The mismatch between current statistical practice and doctoral training in ecology

Ecologists are studying increasingly complex and important issues such as climate change and ecosystem services. These topics often involve large data sets and the application of complicated quantitative models. We evaluated changes in statistics used by ecologists by searching nearly 20,000 published articles in ecology from 1990 to 2013. We found that there has been a rise in sophisticated and computationally intensive statistical techniques such as mixed effects models and Bayesian statistics and a decline in reliance on approaches such as ANOVA or t tests. Similarly, ecologists have shifted away from software such as SAS and SPSS to the open source program R. We also searched the published curricula and syllabi of 154 doctoral programs in the United States and found that despite obvious changes in the statistical practices of ecologists, more than one-third of doctoral programs showed no record of required or optional statistics classes. Approximately one-quarter of programs did require a statistics course, but most of those did not cover contemporary statistical philosophy or advanced techniques. Only one-third of doctoral programs surveyed even listed an optional course that teaches some aspect of contemporary statistics. We call for graduate programs to lead the charge in improving training of future ecologists with skills needed to address and understand the ecological challenges facing humanity.ECU Open Access Publishing Support Fun

Interactions between competition and predation shape early growth and survival of two Neotropical hylid tadpoles [poster]

Background/Question/Methods Recent literature reviews reveal that competition typically has stronger effects on growth than the presence of predators, while predation has larger effects on survival. Further, past studies show that predators typically lessen the negative effect of competition on growth and also make interspecific competition beneficial for the survival of focal species. We examine the independent and combined effects of competition and predation for survival and growth of the tadpoles of two co-occurring Neotropical hylid frogs (Agalychnis callidryas and Dendropsophus ebraccatus). Our experiment crossed tadpole species composition (single and mixed at single total density) with the presence or absence of a free-roaming predator (Anax sp. dragonfly larva) using a 3x2 factorial design. Six replicates were conducted in 300 L mesocosms at the Smithsonian Tropical Research Center, Gamboa, Panama. Results/Conclusions Dragonfly larvae were effective predators of both species, but had larger effects on A. callidryas survival. A. callidryas grew faster in the presence of D. ebraccatus, suggesting it is a more effective competitor. A. callidryas reduced D. ebraccatus growth in the absence of dragonflies; however, this effect disappeared when predators were present. Though our results are largely consistent with similar previous studies, one interesting difference did emerge. Not only did predation have larger effects on survival than competition, but predator presence resulted in a much larger reduction in tadpole growth than competition – even though predation increased per capita resource levels. This can be attributed to either changes in feeding behavior or metabolic costs of alteration of phenotypically plastic traits. Thus, in our study, predator effects dominated survival and growth and highlight the importance of top-down effects, as well as costs associated with phenotypic plasticity, in shaping interactions between these species

Prey Responses to Predator Chemical Cues: Disentangling the Importance of the Number and Biomass of Prey Consumed

To effectively balance investment in predator defenses versus other traits, organisms must accurately assess predation risk. Chemical cues caused by predation events are indicators of risk for prey in a wide variety of systems, but the relationship between how prey perceive risk in relation to the amount of prey consumed by predators is poorly understood. While per capita predation rate is often used as the metric of relative risk, studies aimed at quantifying predator-induced defenses commonly control biomass of prey consumed as the metric of risk. However, biomass consumed can change by altering either the number or size of prey consumed. In this study we determine whether phenotypic plasticity to predator chemical cues depends upon prey biomass consumed, prey number consumed, or both. We examine the growth response of red-eyed treefrog tadpoles (Agalychnis callidryas) to cues from a larval dragonfly (Anax amazili). Biomass consumed was manipulated by either increasing the number of prey while holding individual prey size constant, or by holding the number of prey constant and varying individual prey size. We address two questions. (i) Do prey reduce growth rate in response to chemical cues in a dose dependent manner? (ii) Does the magnitude of the response depend on whether prey consumption increases via number or size of prey? We find that the phenotypic response of prey is an asymptotic function of prey biomass consumed. However, the asymptotic response is higher when more prey are consumed. Our findings have important implications for evaluating past studies and how future experiments should be designed. A stronger response to predation cues generated by more individual prey deaths is consistent with models that predict prey sensitivity to per capita risk, providing a more direct link between empirical and theoretical studies which are often focused on changes in population sizes not individual biomass

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery1,2, spreading efficiently via low-dose fecal-oral transmission3,4. Historically, S. sonnei has been predominantly responsible for dysentery in developed countries, but is now emerging as a problem in the developing world, apparently replacing the more diverse S. flexneri in areas undergoing economic development and improvements in water quality4-6. Classical approaches have shown S. sonnei is genetically conserved and clonal7. We report here whole-genome sequencing of 132 globally-distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and has diversified into several distinct lineages with unique characteristics. Our analysis suggests the majority of this diversification occurred in Europe, followed by more recent establishment of local pathogen populations in other continents predominantly due to the pandemic spread of a single, rapidly-evolving, multidrug resistant lineage

Bacterial microevolution and the Pangenome

The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome. This diversity can be analysed in terms of microevolutionary events that took place since the genomes shared a common ancestor, especially deletion, duplication, and recombination. We review the basic modelling ingredients used implicitly or explicitly when performing such a pangenome analysis. In particular, we describe a basic neutral phylogenetic framework of bacterial pangenome microevolution, which is not incompatible with evaluating the role of natural selection. We survey the different ways in which pangenome data is summarised in order to be included in microevolutionary models, as well as the main methodological approaches that have been proposed to reconstruct pangenome microevolutionary history

Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn't Kill You Makes You Stronger

Infection by a temperate phage can lead to death of the bacterial cell, but sometimes these phages integrate into the bacterial chromosome, offering the potential for a more long-lasting relationship to be established. Here we define three major ecological and evolutionary benefits of temperate phage for bacteria: as agents of horizontal gene transfer (HGT), as sources of genetic variation for evolutionary innovation, and as weapons of bacterial competition. We suggest that a coevolutionary perspective is required to understand the roles of temperate phages in bacterial populations

What traits are carried on mobile genetic elements, and why?

Although similar to any other organism, prokaryotes can transfer genes vertically from mother cell to daughter cell, they can also exchange certain genes horizontally. Genes can move within and between genomes at fast rates because of mobile genetic elements (MGEs). Although mobile elements are fundamentally self-interested entities, and thus replicate for their own gain, they frequently carry genes beneficial for their hosts and/or the neighbours of their hosts. Many genes that are carried by mobile elements code for traits that are expressed outside of the cell. Such traits are involved in bacterial sociality, such as the production of public goods, which benefit a cell's neighbours, or the production of bacteriocins, which harm a cell's neighbours. In this study we review the patterns that are emerging in the types of genes carried by mobile elements, and discuss the evolutionary and ecological conditions under which mobile elements evolve to carry their peculiar mix of parasitic, beneficial and cooperative genes

Prokaryote genome fluidity is dependent on effective population size

Many prokaryote species are known to have fluid genomes, with different strains varying markedly in accessory gene content through the combined action of gene loss, gene gain via lateral transfer, as well as gene duplication. However, the evolutionary forces determining genome fluidity are not yet well understood. We here for the first time systematically analyse the degree to which this distinctive genomic feature differs between bacterial species. We find that genome fluidity is positively correlated with synonymous nucleotide diversity of the core genome, a measure of effective population size Ne. No effects of genome size, phylogeny or homologous recombination rate on genome fluidity were found. Our findings are consistent with a scenario where accessory gene content turnover is for a large part dictated by neutral evolution