Saccharomyces sensu stricto as a model system for evolution and ecology

Baker's yeast, Saccharomyces cerevisiae, is not only an extensively used model system in genetics and molecular biology, it is an upcoming model for research in ecology and evolution. The available body of knowledge and molecular techniques make yeast ideal for work in areas such as evolutionary and ecological genomics, population genetics, microbial biogeography, community ecology and speciation. As long as ecological information remains scarce for this species, the vast amount of data that is being generated using S. cerevisiae as a model system will remain difficult to interpret in an evolutionary context. Here we review the current knowledge of the evolution and ecology of S. cerevisiae and closely related species in the Saccharomyces sensu stricto group, and suggest future research directions.     

Microarray data analysis: a practical approach for selecting differentially expressed genes

Background  

The biomedical community is rapidly developing new methods of data analysis for microarray experiments, with the goal of establishing new standards to objectively process the massive datasets produced from functional genomic experiments. Each microarray experiment measures thousands of genes simultaneously producing an unprecedented amount of biological information across increasingly numerous experiments; however, in general, only a very small percentage of the genes present on any given array are identified as differentially regulated. The challenge then is to process this information objectively and efficiently in order to obtain knowledge of the biological system under study and by which to compare information gained across multiple experiments. In this context, systematic and objective mathematical approaches, which are simple to apply across a large number of experimental designs, become fundamental to correctly handle the mass of data and to understand the true complexity of the biological systems under study.     

Knowledge sharing and collaboration in translational research, and the DC-THERA Directory

Biomedical research relies increasingly on large collections of data sets and knowledge whose generation, representation and analysis often require large collaborative and interdisciplinary efforts. This dimension of 'big data' research calls for the development of computational tools to manage such a vast amount of data, as well as tools that can improve communication and access to information from collaborating researchers and from the wider community. Whenever research projects have a defined temporal scope, an additional issue of data management arises, namely how the knowledge generated within the project can be made available beyond its boundaries and life-time. DC-THERA is a European 'Network of Excellence' (NoE) that spawned a very large collaborative and interdisciplinary research community, focusing on the development of novel immunotherapies derived from fundamental research in dendritic cell immunobiology. In this article we introduce the DC-THERA Directory, which is an information system designed to support knowledge management for this research community and beyond. We present how the use of metadata and Semantic Web technologies can effectively help to organize the knowledge generated by modern collaborative research, how these technologies can enable effective data management solutions during and beyond the project lifecycle, and how resources such as the DC-THERA Directory fit into the larger context of e-science.     

The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains,expansions, and losses

Model organisms such as yeast, fly, and worm have played a defining role in the study of many biological systems. A significant challenge remains in translating this information to humans. Of critical importance is the ability to differentiate those components where knowledge of function and interactions may be reliably inferred from those that represent lineage‐specific innovations. To address this challenge, we use chromatin modification (CM) as a model system for exploring the evolutionary properties of their components in the context of their known functions and interactions. Collating previously identified components of CM from yeast, worm, fly, and human, we identified a “core” set of 50 CM genes displaying consistent orthologous relationships that likely retain their interactions and functions across taxa. In addition, we catalog many components that demonstrate lineage specific expansions and losses, highlighting much duplication within vertebrates that may reflect an expanded repertoire of regulatory mechanisms. Placed in the context of a high‐quality protein–protein interaction network, we find, contrary to existing views of evolutionary modularity, that CM complex components display a mosaic of evolutionary histories: a core set of highly conserved genes, together with sets displaying lineage specific innovations. Although focused on CM, this study provides a template for differentiating those genes which are likely to retain their functions and interactions across species. As such, in addition to informing on the evolution of CM as a system, this study provides a set of comparative genomic approaches that can be generally applied to any biological systems. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Integrating epitope data into the emerging web of biomedical knowledge resources

The recognition of immune epitopes is an important molecular mechanism of the vertebrate immune system to discriminate between self and non-self. Increasing amounts of data on immune epitopes are becoming available due to technological advances in epitope-mapping techniques and the availability of genomic information for pathogens. Organizing this data poses a challenge that is similar to the successful effort that was required to organize genomic data, which needed the establishment of centralized databases that complement the primary literature to make the data readily accessible and searchable by researchers. As described in this Innovation article, the Immune Epitope Database and Analysis Resource aims to achieve the same for the more complex and context-dependent information on immune epitopes, and to integrate this data with existing and emerging knowledge resources.     

Applied conservation services of the evolutionary theory

Having quantitative data to use in a reliable model in conservation can be extremely limiting because of the usual scarcity of such information. The body of theory accumulated so far in evolutionary ecology, and particularly in the evolution of life-history traits, can also come in the aid of conservation practitioners and provide them with some help in the absence of quantitative data. Although some attempts have been made already to bridge the gap between evolution and applied conservation, this interface remains to be properly delineated. Here we present a diverse number of examples of the applicability of evolutionary knowledge to the effective solution of diverse applied conservation problems. We first deal with the opposed strategies of animal and plant species inhabiting survival versus reproduction habitats, and the most adequate management approaches in both cases, with special emphasis in assessing the risks of supplementing food and nest boxes for conservation purposes. Secondly, we deal with invasion biology and suggest that a better understanding of the problem of biological invasions, and a better management of it, is gained if the focus is moved from invasive species characteristics to the properties of the invaded community from an evolutionary perspective. Finally, we show how the management of complex predator–prey interactions can benefit from the application of knowledge on life-history evolution and discuss the particularities of culling programs applied either to short-lived or long-lived species in order to be effective.     

Detecting the genomic signal of polygenic adaptation and the role of epistasis in evolution

Over the last decade, the genomic revolution has offered the possibility to generate tremendous amounts of data that contain valuable information on the genetic basis of phenotypic traits, such as those linked to human diseases or those that allow for species to adapt to a changing environment. Most ecologically relevant traits are controlled by a large number of genes with small individual effects on trait variation, but that are connected with one another through complex developmental, metabolic and biochemical networks. As a result, it has recently been suggested that most adaptation events in natural populations are reached via correlated changes at multiple genes at a time, for which the name polygenic adaptation has been coined. The current challenge is to develop methods to extract the relevant information from genomic data to detect the signature of polygenic evolutionary change. The symposium entitled “Detecting the Genomic Signal of Polygenic Adaptation and the Role of Epistasis in Evolution” held in 2017 at the University of Zürich aimed at reviewing our current state of knowledge. In this review, we use the talks of the invited speakers to summarize some of the most recent developments in this field.     

An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community

The future bioinformatics needs of the Arabidopsis community as well as those of other scientific communities that depend on Arabidopsis resources were discussed at a pair of recent meetings held by the Multinational Arabidopsis Steering Committee and the North American Arabidopsis Steering Committee. There are extensive tools and resources for information storage, curation, and retrieval of Arabidopsis data that have been developed over recent years primarily through the activities of The Arabidopsis Information Resource, the Nottingham Arabidopsis Stock Centre, and the Arabidopsis Biological Resource Center, among others. However, the rapid expansion in many data types, the international basis of the Arabidopsis community, and changing priorities of the funding agencies all suggest the need for changes in the way informatics infrastructure is developed and maintained. We propose that there is a need for a single core resource that is integrated into a larger international consortium of investigators. We envision this to consist of a distributed system of data, tools, and resources, accessed via a single information portal and funded by a variety of sources, under shared international management of an International Arabidopsis Informatics Consortium (IAIC). This article outlines the proposal for the development, management, operations, and continued funding for the IAIC.The Multinational Arabidopsis Steering Committee (MASC) and the North American Arabidopsis Steering Committee (NAASC) hosted workshops in Nottingham, UK (April 15 to 16, 2010) and Washington DC (May 10 to 11, 2010) to consider the future bioinformatics needs of the Arabidopsis community as well as other science communities that depend vitally on Arabidopsis resources. The outcomes of both workshops were presented and discussed at the International Conference on Arabidopsis Research (ICAR) in Yokohama, Japan. The focus of the workshops was on Arabidopsis because of its unique and essential role as a reference organism for all seed plant species. The development of the highly annotated “gold standard” Arabidopsis genome sequence has been an invaluable resource for plant and crop sciences. This platform provides important information and working practices for other species and for comparative genomic and evolutionary studies. Arabidopsis tools and resources for information storage, curation, and retrieval have been developed over recent years primarily through the activities of The Arabidopsis Information Resource (TAIR), the Nottingham Arabidopsis Stock Centre (NASC), and the Arabidopsis Biological Resource Center, among others. However, the Arabidopsis community and funding agencies recognize the need for a single data management infrastructure. The key challenge is to develop and fund this resource in a sustainable and transparent manner.Global challenges surrounding food and energy security require intelligent plant breeding strategies that will be dependent on a central Arabidopsis information resource to aid our understanding of gene function and associated phenotype in many different environments. The knowledge accrued in Arabidopsis informs our understanding of the genetic basis of plant processes and crop traits. To date, this has accumulated primarily through analysis of single genes. However, gene products do not act alone but rather in complex interacting networks. Thus, the challenge for the Arabidopsis community is to understand this higher level of complexity, to a significant extent through the application of new high volume, quantitative experimental techniques. The goals of these efforts are to develop gene/protein/metabolite networks that will enable systems-level modeling of plant processes and ultimately to translate these findings to crop plants. To achieve these goals, we must develop novel approaches to data management, integration, and access.The UK workshop addressed three principal issues: the types of data generated by the Arabidopsis community, the types of data used by the community, and future needs of the community. The objective was to produce recommendations for the type of infrastructure necessary to address the challenges and opportunities associated with the application of new technologies and recommendations for a sustainable funding model to support this infrastructure. These recommendations were considered and expanded upon at the US workshop with the ultimate goal of generating solutions to the issues discussed in the first meeting. It was recognized that cohesive, cooperative, and long-term international collaboration will be critical to successfully maintain an Arabidopsis database infrastructure that is essential for plant biology research worldwide.The workshop participants concluded that there is a continued need for a central Arabidopsis information resource, based on the productivity of the Arabidopsis community and the critical importance of the findings generated by this community. For example, ∼3000 Arabidopsis publications are currently published in peer-reviewed journals each year, a nearly 10-fold increase since the early 1990s; and in 2009, TAIR was accessed by 335,692 unique visitors and had nearly 20 million page views. Furthermore, the importance of a current, well-organized, and carefully curated Arabidopsis genome to researchers studying other plants, including crops, cannot be overstated. In the future, this resource should be part of a larger infrastructure that would be dynamic and responsive to new directions in plant biology research.     

The challenge of plant regeneration after fire in the Mediterranean Basin: scientific gaps in our knowledge on plant strategies and evolution of traits

Though observations on re-colonisation of post-fire sites in the Mediterranean Basin are plentiful, there still is an ongoing debate on the interrelation of fire regimes and species traits related to fire adaptation. Most of the studies found are restricted to particular species or claim to present community attributes. Therefore they often lack information for the evaluation of evolutionary evidence and historical contingency of the local fire regime and other abiotic conditions, which may act as selective pressure for plant regeneration strategies. Indeed, knowledge about the success of regeneration mechanisms and their interrelation with ecological factors is essential for the interpretation of the high spatio-temporal variability found in post-fire species performance. Such knowledge would be necessary to assess the potential of different regeneration mechanisms to cope with ongoing land-use and climate change—a crucial scientific challenge. A summary is given of the knowledge about the limits and potential of plant regeneration mechanisms after fire in the Mediterranean Basin, along with corresponding studies conducted in other parts of the world with similar climatic conditions in order to present the fullest possible picture. Moreover, the positive or negative impacts of particular parameters of a fire regime on different regeneration strategies (post-fire seeders, resprouters, and facultative resprouters) are explained and discussed in the light of published literature. To conclude, reference is made to scientific gaps that need to be filled in order to analyse species resistance and community resilience absorbing possible climate or land use changes.     

What processes must we understand to forecast regional-scale population dynamics?

An urgent challenge facing biologists is predicting the regional-scale population dynamics of species facing environmental change. Biologists suggest that we must move beyond predictions based on phenomenological models and instead base predictions on underlying processes. For example, population biologists, evolutionary biologists, community ecologists and ecophysiologists all argue that the respective processes they study are essential. Must our models include processes from all of these fields? We argue that answering this critical question is ultimately an empirical exercise requiring a substantial amount of data that have not been integrated for any system to date. To motivate and facilitate the necessary data collection and integration, we first review the potential importance of each mechanism for skilful prediction. We then develop a conceptual framework based on reaction norms, and propose a hierarchical Bayesian statistical framework to integrate processes affecting reaction norms at different scales. The ambitious research programme we advocate is rapidly becoming feasible due to novel collaborations, datasets and analytical tools.     

Biological traits approaches in benthic marine ecology: Dead ends and new paths

Biological traits analysis (BTA) links community structure to both ecological functions and response to environmental drivers through species’ attributes. In consequence, it has become a popular approach in marine benthic studies. However, BTA will reach a dead end if the scientific community does not acknowledge its current shortcomings and limitations: (a) uncertainties related to data origins and a lack of standardized reporting of trait information; (b) knowledge gaps on the role of multiple interacting traits on driving the organisms’ responses to environmental variability; (c) knowledge gaps regarding the mechanistic links between traits and functions; (d) a weak focus on the spatial and temporal variability that is inherent to the trait expression of species; and, last but not least, (e) the large reliance on expert knowledge due to an enormous knowledge gap on the basic ecology of many benthic species. BTA will only reach its full potential if the scientific community is able to standardize and unify the reporting and storage of traits data and reconsider the importance of baseline observational and experimental studies to fill knowledge gaps on the mechanistic links between biological traits, functions, and environmental variability. This challenge could be assisted by embracing new technological advances in marine monitoring, such as underwater camera technology and artificial intelligence, and making use of advanced statistical approaches that consider the interactive nature and spatio‐temporal variability of biological systems. The scientific community has to abandon some dead ends and explore new paths that will improve our understanding of individual species, traits, and the functioning of benthic ecosystems.     

Breathing life into climate change adaptation

The exploration of evolutionary biology and biological adaptation can inform society's adaptation to climate change, particularly the mechanisms that bring about adaptability, such as phenotypic plasticity, epigenetics, and horizontal gene transfer. Learning from unplanned autonomous biological adaptation may be considered undesirable and incompatible with human endeavor. However, it is argued that there is no need for agency, and planned adaptation is not necessarily preferable over autonomous adaptation. What matters is the efficacy of adaptive mechanisms and their capacity to increase societal resilience to current and future impacts. In addition, there is great scope for industrial ecology (IE) to contribute approaches to climate change adaptation that generate system models and baseline data to inform decision making. The problem of “uncertainty” was chosen as an example of a challenge that is shared by biological systems, IE, and climate change adaptation to show how biological adaptation might contribute solutions. Finally, the Coastal Climate Adaptation Decision Support tool was used to demonstrate how IE and biological adaptation approaches may be mainstreamed in climate change adaptation planning and practice. In conclusion, there is close conceptual alignment between evolutionary biology and IE. The integration of biological adaptation thinking can enrich IE, add new perspectives to climate change adaptation science, and support IE's engagement with climate change adaptation. There should be no major obstacles regarding the collaboration of industrial ecologists with the climate change adaptation community, but mainstreaming of biological adaptation solutions depends greatly on successful knowledge transfer and the engagement of open‐minded and informed adaptation stakeholders.     

Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time

A key challenge in ecological research is to integrate data from different scales to evaluate the ecological and evolutionary mechanisms that influence current patterns of biological diversity. We build on recent attempts to incorporate phylogenetic information into traditional diversity analyses and on existing research on beta diversity and phylogenetic community ecology. Phylogenetic beta diversity (phylobetadiversity) measures the phylogenetic distance among communities and as such allows us to connect local processes, such as biotic interactions and environmental filtering, with more regional processes including trait evolution and speciation. When combined with traditional measures of beta diversity, environmental gradient analyses or ecological niche modelling, phylobetadiversity can provide significant and novel insights into the mechanisms underlying current patterns of biological diversity.     

Techniques for integrating ‐omics data

The challenge for -omics research is to tackle the problem of fragmentation of knowledge by integrating several sources of heterogeneous information into a coherent entity. It is widely recognized that successful data integration is one of the keys to improve productivity for stored data. Through proper data integration tools and algorithms, researchers may correlate relationships that enable them to make better and faster decisions. The need for data integration is essential for present ‐omics community, because ‐omics data is currently spread world wide in wide variety of formats. These formats can be integrated and migrated across platforms through different techniques and one of the important techniques often used is XML. XML is used to provide a document markup language that is easier to learn, retrieve, store and transmit. It is semantically richer than HTML. Here, we describe bio warehousing, database federation, controlled vocabularies and highlighting the XML application to store, migrate and validate -omics data.     

Biomedical Discovery Acceleration, with Applications to Craniofacial Development

The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning, and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or using biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. An implementation of this approach, called the Hanalyzer, is demonstrated on a large-scale gene expression array dataset relevant to craniofacial development. The use of the tool was critical in the creation of hypotheses regarding the roles of four genes never previously characterized as involved in craniofacial development; each of these hypotheses was validated by further experimental work.     

The conserved genome organisation of non-falciparum malaria species: the need to know more

The current knowledge on genomes of non-falciparum malaria species and the potential of model malaria parasites for functional analyses are reviewed and compared with those of the most pathogenic human parasite, Plasmodium falciparum. There are remarkable similarities in overall genome composition among the different species at the level of chromosome organisation and chromosome number, conserved order of individual genes, and even conserved functions of specific gene domains and regulatory control elements. With the initiative taken to sequence the genome of P. falciparum, a wealth of information is already becoming available to the scientific community. In order to exploit the biological information content of a complete genome sequence, simple storage of the bulk of sequence data will be inadequate. The requirement for functional analyses to determine the biological role of the open reading frames is commonly accepted and knowledge of the genomes of the animal model malaria species will facilitate these analyses. Detailed comparative genome information and sequencing of additional Plasmodium genomes will provide a deeper insight into the evolutionary history of the species, the biology of the parasite, and its interactions with the mammalian host and mosquito vector. Therefore, an extended and integrated approach will enhance our knowledge of malaria and will ultimately lead to a more rational approach that identifies and evaluates new targets for anti-malarial drug and vaccine development.     

An integrative model of evolutionary covariance: a symposium on body shape in fishes

A major direction of current and future biological research is to understand how multiple, interacting functional systems coordinate in producing a body that works. This understanding is complicated by the fact that organisms need to work well in multiple environments, with both predictable and unpredictable environmental perturbations. Furthermore, organismal design reflects a history of past environments and not a plan for future environments. How complex, interacting functional systems evolve, then, is a truly grand challenge. In accepting the challenge, an integrative model of evolutionary covariance is developed. The model combines quantitative genetics, functional morphology/physiology, and functional ecology. The model is used to convene scientists ranging from geneticists, to physiologists, to ecologists, to engineers to facilitate the emergence of body shape in fishes as a model system for understanding how complex, interacting functional systems develop and evolve. Body shape of fish is a complex morphology that (1) results from many developmental paths and (2) functions in many different behaviors. Understanding the coordination and evolution of the many paths from genes to body shape, body shape to function, and function to a working fish body in a dynamic environment is now possible given new technologies from genetics to engineering and new theoretical models that integrate the different levels of biological organization (from genes to ecology).     

Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research

It is now well recognized that considering species evolutionary history is crucial for understanding the processes driving community assembly (Cavender‐Bares et al. 2009 ). Considerable efforts have been made to integrate phylogenetics and community ecology into a single theoretical framework. Yet, assessing phylogenetic structure at the community scale remains a great challenge, in particular for poorly known organisms. While DNA metabarcoding is increasingly used for assessing taxonomic composition of complex communities from environmental samples, biases and limitations of this technique can preclude the retrieval of information on phylogenetic community structure. In this issue of Molecular Ecology, Andújar et al. (2015) demonstrate that shotgun sequencing of bulk samples of soil beetles and subsequent reconstruction of mitochondrial genomes can provide a solid phylogenetic framework to estimate species diversity and gain insights into the mechanisms underlying the spatial turnover of soil mesofaunal assemblages. This work highlights the enormous potential of ‘metagenome skimming’ not only for improving the current standards of DNA‐based biodiversity assessment but also for opening up the application of phylogenetic community ecology to hyperdiverse and poorly known biota, which was heretofore inconceivable.     

Self-deception does not explain high-risk sexual behavior in the face of HIV/AIDS: A test from northern Kenya

Throughout sub-Saharan Africa, there is resistance to changing sexual behavior despite survey data indicating high levels of knowledge about HIV transmission patterns and high-risk behavior. Previous explanations for this paradox emphasize indigenous cultural models. An alternative explanation is that, due to a strong natural selection for sexual gratification, individuals evoke the evolved trait of self-deception to continue practicing high-risk sexual behavior. This alternative is tested using survey data from an Ariaal community in Marsabit District, northern Kenya. Results indicate that respondents make highly accurate self-assessments of HIV risk, negating the concept of self-deception in this study. These results are discussed within the larger context of the applicability of evolutionary theory to the AIDS pandemic.     

Transgenerational plasticity of inducible defences: Combined effects of grand‐parental,parental and current environments

Phenotypic plasticity can occur across generations (transgenerational plasticity) when environments experienced by the previous generations influenced offspring phenotype. The evolutionary importance of transgenerational plasticity, especially regarding within‐generational plasticity, is a currently hot topic in the plasticity framework. How long an environmental effect can persist across generations and whether multigenerational effects are cumulative are primordial—for the evolutionary significance of transgenerational plasticity—but still unresolved questions. In this study, we investigated how the grand‐parental, parental and offspring exposures to predation cues shape the predator‐induced defences of offspring in the Physa acuta snail. We expected that the offspring phenotypes result from a three‐way interaction among grand‐parental, parental and offspring environments. We exposed three generations of snails without and with predator cues according to a full factorial design and measured offspring inducible defences. We found that both grand‐parental and parental exposures to predator cues impacted offspring antipredator defences, but their effects were not cumulative and depended on the defences considered. We also highlighted that the grand‐parental environment did alter reaction norms of offspring shell thickness, demonstrating an interaction between the grand‐parental transgenerational plasticity and the within‐generational plasticity. We concluded that the effects of multigenerational exposure to predator cues resulted on complex offspring phenotypic patterns which are difficult to relate to adaptive antipredator advantages.