Telomeres:Linking stress and survival,ecology and evolution

Telomeres are protective structures at the ends of eukaryotic chromosomes. The loss of telomeres through cell division and oxidative stress is related to cellular aging, organismal growth and disease. In this way, telomeres link molecular and cellular mechanisms with organismal processes, and may explain variation in a number of important life-history traits. Here, we discuss how telomere biology relates to the study of physiological ecology and life history evolution. We emphasize current knowledge on how ...     

The ecology and evolution of host-plant resistance to insects

Genetic techniques have yielded new insights into plant-herbivore coevolution. Quantitative genetic tests of herbivory theory reveal that in some cases insect herbivores impose selection on resistance traits. Also, some resistance traits are costly while others appear not to be, and genetic models can explain these results. Genetic variation in plant resistance influences insect community structure by modifying interactions of herbivores with competitors and natural enemies. Therefore, models of multispecies coevolution are more realistic than pairwise coevolutionary models. Ecological genetics will facilitate further theoretical and empirical exploration of multispecies coevolution of plants and herbivores.     

Using functional morphology to examine the ecology and evolution of specialization

Researchers strive to understand what makes species different,and what allows them to survive in the time and space that theydo. Many models have been advanced which encompass an arrayof ecological, evolutionary, mathematical, and logical principles.The goal has been to develop ecological theories that can, amongother things, make specific and robust predictions about howand where organisms should live and what organisms should utilize.The role of functional morphology is often an under-appreciatedparameter of these models. A more complete understanding ofhow anatomical features work to allow the organism to accomplishcertain tasks has allowed us to revisit some of these ideaswith a new perspective. We illustrate our view of this rolefor functional morphology in ecology by considering the issueof specialization: we attempt to align several definitions ofspecialization based upon shared ecological and evolutionaryprinciples, and we summarize theoretical predictions regardingwhy an organism might specialize. Kinematic studies of preycapture in several types of fishes are explored with regardto the potential ecological and evolutionary consequences ofspecialization, most notably in the area of trade-offs. We suggestthat a functional morphological perspective can increase ourunderstanding of the ecological concepts of specialization andit consequences. The kinds of data that functional morphologistscollect can help us to quantify organismal performance associatedwith specialization and the union of functional morphology withecology can help us to better understand not just how but whyorganisms interact in the manner that they do.     

Higher-level classification of the Archaea: evolution of methanogenesis and methanogens

We used a phylogenetic approach to analyze the evolution of methanogenesis and methanogens. We show that 23 vertically transmitted ribosomal proteins do not support the monophyly of methanogens, and propose instead that there are two distantly related groups of extant archaea that produce methane, which we have named Class I and Class II. Based on this finding, we subsequently investigated the uniqueness of the origin of methanogenesis by studying both the enzymes of methanogenesis and the proteins that synthesize its specific coenzymes. We conclude that hydrogenotrophic methanogenesis appeared only once during evolution. Genes involved in the seven central steps of the methanogenic reduction of carbon dioxide (CO(2)) are ubiquitous in methanogens and share a common history. This suggests that, although extant methanogens produce methane from various substrates (CO(2), formate, acetate, methylated C-1 compounds), these archaea have a core of conserved enzymes that have undergone little evolutionary change. Furthermore, this core of methanogenesis enzymes seems to originate (as a whole) from the last ancestor of all methanogens and does not appear to have been horizontally transmitted to other organisms or between members of Class I and Class II. The observation of a unique and ancestral form of methanogenesis suggests that it was preserved in two independent lineages, with some instances of specialization or added metabolic flexibility. It was likely lost in the Halobacteriales, Thermoplasmatales and Archaeoglobales. Given that fossil evidence for methanogenesis dates back 2.8 billion years, a unique origin of this process makes the methanogenic archaea a very ancient taxon.     

Phylogeny and evolution of the Archaea: one hundred genomes later

Little more than 30 years since the discovery of the Archaea, over one hundred archaeal genome sequences are now publicly available, of which ～40% have been released in the last two years. Their analysis provides an increasingly complex picture of archaeal phylogeny and evolution with the proposal of new major phyla, such as the Thaumarchaeota, and important information on the evolution of key central cellular features such as cell division. Insights have been gained into the events and processes in archaeal evolution, with a number of additional and unexpected links to the Eukaryotes revealed. Taken together, these results predict that many more surprises will be found as new archaeal genomes are sequenced.     

Distinct functional domains of Ubc9 dictate cell survival and resistance to genotoxic stress

Covalent modification with SUMO alters protein function, intracellular localization, or protein-protein interactions. Target recognition is determined, in part, by the SUMO E2 enzyme, Ubc9, while Siz/Pias E3 ligases may facilitate select interactions by acting as substrate adaptors. A yeast conditional Ubc9P(123)L mutant was viable at 36 degrees C yet exhibited enhanced sensitivity to DNA damage. To define functional domains in Ubc9 that dictate cellular responses to genotoxic stress versus those necessary for cell viability, a 1.75-A structure of yeast Ubc9 that demonstrated considerable conservation of backbone architecture with human Ubc9 was solved. Nevertheless, differences in side chain geometry/charge guided the design of human/yeast chimeras, where swapping domains implicated in (i) binding residues within substrates that flank canonical SUMOylation sites, (ii) interactions with the RanBP2 E3 ligase, and (iii) binding of the heterodimeric E1 and SUMO had distinct effects on cell growth and resistance to DNA-damaging agents. Our findings establish a functional interaction between N-terminal and substrate-binding domains of Ubc9 and distinguish the activities of E3 ligases Siz1 and Siz2 in regulating cellular responses to genotoxic stress.     

Inference in ecology and evolution

Most ecologists and evolutionary biologists continue to rely heavily on null hypothesis significance testing, rather than on recently advocated alternatives, for inference. Here, we briefly review null hypothesis significance testing and its major alternatives. We identify major objectives of statistical analysis and suggest which analytical approaches are appropriate for each. Any well designed study can improve our understanding of biological systems, regardless of the inferential approach used. Nevertheless, an awareness of available techniques and their pitfalls could guide better approaches to data collection and broaden the range of questions that can be addressed. Although we should reduce our reliance on significance testing, it retains an important role in statistical education and is likely to remain fundamental to the falsification of scientific hypotheses.     

The ecology and evolution of bacteriocins

In this review we focus on the ecological and evolutionary forces that determine the frequency and diversity of colicins inEscherichia coli. To begin, we describe that this killing phenotype is ubiquitous inE. coli, with as many as 50% of the isolates from a population producing colicin toxins, and that each population sampled has its own unique distribution of the more than 20 known colicin types. Next, we explore the dynamics of colicinogeny, which exhibits a typical form of frequency dependence, where the likelihood of successful colicin invasion into a population increases as the initial density of colicinogenic cells increases. We then incorporate thoughts on the evolution of chromosomal resistance to colicins and describe how resistance might influence the dynamics of colicinogen invasion and maintenance and the resulting colicin diversity. The final section deals with a genetic and phylogenetic characterization of colicins and a discussion of the evolutionary mechanisms responsible for generating colicin diversity. In this final section we provide details of the different molecular mechanisms known to play a role in generating colicin diversity, including the two most dominant forces in colincin evolution: recombination and positive, deversifying, selection.     

The origin and evolution of Archaea: a state of the art

Environmental surveys indicate that the Archaea are diverse and abundant not only in extreme environments, but also in soil, oceans and freshwater, where they may fulfil a key role in the biogeochemical cycles of the planet. Archaea display unique capacities, such as methanogenesis and survival at temperatures higher than 90 degrees C, that make them crucial for understanding the nature of the biota of early Earth. Molecular, genomics and phylogenetics data strengthen Woese's definition of Archaea as a third domain of life in addition to Bacteria and Eukarya. Phylogenomics analyses of the components of different molecular systems are highlighting a core of mainly vertically inherited genes in Archaea. This allows recovering a globally well-resolved picture of archaeal evolution, as opposed to what is observed for Bacteria and Eukarya. This may be due to the fact that no rapid divergence occurred at the emergence of present-day archaeal lineages. This phylogeny supports a hyperthermophilic and non-methanogenic ancestor to present-day archaeal lineages, and a profound divergence between two major phyla, the Crenarchaeota and the Euryarchaeota, that may not have an equivalent in the other two domains of life. Nanoarchaea may not represent a third and ancestral archaeal phylum, but a fast-evolving euryarchaeal lineage. Methanogenesis seems to have appeared only once and early in the evolution of Euryarchaeota. Filling up this picture of archaeal evolution by adding presently uncultivated species, and placing it back in geological time remain two essential goals for the future.     

Forward from the crossroads of ecology and evolution

Community genetics is a synthesis of community ecology and evolutionary biology. It examines how genetic variation within a species affects interactions among species to change ecological community structure and diversity. The use of community genetics approaches has greatly expanded in recent years and the evidence for ecological effects of genetic diversity is growing. The goal of current community genetics research is to determine the circumstances in which, and the mechanisms by which community genetic effects occur and is the focus of the papers in this special issue. We bring a new group of researchers into the community genetics fold. Using a mixture of empirical research, literature reviews and theoretical development, we introduce novel concepts and methods that we hope will enable us to develop community genetics into the future.     

Network thinking in ecology and evolution

Although pairwise interactions have always had a key role in ecology and evolutionary biology, the recent increase in the amount and availability of biological data has placed a new focus on the complex networks embedded in biological systems. The increased availability of computational tools to store and retrieve biological data has facilitated wide access to these data, not just by biologists but also by specialists from the social sciences, computer science, physics and mathematics. This fusion of interests has led to a burst of research on the properties and consequences of network structure in biological systems. Although traditional measures of network structure and function have started us off on the right foot, an important next step is to create biologically realistic models of network formation, evolution, and function. Here, we review recent applications of network thinking to the evolution of networks at the gene and protein level and to the dynamics and stability of communities. These studies have provided new insights into the organization and function of biological systems by applying existing techniques of network analysis. The current challenge is to recognize the commonalities in evolutionary and ecological applications of network thinking to create a predictive science of biological networks.     

Funding troubles for evolution and ecology

The human population passed the 7 billion mark last month. As the population grows, the environment, which in turn is necessary for our survival, suffers as a result of increased demand for natural resources and global warming. Key to addressing these challenges will be new knowledge provided by the evolutionary and ecological sciences. But, alarmingly, these areas are underfunded, as Cyrus Martin reports.