of the 70 malaria-endemic thanas was approximately 13.5 million in 2007. Incidence of reported cases for both types of malaria was highest in the mountainous south-east of the country (the Chittagong Hill Tracts). Models revealed statistically significant positive associations between the incidence of reported P. vivax and P. falciparum cases and rainfall and maximum temperature. CONCLUSIONS: The risk of P. falciparum and P. vivax was spatially variable across the endemic thanas of Bangladesh and also highly seasonal, suggesting that interventions should be targeted and timed according to the risk profile of the endemic areas. Rainfall, temperature and elevation are major factors driving the spatiotemporal patterns of malaria in Bangladesh.     

The diatoms ingested by freshwater snails: temporal,spatial, and interspecific variation

Seventeen species of diatoms, representing a broad range of sizes, shapes, and growth habits, were collected from rocks in rapidly-flowing sections of the Mitchell River, North Carolina. The diatoms ingested by adult Goniobasis proxima, juvenile Leptoxis carinata, and adult Physa sp. co-occurring in this habitat were indistinguishable from one another, in spite of great differences in radular morphology. All snails sampled the diatom flora almost randomly, with only one or two of the larger diatom species under-represented in the gut contents. Some snails also seemed to selectively ingest the smaller individuals of the larger diatom taxa, and larger individuals of the smaller diatom taxa. The diatoms identifiable in juvenile Goniobasis guts were somewhat more distinctive, although this seemed to be due at least partly to more mechanical breakage. The diatom flora of quiet, muddy pools was much different from that of shallow, rocky areas, but once again, Goniobasis seemed to sample the available flora randomly. Seasonal variation was also apparent in the diatom diet of Goniobasis. We suggest that in some cases, it may be reasonable to use snails to sample the diatom assemblage present in a particular habitat, if more direct methods are impractical.     

Olfactory coding in the insect brain: molecular receptive ranges, spatial and temporal coding

Odor information is coded in the insect brain in a sequence of steps, ranging from the receptor cells, via the neural network in the antennal lobe, to higher order brain centers, among which the mushroom bodies and the lateral horn are the most prominent. Across all of these processing steps, coding logic is combinatorial, in the sense that information is represented as patterns of activity across a population of neurons, rather than in individual neurons. Because different neurons are located in different places, such a coding logic is often termed spatial, and can be visualized with optical imaging techniques. We employ in vivo calcium imaging in order to record odor‐evoked activity patterns in olfactory receptor neurons, different populations of local neurons in the antennal lobes, projection neurons linking antennal lobes to the mushroom bodies, and the intrinsic cells of the mushroom bodies themselves, the Kenyon cells. These studies confirm the combinatorial nature of coding at all of these stages. However, the transmission of odor‐evoked activity patterns from projection neuron dendrites via their axon terminals onto Kenyon cells is accompanied by a progressive sparsening of the population code. Activity patterns also show characteristic temporal properties. While a part of the temporal response properties reflect the physical sequence of odor filaments, another part is generated by local neuron networks. In honeybees, γ‐aminobutyric acid (GABA)‐ergic and histaminergic neurons both contribute inhibitory networks to the antennal lobe. Interestingly, temporal properties differ markedly in different brain areas. In particular, in the antennal lobe odor‐evoked activity develops over slow time courses, while responses in Kenyon cells are phasic and transient. The termination of an odor stimulus is reflected by a decrease in activity within most glomeruli of the antennal lobe and an off‐response in some glomeruli, while in the mushroom bodies about half of the odor‐activated Kenyon cells also exhibit off‐responses.     

Sampling spatial and temporal variation in soil nitrogen availability

There are few studies in natural ecosystems on how spatial maps of soil attributes change within a growing season. In part, this is due to methodological difficulties associated with sampling the same spatial locations repeatedly over time. We describe the use of ion exchange membrane spikes, a relatively nondestructive way to measure how soil resources at a given point in space fluctuate over time. We used this method to examine spatial patterns of soil ammonium (NH⁺ ₄) and nitrate (NO⁻ ₃) availability in a mid-successional coastal dune for four periods of time during the growing season. For a single point in time, we also measured soil NH⁺ ₄ and NO⁻ ₃ concentrations from soil cores collected from the mid-successional dune and from an early and a late successional dune. Soil nitrogen concentrations were low and highly variable in dunes of all ages. Mean NH⁺ ₄ and NO⁻ ₃ concentrations increased with the age of the dune, whereas coefficients of variation for NH⁺ ₄ and NO⁻ ₃ concentrations decreased with the age of the dune. Soil NO⁻ ₃ concentration showed strong spatial structure, but soil NH⁺ ₄ concentration was not spatially structured. Plant-available NH⁺ ₄ and NO⁻ ₃ showed relatively little spatial structure: only NO⁻ ₃ availability in the second sampling period had significant patch structure. Spatial maps of NH⁺ ₄ and NO⁻ ₃ availability changed greatly over time, and there were few significant correlations among soil nitrogen availability at different points in time. NO⁻ ₃ availability in the second sampling period was highly correlated (r = 0.90) with the initial soil NO⁻ ₃ concentrations, providing some evidence that patches of plant-available NO⁻ ₃ may reappear at the same spatial locations at irregular points in time. Received: 20 February 1998 / Accepted: 23 November 1998     

Challenges in integrating Escherichia coli molecular biology data

One key challenge in Systems Biology is to provide mechanisms to collect and integrate the necessary data to be able to meet multiple analysis requirements. Typically, biological contents are scattered over multiple data sources and there is no easy way of comparing heterogeneous data contents. This work discusses ongoing standardisation and interoperability efforts and exposes integration challenges for the model organism Escherichia coli K-12. The goal is to analyse the major obstacles faced by integration processes, suggest ways to systematically identify them, and whenever possible, propose solutions or means to assist manual curation. Integration of gene, protein and compound data was evaluated by performing comparisons over EcoCyc, KEGG, BRENDA, ChEBI, Entrez Gene and UniProt contents. Cross-links, a number of standard nomenclatures and name information supported the comparisons. Except for the gene integration scenario, in no other scenario an element of integration performed well enough to support the process by itself. Indeed, both the integration of enzyme and compound records imply considerable curation. Results evidenced that, even for a well-studied model organism, source contents are still far from being as standardized as it would be desired and metadata varies considerably from source to source. Before designing any data integration pipeline, researchers should decide on the sources that best fit the purpose of analysis and be aware of existing conflicts/inconsistencies to be able to intervene in their resolution. Moreover, they should be aware of the limits of automatic integration such that they can define the extent of necessary manual curation for each application.     

Factors influencing initial larval settlement: temporal, spatial and surface molecular components

The impact of initial surface chemistry on settlement of barnacle, bryozoan, and hydroid larvae was assessed. Temporal (on a scale of weeks to months) and fine scale spatial (centimeter to meter) variation in settlement were quantified. Four arrays of silanized glass surfaces, deployed at ≈2-wk intervals, were monitored after 1 and 3 days of immersion. Settlement of all larval types exhibited strong temporal variation. There was a 25, 22- and 18-fold difference between the highest and lowest Day 1 settlement for barnacles, bryozoans and hydroids, respectively. Bryozoan and hydroid settlement was spatially variable, barnacle settlement was not. Barnacle and bryozoan settlement was influenced by inttial surface chemistry, hydroid settlement was not. For barnacles, there was a 2-fold difference between total settlement over the four arrays on untreated glass and diphenyl-silanized surfaces; for bryozoans, there was a 51-fold difference, and in the opposite direction. There was a negative correlation between barnacle and bryozoan settlement with respect to surface. This result was independent of the presence of the other species. Bryozoan settlement was also spatially and temporally quantified in a separate, single surface 56-h array, and total bryozoan settlement ·h⁻¹ was found to be correlated with light intensity. Patterns of initial colonization were strongly influenced by surface chemistry and spatial temporal variation in larval supply. These effects on initial colonization may influence subsequent community development.     

Rocky intertidal fish communities of California: temporal and spatial variation

Synopsis We examined data from our own and published collections of intertidal and shallow littoral fishes of the North American Pacific Coast with respect to temporal and spatial trends in species composition and dominance. We compared (1) recent and past intertidal collections made five and seven years apart, respectively, for two California localities, (2) intertidal collections from twelve localities in California, Oregon, and British Columbia, and (3) intertidal versus subtidal collections at one California locality. Temporal comparisons indicated substantially lower abundance of the cottid Oligocottus snyderi at two California localities during 1984, at one locality due to depressed abundance of young. Interannual differences in abundances suggested that other tidepool fish assemblages undergo significant changes as well. Geographical comparisons indicated general similarity in species composition, with cottids predominating in tidepools although several other families also were well represented (e.g., Stichaeidae, Scorpaenidae). Eel-shaped stichaeids and pholids occurred at high densities in exposed boulder fields. Both the tidepool and boulder field assemblages showed north-south changes in species abundances. Comparison of collections from the intertidal and subtidal zones at one California locality demonstrated that fishes of these habitats form two essentially distinct assemblages, with most species restricted to or concentrated in one or the other habitat.     

Monitoring rocky-shore communities: a critical look at spatial and temporal variation

Increasingly programmes are being set up to monitor rocky-shore communities in order to provide baseline data which will indicate changes resulting from subsequent pollution. However, these efforts are complicated by several factors. Firstly, there are overall changes in the composition of communities both within and between years. Secondly, there is variation within certain communities due to a mosaic distribution of components, the mosaic format changing continuously with a cycle of several years. This paper reports on studies of a medium-exposed rocky shore in the Isle of Man (U. K.). It describes patterns of spatial and temporal variation, and looks at certain implications for monitoring programmes: (a) the frequency of sampling, and the duration of the sampling programme, in the light of seasonal and long-term variation; (b) the efficiency, in terms of the minimisation of variability, of sampling the same area by different strategies — belt transects, small random quadrats, single large quadrat; (c) the effect of the distribution patterns of some commoner species on the variation between samples.     

Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity

Background

Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats.

Methodology/Principal Findings

A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various saber-toothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats.

Conclusions/Significance

Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional diversity studies, and may reveal novel patterns of morphospace occupation.     

Concordance of molecular and morphological data: The example of the Acoela

Morphological features of the Acoela appear to be quite plastic, including those of the copulatory organs, which provide the principle characteristics used for the systematics of this group. Consequently, classification schemes of the Acoela comprise numerous polyphyletic groupings. In this review, we detail recent revisions of acoel systematics using molecular sequence data and new and reevaluated morphological characteristics. Gene trees are discordant with traditional systematic schemes but strongly concordant with new morphological characteristics obtained through the use of transmission electron microscopy and confocal laser scanning microscopy, namely, characteristics of body-wall and copulatory organ musculature, sperm, sperm ducts, sagittocysts, and immunocytochemistry of the nervous system. This merger of molecular and morphological data has led to significant changes in acoel classification, including a major emendation of the largest family of the Acoela, the Convolutidae, whereby half of its members were transferred to a newly created family, the Isodiametridae.     

Resource storage and competition with spatial and temporal variation in resource availability

This study addresses interspecific competition for a nutrient resource that is stored within individuals in habitats with both temporal and spatial variation. In such environments, population structure is induced by the mixture at any location of individuals with different amounts of stored nutrient, acquired elsewhere in the habitat. Focusing on phytoplankton competing for phosphorus in a partially mixed water column, an individual-based Lagrangian model is used to represent this population structure, and partial differential equations that approximate competitive dynamics are constructed by averaging over this population structure. Although the approximation model overestimates the benefit of resource storage to competitive fitness, both approaches predict that species with high storage capacity are favored by periodic resource pulses that are short lived but large in magnitude. Such storage specialists can competitively exclude or coexist with species that have advantages in maximal nutrient uptake and population growth rates. For very infrequent resource pulses, competitive dynamics become close to neutral. Thus, persistence of diverse species that are differentiated in nutrient storage and uptake capabilities is favored by resource pulses occurring with periods that are many times the average generation time of competitors.     

Prediction of drug combinations by integrating molecular and pharmacological data

Combinatorial therapy is a promising strategy for combating complex disorders due to improved efficacy and reduced side effects. However, screening new drug combinations exhaustively is impractical considering all possible combinations between drugs. Here, we present a novel computational approach to predict drug combinations by integrating molecular and pharmacological data. Specifically, drugs are represented by a set of their properties, such as their targets or indications. By integrating several of these features, we show that feature patterns enriched in approved drug combinations are not only predictive for new drug combinations but also provide insights into mechanisms underlying combinatorial therapy. Further analysis confirmed that among our top ranked predictions of effective combinations, 69% are supported by literature, while the others represent novel potential drug combinations. We believe that our proposed approach can help to limit the search space of drug combinations and provide a new way to effectively utilize existing drugs for new purposes.