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.     

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.     

The evolution of parental care in shorebirds: life histories, ecology, and sexual selection

Parental care is expected to evolve according to a trade-offbetween the benefits of increased survival of offspring andcosts of reduced survival and future reproduction of adults.Here we investigate the components of this life-history trade-offin shorebirds (Charadriides, excluding Laroidea), an avian infraorderdisplaying an unusual diversity in extent of care by each sex.We show that evolutionary increases in the duration of carein one sex are associated with decreased care by the other.We found no evidence that various hypothesised benefits of careprovide a general explanation for the duration of care by eitheror both sexes, although parental feeding of the young was tooconservative for comparisons. Sexual dimorphism in body sizehad a similar relationship to parental care in both sexes: reductionsin duration of care by either sex were matched by increasesin the size of that sex relative to the other. Whereas thispattern could be explained by sexual selection in males, itwas retained within socially monogamous females. Reduced carein males (but not in females) appears to have facilitated theevolution of greater migration distances. These results suggestthat parental care has had different causes and consequencesin each sex. Benefits of desertion due to sexual selection aremore clearly demonstrable for males, whereas correlates of careare less clear for females     

Olfactory evolution and behavioral ecology in primates

Primates are usually thought of as "visual" mammals, and several comparative studies have emphasized the role of vision in primate neural and sociocognitive specialization. Here I explore the role of olfactory systems, using phylogenetic analysis of comparative volumetric data. The relative sizes of the main olfactory bulb (MOB) and accessory olfactory bulb (AOB) tend to show different evolutionary patterns in accordance with their different functions. Although there is some evidence of correlated evolution of the two systems, this is apparent in only one clade (the strepsirhines). As predicted, the MOBs correlate predominantly with ecological factors (activity period and diet), while the AOBs correlate with social and mating systems. Related olfactory structures (i.e., the piriform cortex and amygdala) exhibit correlated evolution with the AOBs but not with the MOBs, and the corticobasolateral part of the amygdala exhibits a correlation with social group size in platyrrhines similar to that observed for the AOB. These social system correlations support the idea that there is an olfactory dimension to the concept of the social brain.     

Community genomics in microbial ecology and evolution

It is possible to reconstruct near-complete, and possibly complete, genomes of the dominant members of microbial communities from DNA that is extracted directly from the environment. Genome sequences from environmental samples capture the aggregate characteristics of the strain population from which they were derived. Comparison of the sequence data within and among natural populations can reveal the evolutionary processes that lead to genome diversification and speciation. Community genomic datasets can also enable subsequent gene expression and proteomic studies to determine how resources are invested and functions are distributed among community members. Ultimately, genomics can reveal how individual species and strains contribute to the net activity of the community.     

Emergent and effective properties in ecology and evolution

Emergent properties are often discussed in arguments concerning relationships among different levels. However, the different definitions of emergent properties sometimes confuse the arguments about macro-level phenomena, since some authors regard emergent properties not only as observable global patterns but as properties that affect and cause change in ecological and evolutionary processes. Thus it is important to distinguish higher-level or larger-scale properties that can influence particular ecological and evolutionary processes from those that cannot. I call the former properties effective properties. I gave examples that show why the distinctions between effective and non-effective properties are important.

     

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.     

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.     

Yeast evolution and ecology meet genomics

The first EMBO Conference on Experimental Approaches to Evolution and Ecology in Yeast was held in Heidelberg, Germany, at the end of September 2010. What might sound like a rather narrow topic actually covered a broad range of interests, approaches, and systems and generated a great deal of excitement among participants. The applications of genomic methods to ecological and evolutionary questions emphasize that the yeasts are poised to make significant contributions to these fields.