Molecular approaches to the study of evolution and phylogeny of the Nemertina

Molecular biological tools currently available to us are revolutionizing the way in which we can address questions in evolutionary biology. The purpose of this article is to provide an overview of molecular techniques and applications available to biologists who are interested in evolutionary studies but who have little acquaintance with molecular biology. In evolutionary biology, techniques designed to determine degree of nucleic acid similarity are in common use and will be dealt with first. Another approach, namely gene expression studies, has strong implications for evolutionary biology but generally requires substantial familiarity with molecular biological tools. Expression studies provide powerful tools for discerning processes of speciation, as in the selection of genetic variants, as well as discerning lineages, e.g., expression of specific homeobox genes during segment formation. For investigations where either nucleic acid identity or gene expression are the ultimate goal, detailed information, protocols and appropriate controls are beyond the scope of this work but, where possible, recent review articles are cited.     

Ecology and evolution of plant�Cpollinator interactions

Background

Some of the most exciting advances in pollination biology have resulted from interdisciplinary research combining ecological and evolutionary perspectives. For example, these two approaches have been essential for understanding the functional ecology of floral traits, the dynamics of pollen transport, competition for pollinator services, and patterns of specialization and generalization in plant–pollinator interactions. However, as research in these and other areas has progressed, many pollination biologists have become more specialized in their research interests, focusing their attention on either evolutionary or ecological questions. We believe that the continuing vigour of a synthetic and interdisciplinary field like pollination biology depends on renewed connections between ecological and evolutionary approaches.

Scope

In this Viewpoint paper we highlight the application of ecological and evolutionary approaches to two themes in pollination biology: (1) links between pollinator behaviour and plant mating systems, and (2) generalization and specialization in pollination systems. We also describe how mathematical models and synthetic analyses have broadened our understanding of pollination biology, especially in human-modified landscapes. We conclude with several suggestions that we hope will stimulate future research. This Viewpoint also serves as the introduction to this Special Issue on the Ecology and Evolution of Plant–Pollinator Interactions. These papers provide inspiring examples of the synergy between evolutionary and ecological approaches, and offer glimpses of great accomplishments yet to come.Key words: Floral traits, generalization and specialization, global change, male fitness, mating systems, multiple paternity, plant–pollinator networks, pollen and gene dispersal, pollinator behaviour, pollination syndromes, pollination webs, self-fertilization     

Climate change,collections and the classroom: using big data to tackle big problems

Preparing students to explore, understand, and resolve societal challenges such as global climate change is an important task for evolutionary and ecological biologists that will require novel and innovative pedagogical approaches. Recent calls to reform undergraduate science education emphasize the importance of engaging students in inquiry-driven, active, and authentic learning experiences. We believe that the vast digital resources (i.e., “big data”) associated with natural history collections provide invaluable but underutilized opportunities to create such experiences for undergraduates in biology. Here, we describe an online, open-access educational module that we have developed that harnesses the power of collections-based information to introduce students to multiple conceptual and analytical elements of climate change, evolutionary, and ecological biology research. The module builds upon natural history specimens and data collected over the span of nearly a century in Yosemite National Park, California, to guide students through a series of exercises aimed at testing hypotheses regarding observed differences in response to climate change by two closely related and partially co-occurring species of chipmunks. The content of the module can readily be modified to meet the pedagogical goals and instructional levels of different courses while the analytical strategies outlined can be adapted to address a wide array of questions in evolutionary and ecological biology. In sum, we believe that specimen-based natural history data represent a powerful platform for reforming undergraduate instruction in biology. Because these efforts will result in citizens who are better prepared to understand complex biological relationships, the benefits of this approach to undergraduate education will have widespread benefits to society.     

The naturalist in a world of genomics

Functional genomics provides new opportunities to address issues of fundamental interest in evolutionary biology and suggests many new research directions that are ripe for evolutionary investigation. New types of data, and the ability to study biological processes from a whole genome perspective, are likely to have a profound impact on evolutionary biology and ecology. To illustrate, we discuss how genomewide gene expression studies can be used to reformulate questions about trade-offs and pleiotropy. We then touch on some of the new research opportunities that the application of functional genomics affords to evolutionary biologists. We end with some brief notes about how evolutionary biology and comparative approaches will probably have an impact on functional genomics.     

Toward a stoichiometric framework for evolutionary biology

Ecological stoichiometry, the study of the balance of energy and materials in living systems, may serve as a useful synthetic framework for evolutionary biology. Here, we review recent work that illustrates the power of a stoichiometric approach to evolution across multiple scales, and then point to important open questions that may chart the way forward in this new field. At the molecular level, stoichiometry links hereditary changes in the molecular composition of organisms to key phenotypic functions. At the level of evolutionary ecology, a simultaneous focus on the energetic and material underpinnings of evolutionary tradeoffs and transactions highlights the relationship between the cost of resource acquisition and the functional consequences of biochemical composition. At the macroevolutionary level, a stoichiometric perspective can better operationalize models of adaptive radiation and escalation, and elucidate links between evolutionary innovation and the development of global biogeochemical cycles. Because ecological stoichiometry focuses on the interaction of energetic and multiple material currencies, it should provide new opportunities for coupling evolutionary dynamics across scales from genomes to the biosphere.     

What is speciation and how should we study it?

To understand speciation, we first need to know what species are. Yet debates over species concepts have seemed endless, with little obvious relevance to the study of speciation. Recently, there has been progress in resolving these debates, favoring a lineage-based, evolutionary species concept. This progress calls for reconsideration of the study of speciation. Traditional speciation research based on the biological species concept has led to great advances in understanding how nonallopatric speciation occurs and how species diverge and remain separate from each other. However, this research has neglected the question of how new species arise in the first place for the most common geographic mode (allopatric). A new and very different research program is needed to understand the ecological and evolutionary processes that split an ancestral species into new allopatric lineages. This research program will connect speciation to many other fundamental questions in evolutionary biology, ecology, biogeography, and conservation biology.     

Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology

Phylogenetics has inherent utility in evolutionary developmental biology (EDB) as it is an established methodology for estimating evolutionary relationships and for making comparisons between levels of biological organization. However, explicit phylogenetic methods generally have been limited to two levels of organization in EDB-the species and the gene. We demonstrate that phylogenetic methods can be applied broadly to other organizational levels, such as morphological structures or cell types, to identify evolutionary patterns. We present examples at and between different hierarchical levels of organization to address questions central to EDB. We argue that this application of "hierarchical phylogenetics" can be a unifying analytical approach to the field of EDB.     

The morphogenesis of evolutionary developmental biology

The early studies of evolutionary developmental biology (Evo-Devo) come from several sources. Tributaries flowing into Evo-Devo came from such disciplines as embryology, developmental genetics, evolutionary biology, ecology, paleontology, systematics, medical embryology and mathematical modeling. This essay will trace one of the major pathways, that from evolutionary embryology to Evo-Devo and it will show the interactions of this pathway with two other sources of Evo-Devo: ecological developmental biology and medical developmental biology. Together, these three fields are forming a more inclusive evolutionary developmental biology that is revitalizing and providing answers to old and important questions involving the formation of biodiversity on Earth. The phenotype of Evo-Devo is limited by internal constraints on what could be known given the methods and equipment of the time and it has been framed by external factors that include both academic and global politics.     

Individual variation in endocrine systems: moving beyond the 'tyranny of the Golden Mean'

Twenty years ago, Albert Bennett published a paper in the influential book New directions in ecological physiology arguing that individual variation was an 'underutilized resource'. In this paper, I review our state of knowledge of the magnitude, mechanisms and functional significance of phenotypic variation, plasticity and flexibility in endocrine systems, and argue for a renewed focus on inter-individual variability. This will provide challenges to conventional wisdom in endocrinology itself, e.g. re-evaluation of relatively simple, but unresolved questions such as structure-function relationships among hormones, binding globulins and receptors, and the functional significance of absolute versus relative hormone titres. However, there are also abundant opportunities for endocrinologists to contribute solid mechanistic understanding to key questions in evolutionary biology, e.g. how endocrine regulation is involved in evolution of complex suites of traits, or how hormone pleiotropy regulates trade-offs among life-history traits. This will require endocrinologists to embrace the raw material of adaptation (heritable, individual variation and phenotypic plasticity) and to take advantage of conceptual approaches widely used in evolutionary biology (selection studies, reaction norms, concepts of evolutionary design) as well as a more explicit focus on the endocrine basis of life-history traits that are of primary interest to evolutionary biologists (cf. behavioural endocrinology).     

对我国分子生态学研究近期发展战略的一些思考

分子生态学是多学科交叉的整合性研究领域, 是运用进化生物学理论解决宏观生物学问题的科学。经过半个多世纪的发展, 本学科已日趋成熟, 它不仅已经广泛渗透到宏观生物学的众多学科领域, 而且已经成为连接和融合很多不同学科的桥梁, 是目前最具活力的研究领域之一。其研究的范畴, 从最基础的理论和方法技术, 到格局和模式的发现和描述, 到对过程和机制的深入探讨, 再到付诸于实践的行动和规划指导等各个层次。分子生态学的兴起给宏观生物学带来了若干飞跃性的变化, 使宏观生物学由传统的以观察、测量和推理为主的描述性研究转变为以从生物和种群的遗传构成的变化和历史演化背景上检验、证明科学假设及揭示机制和规律为主的机制性/解释性研究, 因而使得对具有普遍意义的科学规律、生态和进化过程及机制的探索成为可能。分子生态学已经进入组学研究时代, 这使得阐明复杂生态过程、生物地理过程和适应性演化过程的机制性研究由原来难以企及的梦想变成完全可以实现的探求; 它也带来了全新的挑战, 其中最有深远影响的将是对分子生态学研究至关重要的进化生物学基础理论方面的突破, 例如遗传变异理论、种群分化理论、表观遗传因素的作用, 乃至进化生物学的基本知识构架等等。这些方面的进展必将使宏观生物学迎来一场空前的革命, 并对生态学的所有分支学科产生重大影响, 甚至催生诸如生态表观组学这样的新分支学科。对于中国科学家来说, 分子生态学组学时代的开启, 更是一个千载难逢的机遇, 为提出和建立生命科学的新方法、新假说、新思想和新理论提供了莫大的探索空间——此前我们对宏观生物学方法、理论和思想的发展贡献很小。然而, 限制组学时代重大突破的关键因素是理论、概念、理念、实验方法或分析方法方面的创新和突破, 这正是我国分子生态学研究最薄弱的环节。我国教育部门应尽快调整生命科学本科生培养的理念和方法, 以培养具备突出创新潜力的年轻一代后备人才; 同时, 科研项目资助部门和研究人员不仅应清醒地认识本学科领域的发展态势, 更要及时调整思路, 树立新的项目管理理念和治学 理念。     

Forecasting Ecological Genomics: High-Tech Animal Instrumentation Meets High-Throughput Sequencing

Recent advancements in animal tracking technology and high-throughput sequencing are rapidly changing the questions and scope of research in the biological sciences. The integration of genomic data with high-tech animal instrumentation comes as a natural progression of traditional work in ecological genetics, and we provide a framework for linking the separate data streams from these technologies. Such a merger will elucidate the genetic basis of adaptive behaviors like migration and hibernation and advance our understanding of fundamental ecological and evolutionary processes such as pathogen transmission, population responses to environmental change, and communication in natural populations.     

Units and passages: A view for evolutionary biology and ecology

Many authors, including paleobiologists, cladists and so on, adopt a nested hierarchical viewpoint to examine the relationships among different levels of biological organization. Furthermore, species are often considered to be unique entities in functioning evolutionary processes and one of the individuals forming a nested hierarchy.I have attempted to show that such a hierarchical view is inadequate in evolutionary biology. We should define units depending on what we are trying to explain. Units that play an important role in evolution and ecology do not necessarily form a nested hierarchy. Also the relationships among genealogies at different levels are not simply nested. I have attempted to distinguish the different characteristics of passages when they are used for different purposes of explanation. In my analysis, species and monophyletic taxa cannot be uniquely defined as single units that function in ecological and evolutionary processes.The view discussed in this paper may provide a more general basis for testing competing theories in evolution, and provide new insights for future empirical studies.     

Mitochondrial gene rearrangements: new paradigm in the evolutionary biology and systematics

Mitochondrial (mt) genomic study may reveal significant insight into the molecular evolution and several other aspects of genome evolution such as gene rearrangements evolution, gene regulation, and replication mechanisms. Other questions such as patterns of gene expression mechanism evolution, genomic variation and its correlation with physiology, and other molecular and biochemical mechanisms can be addressed by the mt genomics. Rare genomic changes have attracted evolutionary biology community for providing homoplasy free evidence of phylogenetic relationships. Gene rearrangements are considered to be rare evolutionary events and are being used to reconstruct the phylogeny of diverse group of organisms. Mt gene rearrangements have been established as a hotspot for the phylogenetic and evolutionary analysis of closely as well as distantly related organisms.     

Engineering gene overlaps to sustain genetic constructs in vivo

Evolution is often an obstacle to the engineering of stable biological systems due to the selection of mutations inactivating costly gene circuits. Gene overlaps induce important constraints on sequences and their evolution. We show that these constraints can be harnessed to increase the stability of costly genes by purging loss-of-function mutations. We combine computational and synthetic biology approaches to rationally design an overlapping reading frame expressing an essential gene within an existing gene to protect. Our algorithm succeeded in creating overlapping reading frames in 80% of E. coli genes. Experimentally, scoring mutations in both genes of such overlapping construct, we found that a significant fraction of mutations impacting the gene to protect have a deleterious effect on the essential gene. Such an overlap thus protects a costly gene from removal by natural selection by associating the benefit of this removal with a larger or even lethal cost. In our synthetic constructs, the overlap converts many of the possible mutants into evolutionary dead-ends, reducing the evolutionary potential of the system and thus increasing its stability over time.     

Computational methods in synthetic biology

We discuss how a theoretical synthetic biology research programme may liberate empiricism in biological sciences beyond the unaided human brain. Because synthetic biological systems are relatively small and largely independent of evolutionary contexts, they can be represented with mathematical models strongly founded on first principles of molecular biology and laws of statistical thermodynamics. A universal mathematical formalism for describing synthetic constructs may then be plausibly used to explain in unambiguous, quantitative terms how biological phenotypic complexity emerges as a result of well-defined biomolecular interactions. SynBioSS, a publicly available software package, is described that implements this mathematical formalism.     

TRIBUTE: In Goethe's Wake: Marvalee Wake's conceptual contributions to the development and evolution of a science of morphology

Decrying the typological approach in much of the teaching of morphology, from the outset of her career Marvalee Wake advocated a synthetic, mechanistic and pluralistic developmental and evolutionary morphology. In this short essay, I do not evaluate Wake's contributions to our knowledge of the morphology of caecilians, nor her contributions to viviparity, both of which are seminal and substantive, nor do I examine her role as mentor, supervisor and collaborator, but assess her broader conceptual contributions to the development and evolution of morphology as a science. One of the earliest morphologists to take on board the concept of constraint, she viewed constraint explicitly in relation to adaptation and diversity. Her approach to morphology as a science was hierarchical – measure form and function in a phylogenetic context; seek explanations at developmental, functional, ecological, evolutionary levels of the biological hierarchy; integrate those explanations to the other levels. The explanatory power of morphology thus practised allows morphology to inform evolutionary biology and evolutionary theory, and paves the way for the integrative biology Wake has long championed.     

Evolutionary Novelty and the Evo-Devo Synthesis: Field Notes

Accounting for the evolutionary origins of morphological novelty is one of the core challenges of contemporary evolutionary biology. A successful explanatory framework requires the integration of different biological disciplines, but the relationships between developmental biology and standard evolutionary biology remain contested. There is also disagreement about how to define the concept of evolutionary novelty. These issues were the subjects of a workshop held in November 2009 at the University of Alberta. We report on the discussion and results of this workshop, addressing questions about (i) how to define evolutionary novelty and understand its significance, (ii) how to interpret evolutionary developmental biology as a synthesis and its relation to neo-Darwinian evolutionary theory, and (iii) how to integrate disparate biological approaches in general.     

Targeted sequence capture as a powerful tool for evolutionary analysis1

Next-generation sequencing technologies (NGS) have revolutionized biological research by significantly increasing data generation while simultaneously decreasing the time to data output. For many ecologists and evolutionary biologists, the research opportunities afforded by NGS are substantial; even for taxa lacking genomic resources, large-scale genome-level questions can now be addressed, opening up many new avenues of research. While rapid and massive sequencing afforded by NGS increases the scope and scale of many research objectives, whole genome sequencing is often unwarranted and unnecessarily complex for specific research questions. Recently developed targeted sequence enrichment, coupled with NGS, represents a beneficial strategy for enhancing data generation to answer questions in ecology and evolutionary biology. This marriage of technologies offers researchers a simple method to isolate and analyze a few to hundreds, or even thousands, of genes or genomic regions from few to many samples in a relatively efficient and effective manner. These strategies can be applied to questions at both the infra- and interspecific levels, including those involving parentage, gene flow, divergence, phylogenetics, reticulate evolution, and many more. Here we provide a brief overview of targeted sequence enrichment, and emphasize the power of this technology to increase our ability to address a wide range of questions of interest to ecologists and evolutionary biologists, particularly for those working with taxa for which few genomic resources are available.     

Revealing evolutionary pathways by fitness landscape reconstruction

The concept of epistasis has since long been used to denote non-additive fitness effects of genetic changes and has played a central role in understanding the evolution of biological systems. Owing to an array of novel experimental methodologies, it has become possible to experimentally determine epistatic interactions as well as more elaborate genotype-fitness maps. These data have opened up the investigation of a host of long-standing questions in evolutionary biology, such as the ruggedness of fitness landscapes and the accessibility of mutational trajectories, the evolution of sex, and the origin of robustness and modularity. Here we review this recent and timely marriage between systems biology and evolutionary biology, which holds the promise to understand evolutionary dynamics in a more mechanistic and predictive manner.     

Ecological genetics of invasive alien species

There is growing realisation that integrating genetics and ecology is critical in the context of biological invasions, since the two are explicitly linked. So far, the focus of ecological genetics of invasive alien species (IAS) has been on determining the sources and routes of invasions, and the genetic make-up of founding populations, which is critical for defining and testing ecological and evolutionary hypotheses. However an ecological genetics approach can be extended to investigate questions about invasion success and impacts on native, recipient species. Here, we discuss recent progress in the field, provide overviews of recent methodological advances, and highlight areas that we believe are of particular interest for future research. First, we discuss the main insights from studies that have inferred source populations and invasion routes using molecular genetic data, with particular focus on the role of genetic diversity, adaptation and admixture in invasion success. Second, we consider how genetic tools can lead to a better understanding of patterns of dispersal, which is critical to predicting the spread of invasive species, and how studying invasions can shed light on the evolution of dispersal. Finally, we explore the potential for combining molecular genetic data and ecological network modelling to investigate community interactions such as those between predator and prey, and host and parasite. We conclude that invasions are excellent model systems for understanding the role of natural selection in shaping phenotypes and that an ecological genetics approach offers great potential for addressing fundamental questions in invasion biology.