Evolution of the terminal regions of the Streptomyces linear chromosome

Comparative analysis of the Streptomyces chromosome sequences, between Streptomyces coelicolor, Streptomyces avermitilis, and Streptomyces ambofaciens ATCC23877 (whose partial sequence is released in this study), revealed a highly compartmentalized genetic organization of their genome. Indeed, despite the presence of specific genomic islands, the central part of the chromosome appears highly syntenic. In contrast, the chromosome of each species exhibits large species-specific terminal regions (from 753 to 1,393 kb), even when considering closely related species (S. ambofaciens and S. coelicolor). Interestingly, the size of the central conserved region between species decreases as the phylogenetic distance between them increases, whereas the specific terminal fraction reciprocally increases in size. Between highly syntenic central regions and species-specific chromosomal parts, there is a notable degeneration of synteny due to frequent insertions/deletions. This reveals a massive and constant genomic flux (from lateral gene transfer and DNA rearrangements) affecting the terminal contingency regions. We speculate that a gradient of recombination rate (i.e., insertion/deletion events) toward the extremities is the force driving the exclusion of essential genes from the terminal regions (i.e., chromosome compartmentalization) and generating a fast gene turnover for strong adaptation capabilities.     

Biogeographic historical legacies in the net primary productivity of Northern Hemisphere forests

It has been suggested that biogeographic historical legacies in plant diversity may influence ecosystem functioning. This is expected because of known diversity effects on ecosystem functions, and impacts of historical events such as past climatic changes on plant diversity. However, empirical evidence for a link between biogeographic history and present‐day ecosystem functioning is still limited. Here, we explored the relationships between Late‐Quaternary climate instability, species‐pool size, local species and functional diversity, and the net primary productivity (NPP) of Northern Hemisphere forests using structural equation modelling. Our study confirms that past climate instability has negative effects on plant functional diversity and through that on NPP, after controlling for present‐day climate, soil conditions, stand biomass and age. We conclude that global models of terrestrial plant productivity need to consider the biogeographical context to improve predictions of plant productivity and feedbacks with the climate system.     

The context dependence of non‐consumptive predator effects

Non‐consumptive predator effects (NCEs) are now widely recognised for their capacity to shape ecosystem structure and function. Yet, forecasting the propagation of these predator‐induced trait changes through particular communities remains a challenge. Accordingly, focusing on plasticity in prey anti‐predator behaviours, we conceptualise the multi‐stage process by which predators trigger direct and indirect NCEs, review and distil potential drivers of contingencies into three key categories (properties of the prey, predator and setting), and then provide a general framework for predicting both the nature and strength of direct NCEs. Our review underscores the myriad factors that can generate NCE contingencies while guiding how research might better anticipate and account for them. Moreover, our synthesis highlights the value of mapping both habitat domains and prey‐specific patterns of evasion success (‘evasion landscapes’) as the basis for predicting how direct NCEs are likely to manifest in any particular community. Looking ahead, we highlight two key knowledge gaps that continue to impede a comprehensive understanding of non‐consumptive predator–prey interactions and their ecosystem consequences; namely, insufficient empirical exploration of (1) context‐dependent indirect NCEs and (2) the ways in which direct and indirect NCEs are shaped interactively by multiple drivers of context dependence.     

Community assembly: alternative stable states or alternative transient states?

The concept of alternative stable states has long been a dominant framework for studying the influence of historical contingency in community assembly. This concept focuses on stable states, yet many real communities are kept in a transient state by disturbance, and the utility of predictions for stable states in explaining transient states remains unclear. Using a simple model of plant community assembly, we show that the conditions under which historical contingency affects community assembly can differ greatly for stable versus transient states. Differences arise because the contribution of such factors as mortality rate, environmental heterogeneity and plant-soil feedback to historical contingency changes as community assembly proceeds. We also show that transient states can last for a long time relative to immigration rate and generation time. These results argue for a conceptual shift of focus from alternative stable states to alternative transient states for understanding historical contingency in community assembly.     

The Power Function of the Test for ‘No Three Factor Interaction’ in 2×2×2 Contingency Tables

Three approximations to the power function of the chi-square test for the hypotheses of ‘no three factor interaction’ in a 2 × 2 × 2 contingency table are introduced and compared. The first method is based on the sampling distribution of the logarithm of the odds ratio, the second-on the non-central X² distribution and the third—on the conditional distribution of a cell entry. The last method is found to provide the closest approximation under various alternative hypotheses and sample sizes.     

HOW REPEATABLE IS ADAPTIVE EVOLUTION? THE ROLE OF GEOGRAPHICAL ORIGIN AND FOUNDER EFFECTS IN LABORATORY ADAPTATION

The importance of contingency versus predictability in evolution has been a long-standing issue, particularly the interaction between genetic background, founder effects, and selection. Here we address experimentally the effects of genetic background and founder events on the repeatability of laboratory adaptation in Drosophila subobscura populations for several functional traits. We found disparate starting points for adaptation among laboratory populations derived from independently sampled wild populations for all traits. With respect to the subsequent evolutionary rate during laboratory adaptation, starvation resistance varied considerably among foundations such that the outcome of laboratory evolution is rather unpredictable for this particular trait, even in direction. In contrast, the laboratory evolution of traits closely related to fitness was less contingent on the circumstances of foundation. These findings suggest that the initial laboratory evolution of weakly selected characters may be unpredictable, even when the key adaptations under evolutionary domestication are predictable with respect to their trajectories.     

Historical and contingent factors affect re-evolution of a complex feature lost during mass extinction in communities of digital organisms

Re-evolution of complex biological features following the extinction of taxa bearing them remains one of evolution's most interesting phenomena, but is not amenable to study in fossil taxa. We used communities of digital organisms (computer programs that self-replicate, mutate and evolve), subjected to periods of low resource availability, to study the evolution, loss and re-evolution of a complex computational trait, the function EQU (bit-wise logical equals). We focused our analysis on cases where the pre-extinction EQU clade had surviving descendents at the end of the extinction episode. To see if these clades retained the capacity to re-evolve EQU, we seeded one set of multiple subreplicate 'replay' populations using the most abundant survivor of the pre-extinction EQU clade, and another set with the actual end-extinction ancestor of the organism in which EQU re-evolved following the extinction episode. Our results demonstrate that stochastic, historical, genomic and ecological factors can lead to constraints on further adaptation, and facilitate or hinder re-evolution of a complex feature.     

Global concordance in diversity patterns of vascular plants and terrestrial vertebrates

The factors that determine large-scale patterns of species richness are poorly understood. In particular, biologists have not determined the relative roles of taxon-specific characteristics that influence diversification and distribution, and region-specific features that promote and constrain diversity. We show that the numbers of species of vascular plants and of four terrestrial vertebrate taxa (mammals, birds, reptiles and amphibians) vary in parallel across 296 geographic areas covering most of the globe, even after accounting for sample area, climate, topographic heterogeneity and differences between continents. Thus, a common set of regional characteristics and processes appears to shape patterns of species richness in a diverse set of taxa, despite substantial differences in their biological traits.     

Effect of extra running on running-based taste aversion in rats

Voluntary running in an activity wheel endowed rats with aversion to a taste solution consumed before the running. This running-based taste aversion was attenuated by extra running opportunities interspersed among the taste–running pairings, but the attenuating effect was reduced by signaling the extra running by another taste cue. These results correspond to the so-called degraded contingency effect and cover-cue effect in the traditional preparations of Pavlovian conditioning.     

An introduction to microevolution: rate,pattern, process

This special issue of Genetica brings together a diverse collection of contributions that examine evolution within and among populations (i.e., microevolution), and the role that microevolution plays in the formation of new species and morphological forms (i.e., macroevolution). Many of the papers present evidence of microevolution occuring over contemporary time frames, further validating the near ubiquity of ongoing evolution in the world around us. Several synthetic reviews of empirical work help to define the conditions under which microevolution is or is not likely to occur. Some of the studies speak directly to current controversies in evolutionary biology, such as the relative roles of determinism and contigency, and the nature of the relationship between microevolution and macroevolution. In general, microevolution seems driven largely by deterministic mechanisms, particularly natural selection, but contingency plays a role in (1) determining whether or not suitable conditions are present for evolution to proceed, and (2) guiding the precise manner by which evolution proceeds. Several theoretical treatments and empirical reviews confirm previous research in showing that microevolutionary processes are at least capable of generating macroevolutionary trends. Macroevolution may indeed reflect microevolution writ large but the pattern by which it arises is perhaps best charcaterized as microevolution writ in fits and starts.