Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes

Comparative genomics of multiple related species is a powerful methodology for the discovery of functional genomic elements, and its power should increase with the number of species compared. Here, we use 12 Drosophila genomes to study the power of comparative genomics metrics to distinguish between protein-coding and non-coding regions. First, we study the relative power of different comparative metrics and their relationship to single-species metrics. We find that even relatively simple multi-species metrics robustly outperform advanced single-species metrics, especially for shorter exons (≤240 nt), which are common in animal genomes. Moreover, the two capture largely independent features of protein-coding genes, with different sensitivity/specificity trade-offs, such that their combinations lead to even greater discriminatory power. In addition, we study how discovery power scales with the number and phylogenetic distance of the genomes compared. We find that species at a broad range of distances are comparably effective informants for pairwise comparative gene identification, but that these are surpassed by multi-species comparisons at similar evolutionary divergence. In particular, while pairwise discovery power plateaued at larger distances and never outperformed the most advanced single-species metrics, multi-species comparisons continued to benefit even from the most distant species with no apparent saturation. Last, we find that genes in functional categories typically considered fast-evolving can nonetheless be recovered at very high rates using comparative methods. Our results have implications for comparative genomics analyses in any species, including the human.     

Importance of canopy structure on photosynthesis in single- and multi-species assemblages of marine macroalgae

Plant communities utilize available irradiance with different efficiency depending not only on their photosynthetic characteristics but also on the canopy structure and density. The importance of canopy structure are well studied in terrestrial plant communities but poorly studied in aquatic plant communities. The objective of this study was to evaluate macroalgal community photosynthesis in artificial constructed communities of one to four species with different morphologies along a range of leaf (i.e.=thallus) area densities. In a laboratory set-up we measured net photosynthesis and dark respiration in constructed assemblages of macroalgae, excluding effects other than photosynthesis of individual tissue and distribution of photons in the canopy from influencing metabolism. We hypothezised that 1) canopy structure determines the actual rates of photosynthesis relative to the optimal rates and 2) multi-species communities attain higher maximum photosynthetic rates than single species communities. We found that differences in canopy structure outweighed large differences in tissue photosynthesis resulting in relatively similar maximum community photosynthetic rates among the different single and multi-species assemblages (20.1–40.5 μmol O₂ m⁻² s⁻¹). Canopy structure influenced community photosynthesis both at low and high leaf area densities because it determines the ability of macroalgae to use the photosynthetic potential of their individual tissues. Due to an averaging effect the photosynthetic rate at high leaf area density was more similar among multi-species community than among single-species communities. Multi-species communities had, on average, a slightly higher photosynthetic production than expected from photosynthesis of single species communities. Moreover multi-species communities were capable of exposing new tissue to irradiance up to high densities thereby avoiding a decrease in net photosynthesis. This finding suggests that multi-species communities may be able to maintain higher biomass per unit ground area than single-species communities.     

The Madingley general ecosystem model predicts bushmeat yields,species extinction rates and ecosystem-level impacts of bushmeat harvesting

Traditional approaches to guiding decisions about harvesting bushmeat often employ single-species population dynamic models, which require species- and location-specific data, are missing ecological processes such as multi-trophic interactions, cannot represent multi-species harvesting and cannot predict the broader ecosystem impacts of harvesting. In order to explore an alternative approach to devising sustainable harvesting strategies, we employ the Madingley general ecosystem model, which can simulate ecosystem dynamics in response to multi-species harvesting given nothing other than location-specific climate data. We used the model to examine yield, extinctions and broader ecosystem impacts, for a range of harvesting intensities of duiker-sized endothermic herbivores. Duiker antelope (such as Cephalophus callipygus and Cephalophus dorsalis) are the most heavily hunted species in sub-Saharan Africa, contributing 34–95% of all bushmeat in the Congo Basin. Across a range of harvesting rates, the Madingley model gave estimates for optimal harvesting rate, and extinction rate, that were qualitatively and quantitatively similar to the estimates from conventional single-species Beverton–Holt model. Predicted yields were somewhat greater (around five times, on average) for the Madingley model than the Beverton–Holt, which is partly attributable to the fact that the Madingley simulates multi-species harvesting from an initially pristine ecosystem. Also, the Madingley model predicted a background local extinction probability for the target species of at least 10%. At medium and high levels of harvesting of duiker-sized herbivores, the Madingley model predicted statistically significant, but moderate, reductions in the densities of the targeted functional group; increases in small-bodied herbivores; decreases in large-bodied carnivores; and minimal ecosystem-level impacts overall. The results illustrate how general ecosystem models such as the Madingley model could potentially be used more widely to help estimate sustainable harvesting rates, bushmeat yields and broader ecosystem impacts across different locations and target species.     

Crayfish as geomorphic agents and ecosystem engineers: effect of a biomass gradient on baseflow and flood-induced transport of gravel and sand in experimental streams

SUMMARY 1. Using experimental streams, we studied the impact of the crayfish Orconectes limosus on (i) the transport of gravel and sand at baseflow; (ii) the sediment surface (bedform, particle consolidation, proportion of sand, algal and gravel cover); and (iii) the critical shear stress (τ_C) causing incipient gravel and sand motion during simulated floods. We examined (i) and (ii) in experimental outdoor flumes that replicated riffle‐pool sequences and (iii) in a larger laboratory flume, in which we exposed sediments retrieved from the outdoor flumes to a progressively increasing discharge. 2. Habitat changes induced by crayfish, such as bedform alterations in riffles (downstream displacement of riffle heads) and the increase of gravel on sand dunes in pools, had major impacts on the spatial and temporal patterns of the baseflow transport of gravel and sand. 3. In addition to their impact on bedform in riffles and on gravel cover in pools, crayfish prevented the physical consolidation of particles in riffles and reduced the algal cover and the proportion of sand in the surface layer in both riffles and pools. These crayfish impacts on sediment surface variables had complex, interacting effects on the mobilisation of gravel and sand during subsequent flood simulations. For sand, crayfish progressively decreased the τ_C (i.e. the sum of bedform drag and skin friction) by about 50% along the entire biomass gradient in pools, whereas the presence of crayfish abruptly decreased the τ_C by about 75% in riffles. For gravel, the discharge causing motion in riffles produced a shear stress (in terms of skin friction) on an even bedform that was about 75% lower in all flumes with crayfish compared with the flumes without crayfish. Crayfish had no impact on τ_C for gravel in pools. 4. Scaling‐up these experimental results to real streams suggests that crayfish could affect the patch dynamics of major sediment transport events and habitat suitability for other organisms that, at larger spatial scales, could increase the overall spatio‐temporal habitat diversity and thus the overall structural and functional biodiversity of lotic communities.     

Persistence and permanence in a metapopulation model with space-limited recruitment

In this paper we analyze a metapopulation model with space-limited recruitment. The model describes the population dynamics of sessile adult and planktonic larvae in a common larval pool. We introduce the basic reproduction number of each species which is the expected number of future larvae reproduced by one larva. We consider the conditions for the persistence of the multi-species and multi-habitats model and the permanence of the single-species model. Subsequently, we consider the conditions for the existence of the non-trivial steady state of the single-species model and its global stability, and the permanence of the two species and two habitats model.     

Body length variation within multi-species fish shoals: the effects of shoal size and number of species

Theory predicts that selection should favour phenotypic homogeneity in fish shoals, and field studies have indeed confirmed that variation in body length within fish shoals is significantly lower than expected from a random distribution of fish among shoals. We investigated the extent to which variation in fish body length within shoals is determined by the shoal mean of body length, the number of species in a shoal, and the overall shoal size. We collected 34 fish shoals, ranging in size from 6 to 776 individuals, from the littoral zone of a Canadian lake. Shoals consisted of up to four different species, with multi-species shoals being larger and more frequent than single-species ones. The strongest determinant of body length variation within shoals was the shoal mean of body length, followed by the number of fish species in a shoal; i.e. multi-species shoals were less size-assorted than single-species ones. A more detailed analysis showed that the higher body length variation observed in multi-species shoals was due to increased body length variation both within and between component species. Shoal size had no significant effect on body length variation within shoals. Potential explanations of the positive relationship between body length variation and the number of species in a shoal are suggested. The implications of the above results for the evolution of multi-species shoals are discussed. Received: 6 May 1997 / Accepted: 14 October 1997     

Evolution in metacommunities

A metacommunity can be defined as a set of communities that are linked by migration, and extinction and recolonization. In metacommunities, evolution can occur not only by processes that occur within communities such as drift and individual selection, but also by among-community processes, such as divergent selection owing to random differences among communities in species composition, and group and community-level selection. The effect of these among-community-level processes depends on the pattern of migration among communities. Migrating units may be individuals (migrant pool model), groups of individuals (single-species propagule pool model) or multi-species associations (multi-species propagule pool model). The most interesting case is the multi-species propagule pool model. Although this pattern of migration may a priori seem rare, it becomes more plausible in small well-defined 'communities' such as symbiotic associations between two or a few species. Theoretical models and experimental studies show that community selection is potentially an effective evolutionary force. Such evolution can occur either through genetic changes within species or through changes in the species composition of the communities. Although laboratory studies show that community selection can be important, little is known about how important it is in natural populations.     

Overyielding in grassland communities: testing the sampling effect hypothesis with replicated biodiversity experiments

We derive and test some assumptions and predictions of the Sampling Effect Hypothesis (SEH) by examining the relationship between the traits of species in monoculture and their relative abundance in mixture, and by comparing polyculture performance with single-species plots. Although we found a positive relationship between production in monoculture and dominance in mixtures as predicted by the SEH, the relationship had low explanatory power. Counter to predictions, the species with the highest monoculture biomass were not able to strongly dominate all mixtures; instead the dominance of these species decreased with increasing species richness. On average, polycultures did not achieve greater biomass than (transgressively overyield) the species in each mixture, or at each site, that was most productive in monoculture. However, mixture yields did transgressively overyield both the monoculture biomass of the dominant species in the mixtures, and the weighted average of all monocultures (non-transgressive overyielding), both of which were positively related to increasing species richness. The varying responses of different overyielding tests resulted because resource partitioning and positive interactions were often counter-balanced by selection for species with lower biomass than the highest-yielding monocultures. Judging whether or not mixtures overyield therefore depends in part upon which species is the basis for comparison. We present a new general framework for overyielding analysis where every monoculture provides a potential comparison and from which the most relevant tests can be selected.     

Current Issues in Statistics and Models for Ecotoxicological Risk Assessment

A review is given on statistical and modelling issues in ecotoxicology. The issues discussed are: 1. How to estimate an (almost) no effect concentration chemicals in the laboratory. 2. Combining single-species acceptable effect levels to an acceptable effect level for a multi-species ecosystem. 3. The combined effect of exposure to several chemicals. 4. Bioavailability in the natural environment and food-web models. Most current procedures in setting standards allow the environmental concentration to be above the acceptable effect concentration for a small fraction of the species. It is shown that a considerable part of the fraction of the affected species will suffer a severe effect.     

A case for multi-species management of sympatric herbivore pest impacts in the central Southern Alps, New Zealand

Five herbivorous introduced mammals are sympatric in the central Southern Alps. All of these species have the potential to affect conservation values, yet the Department of Conservation at present monitors and mitigates the impacts of only one. We outline ecological arguments for multi-species management of sympatric herbivore pest impacts and use the two- species system of sympatric thar and chamois to highlight the need for multi-species management of the central Southern Alps alpine pest community.     

Uninvadability in N-species frequency models for resident-mutant systems with discrete or continuous time

The uninvadability concept, that was originally introduced through static comparisons of individual fitness in resident-mutant systems for a single species, is developed for multi-species models with frequency-dependent fitness by extending its equivalent single-species dynamic characterization. This multi-species definition is then reinterpreted in terms of individual fitness functions based on intra and interspecific interactions. The resultant concept is discussed in relation to that of an N-species ESS (evolutionarily stable strategy) and to dynamic stability of monomorphic and polymorphic evolutionary systems.     

Seasonal variation in the diet of stoats in a breeding colony of Hutton's shearwaters

Abstract

Two advantages could be gained by developing multi-species control by aerial baiting. It should assist pest managers to achieve sustainable resource management by improving the efficiency of operations; and it should reduce the likelihood of unwanted ecological side-effects (such as prey-switching) that sometimes follow when pest species are controlled individually. The technology to achieve efficient multi-species control is already well advanced, aided particularly by the refinement of aerial control of possums and by the development of baits for individual species. More effort will, however, be required to develop predictive models for planning the integration of multi-species control with conventional single-species control, and for predicting the ecological effects of such intervention.     

Non-indigenous invasive bivalves as ecosystem engineers

Several non-indigenous bivalve species have been colonising aquatic ecosystems worldwide, in some cases with great ecological and economic impacts. In this paper, we focus on the ecosystem engineering attributes of non-indigenous invasive bivalves (i.e., the capacities of these organisms to directly or indirectly affect the availability of resources to other species by physically modifying the environment). By reviewing the ecology of several invasive bivalves we identify a variety of mechanisms via which they modify, maintain and/or create habitats. Given the usually high densities and broad spatial distributions of such bivalves, their engineering activities can significantly alter ecosystem structure and functioning (e.g., changes in sediment chemistry, grain size, and organic matter content via bioturbation, increased light penetration into the water column due to filter feeding, changes in near bed flows and shear stress due to the presence of shells, provision of colonisable substrate and refuges by shells). In addition, changes in ecosystem structure and functioning due to engineering by invasive bivalves often have very large economic impacts. Given the worldwide spread of non-indigenous bivalves and the varied ways in which they physically modify habitats, their engineering effects should receive more serious consideration in restoration and management initiatives.     

Shear stress and sediment resuspension in relation to submersed macrophyte biomass

We examined the impacts of macrophyte beds dominated by a canopy-forming (Myriophyllum sibiricum) and a meadow-forming (Chara canescens) species on bottom shear stress (τ) and resuspension in shallow Lake Christina, Minnesota (U.S.A.). Studies were conducted in late summer, 1998, when macrophyte biomass levels exceeded 200 g m^?2, and in early summer, 2000, when biomass was greatly reduced (<20 g m^?2) in both plant beds. The critical shear stress (τ_c) of sediments, measured experimentally in the laboratory, was low (1.4 dynes cm^?2) indicating potential for resuspension in the absence of macrophytes. During 1998, turbidity was low at the M. sibiricum and Chara station, rarely increasing when calculated bottom τ (calculated from wave theory assuming no biomass obstruction) exceeded τsub c sub, indicating that both beds reduced sediment resuspension at high biomass levels. In situτ (estimated τ), measured via gypsum sphere dissolution, did not exceed τ_c above the sediment interface in either bed during 1998. In contrast, sediment resuspension occurred in both beds during similar high winds in 2000. However, estimated τ was lower than calculated bottom τ, suggesting that at low biomass, macrophytes were having some impact on τ.     

Comparative microbial modules resource: generation and visualization of multi-species biclusters

The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html). The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures - results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation.     

Differential virulence in a multiple‐host parasite of bumble bees: resolving the paradox of parasite survival?

Parasite virulence determines both the impact that parasites have on their hosts and parasite fitness. While most studies of virulence have involved single-species host–parasite interactions, the majority of parasites are likely to use multiple concurrent host species. Our understanding of how this impacts on parasite epidemiology and virulence is limited. Using the bumble bee Bombus lucorum , which exists in sympatry with B. terrestris in multi-species assemblages, and their generalist micosporidian parasite Nosema bombi , we tested whether the apparent paradox of parasite maintenance due to parasite virulence in a single host, B. terrestris , could be resolved through understanding the parasite's virulence in this sympatric host species. Nosema bombi significantly impacted colony growth, individual longevity, and individual development in B. lucorum . However, these effects were different both qualitatively and quantitatively to the parasite's impact in B. terrestris . Infected colonies of B. lucorum successfully produced both male and female reproductives, and infected female reproductives were capable of successful mating. Variation in life-history across host species may explain differences in the virulence, or impact of the parasite in B. terrestris and B. lucorum , with species with shorter life-cycles being more likely to transfer the parasite from one annual generation to the next. These results suggest that to understand the virulence and epidemiology of multi-host parasites we need to examine their ecological interactions across their various host species.     

Potential Parasite Transmission in Multi-Host Networks Based on Parasite Sharing

Epidemiological networks are commonly used to explore dynamics of parasite transmission among individuals in a population of a given host species. However, many parasites infect multiple host species, and thus multi-host networks may offer a better framework for investigating parasite dynamics. We investigated the factors that influence parasite sharing – and thus potential transmission pathways – among rodent hosts in Southeast Asia. We focused on differences between networks of a single host species and networks that involve multiple host species. In host-parasite networks, modularity (the extent to which the network is divided into subgroups of rodents that interact with similar parasites) was higher in the multi-species than in the single-species networks. This suggests that phylogeny affects patterns of parasite sharing, which was confirmed in analyses showing that it predicted affiliation of individuals to modules. We then constructed “potential transmission networks” based on the host-parasite networks, in which edges depict the similarity between a pair of individuals in the parasites they share. The centrality of individuals in these networks differed between multi- and single-species networks, with species identity and individual characteristics influencing their position in the networks. Simulations further revealed that parasite dynamics differed between multi- and single-species networks. We conclude that multi-host networks based on parasite sharing can provide new insights into the potential for transmission among hosts in an ecological community. In addition, the factors that determine the nature of parasite sharing (i.e. structure of the host-parasite network) may impact transmission patterns.     

Shear‐induced detachment of biofilms from hollow fiber silicone membranes

A suite of techniques was utilized to evaluate the correlation between biofilm physiology, fluid‐induced shear stress, and detachment in hollow fiber membrane aerated bioreactors. Two monoculture species biofilms were grown on silicone fibers in a hollow fiber membrane aerated bioreactors (HfMBR) to assess detachment under laminar fluid flow conditions. Both physiology (biofilm thickness and roughness) and nutrient mass transport data indicated the presence of a steady state mature biofilm after 3 weeks of development. Surface shear stress proved to be an important parameter for predicting passive detachment for the two biofilms. The average shear stress at the surface of Nitrosomonas europaea biofilms (54.5 ± 3.2 mPa) was approximately 20% higher than for Pseudomonas aeruginosa biofilms (45.8 ± 7.7 mPa), resulting in higher biomass detachment. No significant difference in shear stress was measured between immature and mature biofilms of the same species. There was a significant difference in detached biomass for immature vs. mature biofilms in both species. However, there was no difference in detachment rate between the two species. Biotechnol. Bioeng. 2013; 110: 525–534. © 2012 Wiley Periodicals, Inc.     

Bioturbation by a dominant detritivore in a headwater stream: litter excavation and effects on community structure

Bioturbation can affect community structure by influencing resource distribution and habitat heterogeneity. Bioturbation by detritivores in small headwater streams could affect community structure by reintroducing buried detrital resources into the food web and could also affect the distribution of various taxa on detritus. We evaluated the ability of the caddisfly Pycnopsyche gentilis to uncover experimentally buried leaves in a headwater stream. Packs of leaves were placed in enclosures and covered with a known volume of sediment. We added 0, 3 or 6 large Pycnopsyche to the enclosures which were permeable to most other invertebrate taxa. Leaf packs were sampled after 23 days and leaf pack mass, the amount of sediment covering the leaf packs, and macro‐ and microinvertebrate densities on leaf packs were quantified. There was a significant negative relationship between Pycnopsyche density and leaf pack mass. Pycnopsyche also reduced the volume of sediment covering leaf packs. Pycnopsyche had complex effects on the abundance of invertebrate taxa associated with the leaves. Some taxa exhibited their highest abundance in the 3 Pycnopsyche treatment while others exhibited non‐significant increases as Pycnopsyche density increased. These results suggest that the beneficial effects of Pycnopsyche (e.g. uncovering leaves which increases the availability of habitat and food) outweigh any negative effects (e.g. disturbance, encounter competition) of the caddisfly when it is present at lower densities. However, the negative impacts of Pycnopsyche appear to outweigh the positive effects via sediment removal at higher caddisfly densities for some taxa. Our results suggest that bioturbating organisms in streams have the potential to reintroduce organic matter to detrital food webs and affect the distribution and abundance of benthic taxa associated with organic matter.     

Nitrogen and Phosphorus Release from Mixed Litter Layers is Lower than Predicted from Single Species Decay

Ecosystem-level nutrient dynamics during decomposition are often estimated from litter monocultures. If species effects are additive, we can statistically predict nutrient dynamics in multi-species systems from monoculture work, and potential consequences of species loss. However, if species effects are dependent on interactions with other litter species (that is, non-additive), predictions based on monoculture data will likely be inaccurate. We conducted a 3-year, full-factorial, mixed-litter decomposition study of four dominant tree species in a temperate forest and measured nitrogen and phosphorus dynamics to explore whether nutrient dynamics in mixtures were additive or non-additive. Following common approaches, we used litterfall data to predict nutrient dynamics at the ecosystem-level. In mixtures, we observed non-additive effects of litter mixing on nutrient dynamics: the presence of nutrient-rich species in mixture facilitated nutrient release, whereas nutrient-poor species facilitated nutrient retention. Fewer nutrients were released from mixtures containing high-quality litter, and more immobilized from mixtures containing low-quality litter, than predicted from monocultures, creating a difference in overall nutrient release between predicted and actual dynamics in litter mixtures. Nutrient release at the ecosystem-level was greatly overestimated when based on monocultures because the effect of species interactions on nutrient immobilization was not accounted for. Our data illustrate that the identity of species in mixtures is key to their role in non-additive interactions, with repercussions for mineral nutrient availability and storage. These results suggest that predictions of ecosystem-level nutrient dynamics using litter monoculture data likely do not accurately represent actual dynamics because the effects of litter species interactions are not incorporated. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.