Modeling the flocking propensity of passerine birds in two Neotropical habitats

We examined the importance of mixed-species flock abundance, individual bird home range size, foraging height, and foraging patch characteristics in predicting the propensity for five Neotropical passerine bird species (Slaty Antwren, Myrmotherula schisticolor; Golden-crowned Warbler, Basileuterus culicivorus; Slate-throated Redstart, Myioborus miniatus; Wilson’s Warbler, Wilsonia pusilla; and Black-and-white Warbler, Mniotilta varia) to forage within flocks, rather than solitarily. We used study plots in primary mid-elevation forest and in shade coffee fields in western Panama. We expected that all species would spend as much time as possible flocking, but that the social and environmental factors listed above would limit compatibility between flock movements and individual bird movements, explaining variability in flocking propensity both within and among species. Flocking propensity was well predicted by home range size and flock abundance together, for four of the five species. While flock abundance was uniform across plots, home range sizes varied among species and plots, so that home range size appeared to be the principle factor limiting flocking propensity. Estimates of flock abundance were still required, however, for calculating flocking propensity values. Foraging height and patch characteristics slightly improved predictive ability for the remaining species, M. miniatus. In general, individual birds tended to join flocks whenever one was available inside their home range, regardless of a flock’s specific location within the home range. Flocking propensities of individual species were lower in shade coffee fields than in forests, and probably vary across landscapes with variations in habitat. This variability affects the stability and species composition of flocks, and may affect survival rates of individual species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Epibenthic colonization of concrete and steel pilings in a cold-temperate embayment: a field experiment

With large-scale development of offshore wind farms, vertical structures are becoming more common in open water areas. To examine how vertical structures of different materials may be colonized by epibenthic organisms, an experiment was carried out using steel and concrete pilings constructed to resemble those commonly used in wind farm constructions as well as in bridges, jetties and oil platforms. The early recruitment and succession of the epibenthic communities were sampled once a month for the first 5 months and then again after 1 year. Further, the fish assemblages associated with the pillars were sampled and compared to natural areas. The main epibenthic species groups, in terms of coverage, differed between the two materials at five out of six sampling occasions. Dominant organisms on steel pillars were the barnacle Balanus improvisus, the calcareous tubeworm Pomatoceros triqueter and the tunicate Ciona intestinalis. On the concrete pillars, the hydroid Laomedea sp. and the tunicates Corella parallelogramma and Ascidiella spp. dominated. However, there was no different in coverage at different heights on the pillars or in biomass and species abundance at different directions (north-east or south-west) 5 months after submergence. Fish showed overall higher abundances and species numbers on the pillars (but no difference between steel and concrete) compared to the surrounding soft bottom habitats but not compared to natural vertical rock walls. Two species were attracted to the pillars, indicating a reef effect; Gobiusculus flavescens and Ctenolabrus rupestris. The bottom-dwelling gobies, Pomatoschistus spp., did not show such preferences. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Redesigning the photosynthetic light reactions to enhance photosynthesis – the PhotoRedesign consortium

In this Perspective article, we describe the visions of the PhotoRedesign consortium funded by the European Research Council of how to enhance photosynthesis. The light reactions of photosynthesis in individual phototrophic species use only a fraction of the solar spectrum, and high light intensities can impair and even damage the process. In consequence, expanding the solar spectrum and enhancing the overall energy capacity of the process, while developing resilience to stresses imposed by high light intensities, could have a strong positive impact on food and energy production. So far, the complexity of the photosynthetic machinery has largely prevented improvements by conventional approaches. Therefore, there is an urgent need to develop concepts to redesign the light-harvesting and photochemical capacity of photosynthesis, as well as to establish new model systems and toolkits for the next generation of photosynthesis researchers. The overall objective of PhotoRedesign is to reconfigure the photosynthetic light reactions so they can harvest and safely convert energy from an expanded solar spectrum. To this end, a variety of synthetic biology approaches, including de novo design, will combine the attributes of photosystems from different photoautotrophic model organisms, namely the purple bacterium Rhodobacter sphaeroides, the cyanobacterium Synechocystis sp. PCC 6803 and the plant Arabidopsis thaliana. In parallel, adaptive laboratory evolution will be applied to improve the capacity of reimagined organisms to cope with enhanced input of solar energy, particularly in high and fluctuating light.     

Fine structure of the ventral nerve centre and interspecific identification of individual neurons in the enigmatic Chaetognatha

The enigmatic arrow worms (Chaetognatha) are marine carnivores and among the most abundant planktonic organisms. Their phylogenetic position has been heavily debated for a long time. Most recent molecular studies still provide a diverging picture and suggest arrow worms to be some kind of basal protostomes. In an effort to understand the organization of the nervous system in this clade for a broad comparison with other Metazoa we analysed the ultrastructure of the ventral nerve centre in Spadella cephaloptera by transmission electron microscopy. We were able to identify six different types of neurons in the bilateral somata clusters by means of the cytoplasmic composition (regarding the structure of the neurite and soma including the shape and eu-/heterochromatin ratio within the nucleus) as well as the size and position of these neurons. Furthermore, our study provides new insights into the neuropil composition of the ventral nerve centre and several other fine structural features. Our second goal was to examine if individually identifiable neurons are present in the ventral nerve centres of four chaetognath species, Sagitta setosa, Sagitta enflata, Pterosagitta draco, and Spadella cephaloptera. For that purpose, we processed whole mount specimens of these species for immunolocalization of RFamide-related neuropeptides and analysed them with confocal laser-scanning microscopy. Our experiments provide evidence for the interspecific homology of individual neurons in the ventral nerve centres of these four chaetognath species suggesting that the potential to generate serially arranged neurons with individual identities is part of their ground pattern.     

Metabolite analysis for the comparison of irrigated and non-irrigated field grown tomato of varying genotype

Every year the consequences of water deficit on crop yield and quality are profound. The observation that many wild species relatives of cultivated crops display a greater stress tolerance and the fact that the cultivated species generally display only a fraction of the allelic diversity available within the tomato clade suggest that crossing of wild species with elite cultivars could improve the stress physiology of modern crops. To assess this from the basis of chemical composition we applied an established GC-MS based metabolite profiling method to fruits from irrigated and non-irrigated tomato plants either of the cultivated tomato (Solanum lycopersicum) or of its hybrid with its wild species relative (Solanum pennellii). Results are discussed in terms of both the metabolic response to drought stress and the potential of utilizing exotic germplasm as a means to improve agronomically important characteristics of crop species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Biomass responses to elevated CO<Subscript>2</Subscript>, soil heterogeneity and diversity: an experimental assessment with grassland assemblages

While it is well-established that the spatial distribution of soil nutrients (soil heterogeneity) influences the competitive ability and survival of individual plants, as well as the productivity of plant communities, there is a paucity of data on how soil heterogeneity and global change drivers interact to affect plant performance and ecosystem functioning. To evaluate the effects of elevated CO₂, soil heterogeneity and diversity (species richness and composition) on productivity, patterns of biomass allocation and root foraging precision, we conducted an experiment with grassland assemblages formed by monocultures, two- and three-species mixtures of Lolium perenne, Plantago lanceolata and Holcus lanatus. The experiment lasted for 90 days, and was conducted on microcosms built out of PVC pipe (length 38 cm, internal diameter 10 cm). When nutrients were heterogeneously supplied (in discrete patches), assemblages exhibited precise root foraging patterns, and had higher total, above- and belowground biomass. Greater aboveground biomass was observed under elevated CO₂. Species composition affected the below:aboveground biomass ratio and interacted with nutrient heterogeneity to determine belowground and total biomass. Species richness had no significant effects, and did not interact with either CO₂ or nutrient heterogeneity. Under elevated CO₂ conditions, the two- and three-species mixtures showed a clear trend towards underyielding. Our results show that differences among composition levels were dependent on soil heterogeneity, highlighting its potential role in modulating diversity–productivity relationships. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible to authorized users.     

Variation in the structure of epifaunal invertebrate assemblages among coral hosts

The high biodiversity of coral reefs is attributable to the many invertebrate groups which live in symbiotic relationships with other reef organisms, particularly those which associate with the living coral habitat. However, few studies have examined the diversity and community structure of coral-dwelling invertebrates and how they vary among coral species. This study quantified the species richness and composition of animals associated with four common species of branching corals (Acropora nasuta, A. millepora, Pocillopora damicornis, and Seriatopora hystrix) at Lizard Island in the northern Great Barrier Reef. One hundred and seventy-eight nominal species from 12 different phyla were extracted across 50 replicate colonies of each coral host. A single coral colony, approximately 20 cm in diameter, harbored as many as 73 individuals and 24 species. There were substantial differences in invertebrate species composition among coral hosts of different families as well as genera. Twenty-seven species (15% of all taxa collected) were found on only one of the four different coral species, which may potentially indicate some level of specialization among coral hosts. The distinct assemblages on different coral species, and the presence of potential specialists, suggests invertebrate communities will be sensitive to the differential loss of branching coral species resulting from coral reef degradation.     

Resource distribution and the trade-off between seed number and seed weight: a comparison across crop species

In grain crops, total sink capacity is usually analysed in terms of two components, seed number and individual seed weight. Seed number and potential individual seed weight are established at a similar timing, around the flowering period, and seed weight at maturity is highly correlated with the potential established earlier. It is known that, within a species, available resources during the seed set period are distributed between both yield components, resulting in a trade-off between seed number and seed weight. Here we tested if this concept could apply for interspecific comparisons, where combinations of numbers and size across species could be related to the total available resources being either allocated to more seed or larger potential individual seed weight during the seed set period. Based on this, species differences in seed weight should be related to resource availability per seed around the period when seed number is determined. Resource availability per seed was estimated as the rate of increase in aboveground biomass per seed around the period of seed set. Data from 15 crop species differing in plant growth, seed number, seed weight and seed composition were analysed from available literature. Because species differed in seed composition, seed weight was analysed following an energy requirement approach. There was an interspecific trade-off relationship between seed number per unit of land area and seed weight (r = 0.92; F(1, 13) = 32.9; n = 15; P < 0.001). Seed weight of different species was positively correlated (r = 0.90; F(1, 13) = 52.9; n = 15; P < 0.001) with resource availability per seed around the seed set period. This correlation included contrasting species like quinoa (Chenopodium quinoa; ∼100000 seeds m⁻², ∼4 mg equivalent-glucose seed⁻¹) or peanut (Arachis hypogaea; ∼800 seeds m⁻², ∼1000 mg equivalent-glucose seed⁻¹). Seed number and individual seed weight combinations across species were related and could be explained considering resource availability when plants are adjusting their seed number to the growth environment and seeds are establishing their storage capacity. Available resources around the seed set period are proportionally allocated to produce either many small seeds or few larger seeds depending on the particular species.     

Variability in Mediterranean annual grassland diversity driven by small-scale changes in fertility and radiation

Using the small-scale gradients in light and fertility imposed by the presence of trees on Mediterranean open oak woodlands, we studied differences in the ecology, floristic diversity and species composition of an annual grassland, and modeled plant relationships with soil properties and radiation using generalized linear models. The strong intra-annual variability in the annual grassland greatly affected overall floristic diversity estimates. Therefore, sampling at least twice during the annual growing period was important to avoid underestimating floristic composition. As has been found in previous studies, different groups of grasses were clearly shaped as a response to the ecological gradient created by the influence of the tree. However, when analyzing specific relationships, only a few individual species directly responded to the studied soil and light availability factors analyzed. Among them, those species considered ‘ruderal’ such as Carduus tenuiflorus, Echium plantagineum, Lolium rigidum, Rumex bucephalophorus, and Tolpis barbata showed a clear response to some nutrients and to light availability but displayed no relationship to N soil content. Our results suggest that individual species are responding to a combination of ecological factors. Therefore, some of the generally accepted assumptions regarding the ecology of specific taxa may not be as straightforward as traditionally considered.     

Identification of a <Emphasis Type="Italic">Lotus</Emphasis> viral pathogen

A virus collection was used to identify a pathogen suitable for laboratory use with the model legume Lotus japonicus. Several Lotus species or L. japonicus accessions were tested and various degrees of susceptibility to the Arabis mosaic virus derived from barley (ArMV-ba) were found. Virus multiplication and persistence in Lotus tissue were examined, as well as plant responses to it. Sensitivity to the virus among the accessions and species is discussed in light of their geographical origin. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effect of different light regimes on fitness of two species of Drosophila montium subgroup

Most organisms possess “biological chronometers” in the form of circadian clocks. Organism possessing circadian clock gains fitness advantage in two ways, by synchronizing its behavior through physiological process and secondly by coordinating its internal metabolic process. Environmental manipulations of circadian clocks have been shown to affect many life-history-related traits. Life-history traits are important components of fitness. To enhance individual fitness, organism has to synchronize the physiology with the surrounding environment. The present investigations were made to understand whether rhythm changes affect fitness of two co-existing species of montium a subgroup of Drosophila. The stocks were maintained at 20 ± 1 °C with 75% RH. Fitness such as fecundity, male lifetime fertility, female lifetime fertility, and longevity was assessed in LD (light/dark), LL (continuous light), and DD (continuous dark) for 15 and 30th generations. Fecundity was assessed in 25 pairs of flies for 20 days, and fertility and longevity was assessed in 10 pairs of flies until lifetime. The result revealed differential effect of light regimes on the two different species of Drosophila. Although the two species are related, effect of the three light regimes, LD, LL, and DD on them was different. It is evident that these two species although genetically related exhibit different responses to different light regimes.     

Pigment composition and photoacclimation as keys to the ecological success of Gonyostomum semen (Raphidophyceae,Stramenopiles)

Aquatic habitats are usually structured by light attenuation with depth resulting in different microalgal communities, each one adapted to a certain light regime by their specific pigment composition. Several taxa contain pigments restricted to one phylogenetic group, making them useful as marker pigments in phytoplankton community studies. The nuisance and invasive freshwater microalga Gonyostomum semen (Raphidophyceae) is mainly found in brown water lakes with sharp vertical gradients in light intensity and color. However, its pigment composition and potential photoadaptations have not been comprehensively studied. We analyzed the photopigment composition of 12 genetically different strains of G. semen by high performance liquid chromatography after acclimation to different light conditions. We confirmed the pigments chl a, chl c1c2, diadinoxanthin, trans‐neoxanthin, cis‐neoxanthin, α and β carotene, which have already been reported for G. semen. In addition, we identified, for the first time, the pigments violaxan‐thin, zeaxanthin, and alloxanthin in this species. Alloxanthin has never been observed in raphidophytes before, suggesting differences in evolutionary plastid acquisition between freshwater lineages and the well‐described marine species. The amount of total chl a per cell generally decreased with increasing light intensity. In contrast, the increasing ratios of the prominent pigments diadinoxanthin and alloxanthin per chl a with light intensity suggest photoprotective functions. In addition, we found significant variation in cell‐specific pigment concentration among strains, grouped by lake of origin, which might correspond to genetic differences between strains and populations.     

Isolation of Bacterial Antagonists of Aspergillus flavus from Almonds

Bacteria were isolated from California almond orchard samples to evaluate their potential antifungal activity against aflatoxin-producing Aspergillus flavus. Fungal populations from the same samples were examined to determine the incidence of aflatoxigenic Aspergillus species. Antagonistic activities of the isolated bacterial strains were screened against a nonaflatoxigenic nor mutant of A. flavus, which accumulates the pigmented aflatoxin precursor norsolorinic acid (NOR) under conditions conducive to aflatoxin production. Using solid and liquid media in coculture assays, 171 bacteria isolated from almond flowers, immature nut fruits, and mature nut fruits showed inhibition of A. flavus growth and/or inhibition of NOR accumulation. Bacterial isolates were further characterized for production of extracellular enzymes capable of hydrolyzing chitin or yeast cell walls. Molecular and physiological identification of the bacterial strains indicated that the predominant genera isolated were Bacillus, Pseudomonas, Ralstonia, and Burkholderia, as well as several plant-associated enteric and nonenteric bacteria. A set of 20 isolates was selected for further study based on their species identification, antifungal phenotypes, and extracellular enzyme production. Quantitative assays using these isolates in liquid coculture with a wild-type, aflatoxin-producing A. flavus strain showed that a number of strains completely inhibited fungal growth in three different media. These results indicate the potential for development of bacterial antagonists as biological control agents against aflatoxigenic aspergilli on almonds.     

Experimental Invasions Using Biological Control Introductions: The Influence of Release Size on the Chance of Population Establishment

Introductions of biological control organisms offer a unique opportunity to experimentally study the process of invasion by exotic species. I used two chrysomelid beetles, Galerucella calmariensis and Galerucella pusilla, which are currently being introduced into North America for the biological control of purple loosestrife (Lythrum salicaria), to determine how the initial size of a release affects the probability that the introduced population grows and persists. I released both species into stands of their host plant at 36 sites scattered throughout central New York State using four release sizes: 20, 60, 180, and 540. I returned to these sites over the next 3 years to census the populations. For both species, the probability of population establishment increased with release size. Population growth rates also depended positively on release size. The implication from these results is that the demographic factors whose influence depends on population size or density such as demographic stochasticity, Allee effects, and genetics play important roles in the establishment of invading populations. A second set of releases was used to determine if it was at all possible for a single gravid female to found a population. Out of twenty individual females released, one female (a G. calmariensis) founded a population that persisted until the end of the study (3 generations). This revised version was published online in July 2006 with corrections to the Cover Date.     

不同组成群落3种共有植物光合生理特征研究

为研究物种在不同群落中光合生理特征的变化,以亚高寒草甸围封恢复地为研究对象,对样地内3个不同组成群落进行样方调查,测定了物种高度及各群落垂直方向上光照强度以及群落中3个共有种披碱草(Elymus dahuricus)、刺儿菜(Cirsium setosum)和紫花苜蓿(Medicago sativa)的净光合速率(Aarea)、叶片氮含量(Nmass)、比叶重(LMA)及光合氮利用效率(PNUE)。结果表明:(1)3个样地的群落组成有明显的差异,豆科植物的增多可以一定程度上改善群落氮养分状况,但植物叶片Nmass还受到群落优势种竞争的影响。(2)同一物种在不同群落的高度不同,不同群落垂直方向上光照强度也不相同,导致同一物种在不同群落中能够获得的光照强度有一定差异。(3)在养分、光照强度有差异的情况下,不同植物的Aarea、LMA及PNUE在不同群落中的变化趋势不尽相同,而Narea与Aarea的关系在总体上、群落间及物种间变化不大,基本上显示了较强的正相关关系。由此可见,群落组成、结构引起的光照及氮素差异是导致同一物种光合生理特征在不同群落中变化的重要因素,但不同物种光合生理特征对光照及氮素变化的响应不同。     

Species effects on nitrogen cycling: a test with perennial grasses

Summary To test for differing effects of plant species on nitrogen dynamics, we planted monocultures of five perennial grasses (Agropyron repens, Agrostis scabra, Poa pratensis, Schizachyrium scoparium, and Andropogon gerardi) on a series of soils ranging from sand to black soil. In situ net N mineralization was measured in the monocultures for three years. By the third year, initially identical soils under different species had diverged up to 10-fold in annual net mineralization. This divergence corresponded to differences in the tissue N concentrations, belowground lignin concentrations, and belowground biomasses of the species. These results demonstrate the potential for strong feedbacks between the species composition of vegetation and N cycling. If individual plant species can affect N mineralization and N availability, then competition for N may lead to positive or negative feedbacks between the processes controlling species composition and ecosystem processes such as N and C cycling. These feedbacks create the potential for alternative stable states for the vegetation-soil system given the same initial abiotic conditions.     

Spatial gradients in species diversity of microscopic animals: the case of bdelloid rotifers at high altitude

Aim Organisms smaller than 2 mm appear not to follow the spatial patterns in richness and diversity commonly observed in macroscopic organisms. We describe spatial patterns in species diversity in a group of microscopic organisms, bdelloid rotifers, living in moss and lichen patches, in order to test the hypotheses of no relationship between species richness and composition and spatial gradients, suggested by previously published patterns in microscopic organisms. Location Moss and lichen patches as habitats for bdelloids, on high‐elevation peaks at altitudes between 2984 and 4527 m a.s.l. across the Italian, French and Swiss Alps, with distances among sample sites ranging from 1 m to 420 km, in comparison with lower‐elevation samples at altitudes from 850 to 1810 m a.s.l. Methods We sampled species assemblages of bdelloid rotifers living in isolated moss and lichen patches in 47 sites. We described the observed α, β and γ diversities; the heterogeneity of species assemblages; and the estimated number of species (incidence‐based coverage estimator). Patterns in species distribution were analysed at three different levels: (1) habitat, comparing species richness on moss and lichen substrates, testing differences in α diversity and heterogeneity (anova ), species composition (analysis of similarities test), and γ diversity (rarefaction curves); (2) altitude, comparing the observed richness with previously published data from locations well below 2000 m; and (3) distances between sites, correlating the matrix of Jaccard dissimilarities and the matrix of geographical distances with a Mantel test. Results Both species richness and species composition of bdelloid rotifers differed significantly between mosses and lichens at high elevations, but no difference was found in the heterogeneity of species assemblages. Alpha diversity was significantly lower at high‐elevation than at low‐elevation sites, but the estimated number of species was not reduced when compared with sites at low elevations. Geographical distance between sites had no effect on species composition in either mosses or lichens. The distribution of species was highly heterogeneous, with a low similarity among assemblages. Main conclusions As expected, bdelloids appear to occupy habitats selectively. The altitudinal gradient in species richness for bdelloid rotifers is limited to a decrease in α diversity only; such a decrease is not caused by a lower number of species (low γ diversity) being able to tolerate harsh conditions, and high‐altitude species are not a subset of species living at lower elevations. The observed values of α, β and γ diversity at high altitudes in the Alps are compatible with the scenario of a very low number of available propagules because of the low density of patches of favourable habitat. Our results suggest that the geographical distribution of animals, and therefore biodiversity patterns, may be strongly influenced by animal size, as small organisms such as bdelloids appear to show spatial patterns that differ from those known in larger animals. Differences in body size should be taken into account carefully in future studies of biodiversity patterns.     

The ecology of ruffe,Gymnocephalus cernuus (Pisces: Percidae) introduced to Mildevatn,western Norway

Synopsis Diet, habitat use, diel and seasonal activity and a number of population parameters were studied on ruffe,Gymnocephalus cernuus, introduced to Mildevatn, western Norway. This lake is sited outside the natural range of the ruffe and has a lower fish diversity and a different fish species composition than within its native range. From June through September the ruffe was planktivorous and mainly caught at 4 to 6 m depth in the benthic zone. At other times of year ruffe was feeding on zoobenthos and caught deeper in the benthic zone. Ruffe was mainly day active. Zooplankton feeding during summer is the clearest difference compared to ruffe populations living within its natural range. Presence of large zooplankton organisms available for ruffe is suggested as the main reason for the difference found in food choice. The availability of large zooplankton is probably due to community structure caused by a predator and lack of interspecific competition for zooplankton in the deeper parts of the lake. Piscivorous brown trout.Salmo trutta, restrict the habitat of threespined stickleback,Gasterosteus aculeatus, to the zone of littoral vegetation, allowing high densities of larger zooplankton species likeBythotrephes longimanus to be present in the lake. Brown trout is present only in the upper light and well oxygenated parts of the lake, leaving a refuge for the ruffe, where they can feed on the rich zooplankton community.     

Effects of gastropod grazers on recruitment and succession of an estuarine assemblage: a multivariate and univariate approach

Grazers have been shown to affect assemblages of species in many habitats. Here we studied the effects of the gastropod grazers, Austrocochlea porcata and Bembicium auratum, on intertidal estuarine assemblages in a sheltered bay in New South Wales, Australia. We examined the effects of gastropods on individual species and on the assemblage as a whole. The multivariate response was compared with data on succession in these assemblages to estimate potential effects of grazers on succession. The experiment was repeated several times to determine the generality of grazer effects in the light of possible variation in the timing or intensity of recruitment. There were different responses of individual species to the presence of grazers. Grazers reduced the abundance of ephemeral algal species, bryozoans, copepods, insect larvae and Balanus spp. barnacles. They had a positive effect on oysters and spirorbids and no effect on the barnacles Elminius covertus and Hexaminius spp. These effects were consistent through time. Multivariate analyses confirmed that grazers caused significant changes to whole assemblages and that these effects were far-reaching and not only caused by changes to algal species. The removal of grazers appeared to neither speed up nor slow down succession, but rather caused a completely different assemblage to develop. Apparent important mechanisms affecting the composition of animal species when grazers were removed included accumulation of sediments and detritus and pre-emption of space by algae. Received: 13 May 1996 / Accepted: 1 September 1996     

OrthoClust: an orthology-based network framework for clustering data across multiple species

Increasingly, high-dimensional genomics data are becoming available for many organisms.Here, we develop OrthoClust for simultaneously clustering data across multiple species. OrthoClust is a computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific. We demonstrate the application of OrthoClust using the RNA-Seq expression profiles of Caenorhabditis elegans and Drosophila melanogaster from the modENCODE consortium. A potential application of cross-species modules is to infer putative analogous functions of uncharacterized elements like non-coding RNAs based on guilt-by-association.

Electronic supplementary material

The online version of this article (doi:10.1186/gb-2014-15-8-r100) contains supplementary material, which is available to authorized users.