Species are hypotheses: avoid connectivity assessments based on pillars of sand

Connectivity among populations determines the dynamics and evolution of populations, and its assessment is essential in ecology in general and in conservation biology in particular. The robust basis of any ecological study is the accurate delimitation of evolutionary units, such as populations, metapopulations and species. Yet a disconnect still persists between the work of taxonomists describing species as working hypotheses and the use of species delimitation by molecular ecologists interested in describing patterns of gene flow. This problem is particularly acute in the marine environment where the inventory of biodiversity is relatively delayed, while for the past two decades, molecular studies have shown a high prevalence of cryptic species. In this study, we illustrate, based on marine case studies, how the failure to recognize boundaries of evolutionary‐relevant unit leads to heavily biased estimates of connectivity. We review the conceptual framework within which species delimitation can be formalized as falsifiable hypotheses and show how connectivity studies can feed integrative taxonomic work and vice versa. Finally, we suggest strategies for spatial, temporal and phylogenetic sampling to reduce the probability of inadequately delimiting evolutionary units when engaging in connectivity studies.     

Pathogen pressure puts immune defense into perspective

The extent to which organisms can protect themselves from disease depends on both the immune defenses they maintain and the pathogens they face. At the same time, immune systems are shaped by the antigens they encounter, both over ecological and evolutionary time. Ecological immunologists often recognize these interactions, yet ecological immunology currently lacks major efforts to characterize the environmental, host-independent, antigenic pressures to which all animals are exposed. Failure to quantify relevant diseases and pathogens in studies of ecological immunology leads to contradictory hypotheses. In contrast, including measures of environmental and host-derived commensals, pathogens, and other immune-relevant organisms will strengthen the field of ecological immunology. In this article, we examine how pathogens and other organisms shape immune defenses and highlight why such information is essential for a better understanding of the causes of variation in immune defenses. We introduce the concept of "operative protection" for understanding the role of immunologically relevant organisms in shaping immune defense profiles, and demonstrate how the evolutionary implications of immune function are best understood in the context of the pressures that diseases and pathogens bring to bear on their hosts. We illustrate common mistakes in characterizing these immune-selective pressures, and provide suggestions for the use of molecular and other methods for measuring immune-relevant organisms.     

Snake diets and the deep history hypothesis

The structure of animal communities has long been of interest to ecologists. Two different hypotheses have been proposed to explain origins of ecological differences among species within present‐day communities. The competition–predation hypothesis states that species interactions drive the evolution of divergence in resource use and niche characteristics. This hypothesis predicts that ecological traits of coexisting species are independent of phylogeny and result from relatively recent species interactions. The deep history hypothesis suggests that divergences deep in the evolutionary history of organisms resulted in niche preferences that are maintained, for the most part, in species represented in present‐day assemblages. Consequently, ecological traits of coexisting species can be predicted based on phylogeny regardless of the community in which individual species presently reside. In the present study, we test the deep history hypothesis along one niche axis, diet, using snakes as our model clade of organisms. Almost 70% of the variation in snake diets is associated with seven major divergences in snake evolutionary history. We discuss these results in the light of relevant morphological, behavioural, and ecological correlates of dietary shifts in snakes. We also discuss the implications of our results with respect to the deep history hypothesis. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 476–486.     

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in a highly systematic way and in a species-neutral manner with the aim of unifying the representation of gene function across different organisms. Each contributing member of the GO Consortium independently associates GO terms to gene products from the organism(s) they are annotating. Here we introduce the Reference Genome project, which brings together those independent efforts into a unified framework based on the evolutionary relationships between genes in these different organisms. The Reference Genome project has two primary goals: to increase the depth and breadth of annotations for genes in each of the organisms in the project, and to create data sets and tools that enable other genome annotation efforts to infer GO annotations for homologous genes in their organisms. In addition, the project has several important incidental benefits, such as increasing annotation consistency across genome databases, and providing important improvements to the GO's logical structure and biological content.     

Introduction. Integration of ecology and endocrinology in avian reproduction: a new synthesis

Birds are some of the most familiar organisms of global ecosystems. Changes in the visibility and abundance of birds are therefore excellent indicators of population and physiological responses to habitat changes and are a major focus for public concern about detrimental environmental changes. In order to understand how birds respond to these challenges, it is essential to determine how the environment affects reproduction under natural conditions. The continuum from environmental variables (cues) to reproductive life-history traits depends upon a cascade of neural and physiological processes that determine the extent and rate at which birds will be able to adapt to changes in their environment. For a full understanding of this ability to adapt, ecologists and endocrinologists need to collaborate and build a common framework. The objective of this theme issue is to bring together a series of papers addressing how evolutionary ecologists and endocrinologists can collaborate directly using avian reproduction as a model system. First, we address the need to integrate ecology and endocrinology and what benefits to biological knowledge will be gained. The papers collected in this issue represent a new synthesis of ecology and endocrinology as discussed in three E-BIRD workshops. The three main foci are trade-offs and constraints, maternal effects and individual variation. Authors within each group present ecological and endocrinological aspects of their topics and many go on to outline testable hypotheses. Finally, we discuss where the major problems remain and how this issue points out where these need collaborative efforts of ecologists and endocrinologists. Specific challenges are raised to future researchers to break through intellectual barriers and explore new frontiers. This framework of topics will ultimately apply to all taxa because the principles involved are universal and hopefully will have direct application to programmes integrating organisms and genes throughout biological sciences.     

动物个性研究进展

"个性"是指不同时空条件下动物种群个体间行为的稳定差异。大量的理论和实验性研究表明,个性差异在动物界普遍存在,其是种群多度和分布、物种共存及群落构建的重要驱动因子。介绍了动物个性的概念、分类及衡量指标,将前人测量个性类型的方法加以总结;随后介绍了动物个性的生态学意义,尤其是个性对动物生活史策略、种群分布与多度、群落结构和动态、生态系统功能和过程以及疾病与信息传播等的影响。在此基础上,进一步分析了在人类活动增加等全球变化背景下,动物个性如何调控动物个体行为、种群和群落动态对这些环境变化的响应。阐述了动物个性的形成与维持机制,并对未来的研究方向进行了展望。     

Fungal genome size and composition reflect ecological strategies along soil fertility gradients

Genomic traits reflect the evolutionary processes that have led to ecological variation among extant organisms, including variation in how they acquire and use resources. Soil fungi have diverse nutritional strategies and exhibit extensive variation in fitness along resource gradients. We tested for trade-offs in genomic traits with mycelial nutritional traits and hypothesize that such trade-offs differ among fungal guilds as they reflect contrasting resource exploitation and habitat preferences. We found species with large genomes exhibited nutrient-poor mycelium and low GC content. These patterns were observed across fungal guilds but with varying explanatory power. We then matched trait data to fungal species observed in 463 Australian grassland, woodland and forest soil samples. Fungi with large genomes and lower GC content dominated in nutrient-poor soils, associated with shifts in guild composition and with species turnover within guilds. These findings highlight fundamental mechanisms that underpin successful ecological strategies for soil fungi.     

Origins and evolution of biological novelty

Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.     

Reducing ambiguity in describing plant–insect interactions: "preference", "acceptability" and "electivity"

Ecologists and evolutionary biologists have a common interest in plant–insect interactions. Ecologists develop terminology describing patterns of association between plants and insects, while evolutionary biologists use the same words to denote potentially heritable traits of individuals. Use of the same terms to describe both traits of the interaction and traits of the organisms hinders communication. An example is "preference", often used by ecologists to denote properties of the plant–insect interaction and by behavioural or evolutionary biologists to denote insect traits. The existing term "electivity" could be incorporated into the lexicon of plant–insect interactions to supplant the ecological use of "preference". The term "preference" would then denote a behavioural trait of the insect. The mirror-image trait of the plant would be "acceptability". This could be a step towards a common terminology that would be usable by both ecologists and evolutionists.     

Toward improved conservation management: a consideration of sensory ecology

All organisms rely on sensory systems to obtain, interpret, and respond to information available in their environment. With rapid alterations of ecosystems occurring across the globe, organisms are being faced with sensory challenges that result in behavioural changes and disruptions with potential population-level consequences. Through a consideration of sensory ecology, it is possible to identify the underlying causes of disturbances at the individual level and use this information to develop better-informed, highly targeted, and more effective management strategies. Indeed, sensory-based approaches have already been successful in response to a variety of conservation issues. This article provides a general discussion of how a consideration of sensory ecology can benefit conservation biology and proceeds to describe three areas of rapid growth and potential for expansion: (1) mitigation of anthropogenic noise disturbance; (2) prevention and amelioration of ecological and other evolutionary traps; (3) targeted population control with special attention to aquatic invasive species. I conclude with general recommendations on how sensory ecologists and conservation biologists can mutually benefit from integrated endeavours.     

中华大仰蝽转录组学研究及SSR新标记开发

【目的】中华大仰蝽Notonecta chinensis为中国和日本冲绳分布的重要水生天敌昆虫,可用于蚊虫的生物防治。本研究旨在建立中华大仰蝽转录组数据库,挖掘其基因信息。【方法】采用高通量测序平台Illumina NextSeq500对中华大仰蝽进行转录组测序、de novo组装及生物信息学分析;利用MISA软件基于转录组unigenes数据进行SSR新分子标记筛选。毛细管电泳检测SSR多态性。【结果】总计获得34782282条clean reads(NCBI SRA数据库登录号:SRR13259254),组装成37801条unigenes,N50为913 bp。将unigenes与已知数据库比对进行基因功能注释,分别有36474,32470,27781,35079和5638条序列注释到nr,Swiss-Prot,GO,eggNOG和KEGG数据库。通过GO数据库注释,unigenes的功能可分为生物学过程、细胞组分和分子功能三大类,其中参与细胞、细胞部分及结合功能的unigenes比例较大。eggNOG数据库注释结果显示,37801条unigenes归到25个基因家族,注释到未知功能的最多。KEGG代谢通路富集分析显示,5638条unigenes注释到245个代谢通路,注释到核糖体的数目最多。此外,用MISA软件在转录组测序数据中的37801条unigenes中搜索到3124个SSR位点(占总unigenes的8.26%),发生频率为7.07%。通过PCR筛选出16个SSR位点。7个中华大仰蝽地理种群3个位点NcCF/NcCR,NcKF/NcKR和NcLF/NcLR的多态信息含量(PIC)分别为0.870,0.902和0.857,具高度多态性。【结论】本研究成功获得了中华大仰蝽转录组数据,为其基因功能分析提供了分子理论基础;SSR新标记的开发为中华大仰蝽遗传多样性分析、隐存种鉴定及基因图谱构建提供了更丰富的候选分子标记。     

Elevational diversity patterns as an example for evolutionary and ecological dynamics in ferns and lycophytes

Evolutionary processes such as adaptation, ecological filtering, and niche conservatism involve the interaction of organisms with their environment and are thus commonly studied along environmental gradients. Elevational gradients have become among the most studied environmental gradients to understand large-scale patterns of species richness and composition because they are highly replicated with different combinations of geographical, environmental and historical factors. We here review the literature on using elevational gradients to understand evolutionary processes in ferns. Some phylogenetic studies of individual fern clades have considered elevation in the analysis or interpretation and postulated that fern diversification is linked to the colonization of mountain habitats. Other studies that have linked elevational community composition and hence ecological filtering with phylogenetic community composition and morphological traits, usually only found limited phylogenetic signal. However, these studies are ultimately only correlational, and there are few actual tests of the evolutionary mechanisms leading to these patterns. We identify a number of challenges for improving our understanding of how evolutionary and ecological processes are linked to elevational richness patterns in ferns: i) limited information on traits and their ecological relevance, ii) uncertainties on the dispersal kernels of ferns and hence the delimitation of regional species pools from which local assemblages are recruited, iii) limited genomic data to identify candidate genes under selection and hence actually document adaptation and selection, and iv) conceptual challenges in developing clear and testable hypotheses to how specific evolutionary processes can be linked to patterns in community composition and species richness.     

Ecological interactions drive evolutionary loss of traits

Loss of traits can dramatically alter the fate of species. Evidence is rapidly accumulating that the prevalence of trait loss is grossly underestimated. New findings demonstrate that traits can be lost without affecting the external phenotype, provided the lost function is compensated for by species interactions. This is important because trait loss can tighten the ecological relationship between partners, affecting the maintenance of species interactions. Here, we develop a new perspective on so-called `compensated trait loss' and how this type of trait loss may affect the evolutionary dynamics between interacting organisms. We argue that: (1) the frequency of compensated trait loss is currently underestimated because it can go unnoticed as long as ecological interactions are maintained; (2) by analysing known cases of trait loss, specific factors promoting compensated trait loss can be identified and (3) genomic sequencing is a key way forwards in detecting compensated trait loss. We present a comprehensive literature survey showing that compensated trait loss is taxonomically widespread, can involve essential traits, and often occurs as replicated evolutionary events. Despite its hidden nature, compensated trait loss is important in directing evolutionary dynamics of ecological relationships and has the potential to change facultative ecological interactions into obligatory ones.     

Between semelparity and iteroparity: Empirical evidence for a continuum of modes of parity

The number of times an organism reproduces (i.e., its mode of parity) is a fundamental life‐history character, and evolutionary and ecological models that compare the relative fitnesses of different modes of parity are common in life‐history theory and theoretical biology. Despite the success of mathematical models designed to compare intrinsic rates of increase (i.e., density‐independent growth rates) between annual‐semelparous and perennial‐iteroparous reproductive schedules, there is widespread evidence that variation in reproductive allocation among semelparous and iteroparous organisms alike is continuous. This study reviews the ecological and molecular evidence for the continuity and plasticity of modes of parity—that is, the idea that annual‐semelparous and perennial‐iteroparous life histories are better understood as endpoints along a continuum of possible strategies. I conclude that parity should be understood as a continuum of different modes of parity, which differ by the degree to which they disperse or concentrate reproductive effort in time. I further argue that there are three main implications of this conclusion: (1) that seasonality should not be conflated with parity; (2) that mathematical models purporting to explain the general evolution of semelparous life histories from iteroparous ones (or vice versa) should not assume that organisms can only display either an annual‐semelparous life history or a perennial‐iteroparous one; and (3) that evolutionary ecologists should base explanations of how different life‐history strategies evolve on the physiological or molecular basis of traits underlying different modes of parity.     

SimHap GUI: An intuitive graphical user interface for genetic association analysis

Background

The expressed sequence tag (EST) methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that do not have the bioinformatics infrastructure of major genome sequencing centres. Therefore, there is a need for user-friendly tools to facilitate the annotation of non-model species EST datasets with well-defined ontologies that enable meaningful cross-species comparisons. To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways.

Results

annot8r automatically downloads all files relevant for the annotation process and generates a reference database that stores UniProt entries, their associated Gene Ontology (GO), Enzyme Commission (EC) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotation and additional relevant data. For each of GO, EC and KEGG, annot8r extracts a specific sequence subset from the UniProt dataset based on the information stored in the reference database. These three subsets are then formatted for BLAST searches. The user provides the protein or nucleotide sequences to be annotated and annot8r runs BLAST searches against these three subsets. The BLAST results are parsed and the corresponding annotations retrieved from the reference database. The annotations are saved both as flat files and also in a relational postgreSQL results database to facilitate more advanced searches within the results. annot8r is integrated with the PartiGene suite of EST analysis tools.

Conclusion

annot8r is a tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and the ease of use of the program make it ideally suited for non-model species EST-sequencing projects.     

Relationships between ecological interaction modifications and diffuse coevolution: similarities, differences, and causal links

A major empirical approach in community ecology is to describe the dynamics of a community by examining small subsets of species. Unfortunately, interaction modifications, which cause pair-wise interaction coefficients to depend on the presence or absence of additional species, can make it difficult to predict the overall dynamics of species within a community from experiments with pairs of species. In a similar fashion, one of the major approaches in evolutionary ecology has been to describe the likely evolutionary dynamics of a single species by focusing on the selection imposed by a limited number of other species within the community. However, recent work on diffuse coevolution indicates that selection pressures due to one species can change in the presence of other species. The magnitude of the difficulty that interaction modifications and diffuse coevolution present for predicting ecological and evolutionary dynamics is an unresolved question. Here we outline the similarities and differences between the two topics, discuss experimental and statistical approaches to studying them, and make predictions about when ecological interaction modifications are likely to cause diffuse coevolution. Since the currencies for interaction modifications are usually fitness components such as growth, fecundity, or survival, is it likely that these will translate into corresponding differences in the relative fitness of individuals or genotypes, and thus in general these two phenomena will occur together. We argue that community ecologists and evolutionary ecologists will both benefit from experiments that test for the effects of interaction modifications, and that studies of the mechanisms driving interaction modifications and diffuse coevolution (e.g., changes in behavior, nonlinear effects on shared resources, genetic covariances) will aid our progress in understanding the ecological and evolutionary dynamics of communities.     

Finding the Needles in the Metagenome Haystack

In the collective genomes (the metagenome) of the microorganisms inhabiting the Earth’s diverse environments is written the history of life on this planet. New molecular tools developed and used for the past 15 years by microbial ecologists are facilitating the extraction, cloning, screening, and sequencing of these genomes. This approach allows microbial ecologists to access and study the full range of microbial diversity, regardless of our ability to culture organisms, and provides an unprecedented access to the breadth of natural products that these genomes encode. However, there is no way that the mere collection of sequences, no matter how expansive, can provide full coverage of the complex world of microbial metagenomes within the foreseeable future. Furthermore, although it is possible to fish out highly informative and useful genes from the sea of gene diversity in the environment, this can be a highly tedious and inefficient procedure. Microbial ecologists must be clever in their pursuit of ecologically relevant, valuable, and niche-defining genomic information within the vast haystack of microbial diversity. In this report, we seek to describe advances and prospects that will help microbial ecologists glean more knowledge from investigations into metagenomes. These include technological advances in sequencing and cloning methodologies, as well as improvements in annotation and comparative sequence analysis. More significant, however, will be ways to focus in on various subsets of the metagenome that may be of particular relevance, either by limiting the target community under study or improving the focus or speed of screening procedures. Lastly, given the cost and infrastructure necessary for large metagenome projects, and the almost inexhaustible amount of data they can produce, trends toward broader use of metagenome data across the research community coupled with the needed investment in bioinformatics infrastructure devoted to metagenomics will no doubt further increase the value of metagenomic studies in various environments.