A comparison of common programming languages used in bioinformatics

Background  

The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python.     

Effects of hummingbird morphology on specialization in pollination networks vary with resource availability

Specialization of species in interaction networks influences network stability and ecosystem functioning. Spatial and temporal variation in resource availability may provide insight into how ecological factors, such as resource abundance, and evolutionary factors, such as phylogenetically conserved morphological traits, influence specialization within mutualistic networks. We used independent measures of hummingbird abundance and resources (nectar), information on hummingbird traits and plant–hummingbird interactions to examine how resource availability and species' morphology influence the specialization of hummingbirds in three habitat types (forest, shrubs, cattle ranch) sampled over 10 sessions across two years in the southern Andes of Ecuador. Specialization of hummingbird species in the networks was measured by three indices: d' (related to niche partitioning), generality (related to niche width) and PSI (related to pollination services). Specialization indices d', generality and PSI of hummingbird species were influenced by resource availability. All indices indicated that specialization of hummingbirds increased when the availability of resources decreased. Variation in d' was also explained by an interaction between resource availability and bill length; hummingbirds with a long bill switched from being more specialized than other species when resource availability was low to being similarly specialized when availability was high. Overall, our results highlight the importance of ecological and evolutionary factors determining the specialization of species in interaction networks. We demonstrate in particular that ecological gradients in resource availability cause substantial changes in consumers' foraging behavior contingent on their morphology. Changes in pollinator specialization along resource gradients can have impacts on ecosystem functions, such as pollination by animals.     

气候变化背景下生物入侵研究态势的文献计量分析

生物入侵严重威胁生物多样性与生态系统健康,对全球环境、经济造成极大损失,而快速的气候变化显著影响外来生物的扩散和入侵进程。探讨气候变化背景下生物入侵研究态势能够从宏观上把握该领域的国际研究现状与热点,为深入理解外来种入侵机制和制定合理的防治策略提供参考。该文基于最近27 a间(1990—2016年)科学文献数据库Web of Science中科学引文索引扩展版(SCI-E)数据,利用TDA等统计工具对气候变化下生物入侵方面的研究进行了文献计量分析。结果表明:27 a间共发表论文1 736篇,论文数量整体保持增长态势,2009年开始进入快速发展阶段;该领域的研究涉及环境科学与生态学、生物多样性保护、植物学等多个学科;澳大利亚莫纳什大学Chown SL教授发文量最高(35篇);美国的总发文量(708篇)和高被引、高影响因子论文数量均居世界首位;发文量最多的研究机构是加利福尼亚大学(93篇),中国科学院发文量居世界第10位(27篇);Biological Invasions是刊文量最大的学术杂志;物种分布模型、生物多样性、全球变暖、风险评估等是近年来该领域的研究热点;中国共发表论文52篇,中国科学院是国内最大的发文机构,其中,动物研究所、武汉植物园、植物研究所的发文量居中科院科研系统前三名;中国在气候变化下生物入侵领域的高被引、高影响因子论文数量及国际合作强度亟待提升。未来需重点关注气候变化下生物入侵的预测与风险评估、生物入侵与生物多样性关系、入侵物种的系统进化、入侵生态系统的多营养级关系、海洋生物入侵、生物入侵与人类健康等问题。     

Bioconductor: open software development for computational biology and bioinformatics

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.     

Agents in bioinformatics, computational and systems biology

The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics (BIOAGENTS) founded during the first AgentLink III Technical Forum meeting on the 2nd of July, 2004, in Rome. The meeting provided an opportunity for seeding collaborations between the agent and bioinformatics communities to develop a different (agent-based) approach of computational frameworks both for data analysis and management in bioinformatics and for systems modelling and simulation in computational and systems biology. The collaborations gave rise to applications and integrated tools that we summarize and discuss in context of the state of the art in this area. We investigate on future challenges and argue that the field should still be explored from many perspectives ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages to be used by information agents, and to the adoption of agents for computational grids.     

Fast parsers for Entrez Gene

NCBI completed the transition of its main genome annotation database from Locuslink to Entrez Gene in Spring 2005. However, to this date few parsers exist for the Entrez Gene annotation file. Owing to the widespread use of Locuslink and the popularity of Perl programming language in bioinformatics, a publicly available high performance Entrez Gene parser in Perl is urgently needed. We present four such parsers that were developed using several parsing approaches (Parse::RecDescent, Parse::Yapp, Perl-byacc and Perl 5 regular expressions) and provide the first in-depth comparison of these sophisticated Perl tools. Our fastest parser processes the entire human Entrez Gene annotation file in under 12 min on one Intel Xeon 2.4 GHz CPU and can be of help to the bioinformatics community during and after the transition from Locuslink to Entrez Gene.     

Trait-mediated interaction leads to structural emergence in mutualistic networks

As asymmetric structures of mutualistic networks can potentially contribute to system resilience, elucidating drivers behind the emergence of particular network architectures remains a major endeavour in ecology. Here, using an eco-evolutionary model for bipartite mutualistic networks with trait-mediated interactions, we explore how particular levels of connectance, nestedness and modularity are affected by three network assembly forces: resource accessibility, tolerance to trait difference between mutualistic pairs and competition intensity. We found that a moderate accessibility to intra-trophic resources and cross-trophic mutualistic support can result in a highly nested web, while low tolerance to trait difference between interacting pairs leads to a high level of modularity. Network-level trait complementarity leads to low connectance and high modularity, while network-level specialization can result in nested structures. Consequently, we argue that the interplay of ecological and evolutionary processes through trait-mediated interactions can explain these widely observed architectures in mutualistic networks.     

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as the relationships between them are parsed and stored in a local MySQL database. A powerful, flexible web search interface with several convenient utilities provides query capabilities not available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export of the entire GEOmetadb database is also available, rendering the entire GEO database accessible with full power of SQL-based queries from within R. AVAILABILITY: The web interface and SQLite databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website.     

Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions

Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization of interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early mutations improve cooperativity by manifesting in synergistic epistasis between genomes of the mutually interacting species. Specifically, we have characterized evolutionary trajectories of syntrophic interactions of Desulfovibrio vulgaris (Dv) with Methanococcus maripaludis (Mm) by longitudinally monitoring mutations accumulated over 1000 generations of nine independently evolved communities with analysis of the genotypic structure of one community down to the single-cell level. We discovered extensive parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance within many evolution lines of a rare lineage of Dv that retained sulfate-respiration (SR+) capability, which is not required for metabolic cross-feeding. An in-depth investigation revealed that synergistic epistasis across pairings of Dv and Mm genotypes had enhanced cooperativity within SR− and SR+ assemblages, enabling their coexistence within the same community. Thus, our findings demonstrate that cooperativity of a mutualism can improve through synergistic epistasis between genomes of the interacting species, enabling the coexistence of mutualistic assemblages of generalists and their specialized variants.Subject terms: Microbial ecology, Population genetics, Symbiosis, Population dynamics, Molecular evolution     

A suite of Perl modules for handling microarray data

We describe PerlMAT, a Perl microarray toolkit providing easy to use object-oriented methods for the simplified manipulation, management and analysis of microarray data. The toolkit provides objects for the encapsulation of microarray spots and reporters, several common microarray data file formats and GAL files. In addition, an analysis object provides methods for data processing, and an image object enables the visualisation of microarray data. This important addition to the Perl developer's library will facilitate more widespread use of Perl for microarray application development within the bioinformatics community. The coherent interface and well-documented code enables rapid analysis by even inexperienced Perl developers. AVAILABILITY: Software is available at http://sourceforge.net/projects/perlmat     

When species become generalists: on‐going large‐scale changes in bird habitat specialization

Aim Species specialization is often considered as a stable species characteristic over the short term. However, this assumption has hardly been tested, even though it may impair our ability to track the impoverishment of biodiversity induced by the rapid replacement of specialists by generalists. We tested whether species specialization in birds varied over a short period of time, and assessed whether variations in species specialization influence community‐level metrics of biotic homogenization. Location France. Methods We studied the variations in specialization to habitat closure of 94 bird species over the period 2002–08, accounting for species variations in mean density, habitat preference and migratory status. We then quantified the temporal changes in a community specialization index, which measures functional homogenization. Results Specialization decreased over time for 35 species (37%), while 46 (49%) showed non‐significant negative trends and 13 (14%) had null or non‐significant positive trends. The more a species was specialized at the beginning of the study, the more it generalized. We additionally found that changes in the specialization level were density dependent: 34 species (36%) became more generalist in years of higher densities while only one became more specialized. At the community level, accounting for this inter‐annual variability in species specialization accentuated the trend in the functional homogenization of bird communities. Main conclusions Habitat specialization is a labile ecological trait, which may change in the short term following habitat degradation, density dependence and source–sink dynamics. Accounting for short‐term temporal variations in observed habitat specialization of species can increase our understanding of the effects of global changes on species strategies and community dynamics.     

Life in the flow lane: differences in pectoral fin morphology suggest transitions in station-holding demand across species of marine sculpin

Aquatic organisms exposed to high flow regimes typically exhibit adaptations to decrease overall drag and increase friction with the substrate. However, these adaptations have not yet been examined on a structural level. Sculpins (Scorpaeniformes: Cottoidea) have regionalized pectoral fins that are modified for increasing friction with the substrate, and morphological specialization varies across species. We examined body and pectoral fin morphology of 9 species to determine patterns of body and pectoral fin specialization. Intact specimens and pectoral fins were measured, and multivariate techniques determined the differences among species. Cluster analysis identified 4 groups that likely represent differences in station-holding demand, and this was supported by a discriminant function analysis. Primarily, the high-demand group had increased peduncle depth (specialization for acceleration) and larger pectoral fins with less webbed ventral rays (specialization for mechanical gripping) compared to other groups; secondarily, the high-demand group had a greater aspect ratio and a reduced number of pectoral fin rays (specialization for lift generation) than other groups. The function of sculpin pectoral fins likely shifts from primarily gripping where demand is likely low, to an equal dependence on gripping and negative lift generation where demand is likely high. Specialization of the ventral pectoral fin region for gripping likely contributes to the recent diversification of some species into high-demand habitats.     

Finding NEMO: nestedness engendered by mutualistic organization in anemonefish and their hosts

The interaction structure of mutualistic relationships, in terms of relative specialization of the partners, is important to understanding their ecology and evolution. Analyses of the mutualistic interaction between anemonefish and their host sea anemones show that the relationship is highly nested in structure, generalist species interacting with one another and specialist species interacting mainly with generalists. This supports the hypothesis that the configuration of mutualistic interactions will tend towards nestedness. In this case, the structure of the interaction is at a much larger scale than previously hypothesized, across more than 180 degrees of longitude and some 60 degrees of latitude, probably owing to the pelagic dispersal capabilities of these species in a marine environment. Additionally, we found weak support for the hypothesis that geographically widespread species should be more generalized in their interactions than species with small ranges. This study extends understanding of the structure of mutualistic relationships into previously unexplored taxonomic and physical realms, and suggests how nestedness analysis can be applied to the conservation of obligate species interactions.     

A neutral‐niche theory of nestedness in mutualistic networks

Recently, there has been a vigorous interest in community ecology about the structure of mutualistic networks and its importance for species persistence and coevolution. However, the mechanisms shaping mutualistic networks have been rarely explored. Here we extend for the first time the neutral theory of biodiversity to a multi trophic system. We focus on nestedness, a distinctive pattern of mutualistic community assembly showing two characteristics, namely, asymmetrical specialization (specialists interacting with generalists) and a generalist core (generalists interacting with generalists). We investigate the importance of relative species abundance (RSA) for the nested assembly of plant–animal mutualistic networks. Our results show that neutral mutualistic communities give rise to networks considerably more nested than real communities. RSA explains 60–70% of nested patterns in two real communities studied here, while 30–40% of nestedness is still unexplained. The nested pattern in real communities is better explained when we introduce interaction‐specific species traits such as forbidden links and intensity of dependence (relative importance of fruits for the diet of a frugivore) in our analysis. The fact that neutral mutualistic communities exhibit a perfectly nested structure and do not show a random or compartmentalized structure, underlines the importance of RSA in the assembly of mutualistic networks.     

Using GOstats to test gene lists for GO term association

MOTIVATION: Functional analyses based on the association of Gene Ontology (GO) terms to genes in a selected gene list are useful bioinformatic tools and the GOstats package has been widely used to perform such computations. In this paper we report significant improvements and extensions such as support for conditional testing. RESULTS: We discuss the capabilities of GOstats, a Bioconductor package written in R, that allows users to test GO terms for over or under-representation using either a classical hypergeometric test or a conditional hypergeometric that uses the relationships among GO terms to decorrelate the results. AVAILABILITY: GOstats is available as an R package from the Bioconductor project: http://bioconductor.org     

Latitudinal gradients in biotic interactions: Are cacti pollination systems more specialized in the tropics?

• Biotic interactions are said to be more specialized in the tropics, and this was also proposed for the pollination systems of columnar cacti from North America. However, this has not yet been tested for a wider set of cactus species. Here, we use the available information about pollination in the Cactaceae to explore the geographic patterns of this mutualistic interaction, and test if there is a latitudinal gradient in its degree of specialization.
• We performed a bibliographic search of all publications on the pollination of cacti species and summarized the information to build a database. We used generalized linear models to evaluate if the degree of specialization in cacti pollination systems is affected by latitude, using two different measures: the number of pollinator guilds (functional specialization) and the number of pollinator species (ecological specialization).
• Our database contained information about the pollination of 148 species. The most frequent pollinator guilds were bees, birds, moths and bats. There was no apparent effect of latitude on the number of guilds that pollinate a cactus species. However, latitude had a small but significant effect on the number of pollinator species that service a given cactus species.
• Bees are found as pollinators of most cactus species, along a wide latitudinal gradient. Bat and bird pollination is more common in the tropics than in the extra-tropics. The available information suggests that cacti pollination systems are slightly more ecologically specialized in the tropics, but it does not support any trend with regard to functional specialization.

     

Interactive effects of elevation,species richness and extreme climatic events on plant–pollinator networks

Plant–pollinator interactions are essential for the functioning of terrestrial ecosystems, but are increasingly affected by global change. The risks to such mutualistic interactions from increasing temperature and more frequent extreme climatic events such as drought or advanced snow melt are assumed to depend on network specialization, species richness, local climate and associated parameters such as the amplitude of extreme events. Even though elevational gradients provide valuable model systems for climate change and are accompanied by changes in species richness, responses of plant–pollinator networks to climatic extreme events under different environmental and biotic conditions are currently unknown. Here, we show that elevational climatic gradients, species richness and experimentally simulated extreme events interactively change the structure of mutualistic networks in alpine grasslands. We found that the degree of specialization in plant–pollinator networks (H2′) decreased with elevation. Nonetheless, network specialization increased after advanced snow melt at high elevations, whereas changes in network specialization after drought were most pronounced at sites with low species richness. Thus, changes in network specialization after extreme climatic events depended on climatic context and were buffered by high species richness. In our experiment, only generalized plant–pollinator networks changed in their degree of specialization after climatic extreme events. This indicates that contrary to our assumptions, network generalization may not always foster stability of mutualistic interaction networks.     

Network structural properties mediate the stability of mutualistic communities

Key advances are being made on the structures of predator–prey food webs and competitive communities that enhance their stability, but little attention has been given to such complexity–stability relationships for mutualistic communities. We show, by way of theoretical analyses with empirically informed parameters, that structural properties can alter the stability of mutualistic communities characterized by nonlinear functional responses among the interacting species. Specifically, community resilience is enhanced by increasing community size (species diversity) and the number of species interactions (connectivity), and through strong, symmetric interaction strengths of highly nested networks. As a result, mutualistic communities show largely positive complexity–stability relationships, in opposition to the standard paradox. Thus, contrary to the commonly-held belief that mutualism's positive feedback destabilizes food webs, our results suggest that interplay between the structure and function of ecological networks in general, and consideration of mutualistic interactions in particular, may be key to understanding complexity–stability relationships of biological communities as a whole.     

Reciprocal specialization in ecological networks

Theories suggest that food webs might consist of groups of species forming 'blocks', 'compartments' or 'guilds'. We consider ecological networks – subsets of complete food webs – involving species at adjacent trophic levels. Reciprocal specializations occur when (say) a pollinator (or group of pollinators) specializes on a particular flower species (or group of such species) and vice versa. Such specializations tend to group species into guilds. We characterize the level of reciprocal specialization for both antagonistic interactions – particularly parasitoids and their hosts – and mutualistic ones – such as insects and the flowers that they pollinate. We also examine whether trophic patterns might be 'palimpsests'– that is, there might be reciprocal specialization within taxonomically related species within a network, but these might be obscured when these relationships are combined. Reciprocal specializations are rare in all these systems when tested against the most conservative null model.     

From antagonistic larvae to mutualistic adults: coevolution of diet niches within life cycles

Population structures largely affect higher levels of organization (community structure, ecosystem functioning), especially when involving ontogenetic changes in habitat or diet. Along life cycles, partners and interaction type may change: for instance Lepidopterans are herbivores as larvae and pollinators as adults. To understand variations in diet niche from larvae to adults, we model a community of two plant species and one stage‐structured insect species consuming plants as juvenile and pollinating them as adult. We model the coevolution of juvenile and adult diet specialization using adaptive dynamics to investigate when one should expect niche partitioning or niche overlap among life stages. We consider ecological and evolutionary implications for the coexistence of species. As predicted based on indirect effects among stages, we find that juvenile diet evolution increases niche overlap and favours the coexistence of plants, while the evolution of the adult diet decreases niche overlap and reduces plant coexistence, because of positive feedbacks emerging from the mutualistic interaction.