When can we distinguish between neutral and non‐neutral processes in community dynamics under ecological drift?

Determining whether the composition of ecological communities (species presence and abundance), can be predicted from species demographic traits, rather than being a result of neutral drift, is a key ecological question. Here we compare the similarity of community composition, from different community assembly models run under identical environmental conditions, where interspecific competition is assumed to be either neutral or niche-based. In both cases, species colonize a focal patch from a network of neighbouring patches in a metacommunity. We highlight the circumstances (rate and spatial scale of dispersal, and the relative importance of ecological drift) where commonly used community similarity metrics or species rank–abundance relationships are likely to give similar results, regardless of the underlying processes (neutral or non-neural) driving species' dynamics. As drift becomes more important in driving species abundances, deterministic niche structure has a smaller influence. Our ability to discriminate between different underlying processes driving community organization depends on the relative importance of different drift processes that operate on different spatial scales.     

How likely is speciation in neutral ecology?

Patterns of biodiversity predicted by the neutral theory rely on a simple phenomenological model of speciation. To further investigate the effect of speciation on neutral biodiversity, we analyze a spatially explicit neutral model based on population genetics. We define the metacommunity as a system of populations exchanging migrants, and we use this framework to introduce speciation with little or no gene flow (allopatric and parapatric speciation). We find that with realistic mutation rates, our metacommunity model driven by neutral processes cannot support more than a few species. Adding natural selection in the population genetics of speciation increases the number of species in the metacommunity, but the level of diversity found in the Barro Colorado Island is difficult to reach.     

When can the cause of a population decline be determined?

Inferring the factors responsible for declines in abundance is a prerequisite to preventing the extinction of wild populations. Many of the policies and programmes intended to prevent extinctions operate on the assumption that the factors driving the decline of a population can be determined. Exogenous factors that cause declines in abundance can be statistically confounded with endogenous factors such as density dependence. To demonstrate the potential for confounding, we used an experiment where replicated populations were driven to extinction by gradually manipulating habitat quality. In many of the replicated populations, habitat quality and density dependence were confounded, which obscured causal inference. Our results show that confounding is likely to occur when the exogenous factors that are driving the decline change gradually over time. Our study has direct implications for wild populations, because many factors that could drive a population to extinction change gradually through time.     

How long before a change in soil organic carbon can be detected?

When planning sampling in an experiment where soil organic carbon (SOC) content is expected to change, it is necessary to know how many samples will need to be taken to demonstrate a change in SOC and after how long this change will be detectable. Much has been published on the number of samples required to demonstrate the minimum detectable difference in SOC, but less on how long it takes for this change to be detectable. In this paper, a model of SOC dynamics is used to estimate the minimum time taken for a change in total SOC content to become measurable under different carbon inputs, land uses and soil types. For free air carbon dioxide enrichment (FACE), and other experiments in which SOC is expected to increase, relationships between the percentage change in C inputs and the time taken to measure a change in SOC are presented, for two levels of sampling intensity corresponding to the maximum that is practically possible in most experiments (～100 samples) and that used regularly in field experiments (10–20 samples). In FACE experiments, where C inputs increase by a maximum of about 20–25%, SOC change could be detected with 90% confidence after about 6–10 years if a sampling regime allowing 3% change in background SOC level (probably requiring a very large number of samples) were used, but could not be detected at all if a sampling regime were used that allowed only a 15% change in background SOC to be detected. If increases in C inputs are much below 15%, it might not be possible to detect a change in soil C without an enormous number of samples. Relationships between the change in C inputs and the time taken to measure a change in SOC are robust over a range of soil types and land uses. The results demonstrate how models of SOC dynamics can be used to complement statistical power analyses for planning when, and how intensively, to sample soils during experiments. An advantage of the modelling approach demonstrated here is that estimates of the minimum time taken for a change in soil carbon to become detectable can be made, even before any detailed soil samples are taken, simply from estimates of the likely increase in carbon inputs to the soil (via expected changes in net primary production).     

When can dispersal synchronize populations?

While spatial synchrony of oscillating populations has been observed in many ecological systems, the causes of this phenomenon are still not well understood. The most common explanations have been the Moran effect (synchronous external stochastic influences) and the effect of dispersal among populations. Since ecological systems are typically subject to large spatially varying perturbations which destroy synchrony, a plausible mechanism explaining synchrony must produce rapid convergence to synchrony. We analyze the dynamics through time of the synchronizing effects of dispersal and, consequently, determine whether dispersal can be the mechanism which produces synchrony. Specifically, using methods new to ecology, we analyze a two patch predator-prey model, with identical weak dispersal between the patches. We find that a difference in time scales (i.e. one population has dynamics occurring much faster than the other) between the predator and prey species is the most important requirement for fast convergence to synchrony.     

What ecological factors shape species-area curves in neutral models?

Understanding factors that shape biodiversity and species coexistence across scales is of utmost importance in ecology, both theoretically and for conservation policies. Species-area relationships (SARs), measuring how the number of observed species increases upon enlarging the sampled area, constitute a convenient tool for quantifying the spatial structure of biodiversity. While general features of species-area curves are quite universal across ecosystems, some quantitative aspects can change significantly. Several attempts have been made to link these variations to ecological forces. Within the framework of spatially explicit neutral models, here we scrutinize the effect of varying the local population size (i.e. the number of individuals per site) and the level of habitat saturation (allowing for empty sites). We conclude that species-area curves become shallower when the local population size increases, while habitat saturation, unless strongly violated, plays a marginal role. Our findings provide a plausible explanation of why SARs for microorganisms are flatter than those for larger organisms.     

When and why do non-neutral metacommunities appear neutral?

Hubbell's neutral theory assumes that all species in a community have the same per capita fitness. Despite the overwhelming evidence against this assumption in most communities the neutral theory has often been, though not always, successful at predicting patterns of diversity in nature. I analyze a non-neutral model in order to suggest conditions under which observed species-abundance distributions (SADs) could be expected to resemble neutral distributions. The non-neutral model consists of two guilds of species such that (1) individuals between guilds do not interact, (2) dynamics within guilds follow Hubbell's model and (3) neutral parameters between guilds differ. This two-guild model generates SADs that appear neutral in some cases and clearly non-neutral in other cases. This result suggests that SADs may be more informative about niche structure than previously thought. The two-guild model could be tested in communities composed of fairly well-defined guilds or functional groups.     

Reconciling economic and ecological sustainability: can non-intensive hunting of red-legged partridges be economically profitable?

The red-legged partridge (Alectoris rufa) is the most important gamebird in Spain. Due to population declines in recent decades, management approaches increasingly include the release of farm-reared partridges and the establishment of so-called intensive estates, where hunting is based on put-and-take partridges. The release of farm-reared partridges is controversial because these birds negatively affect wild populations. However, according to managers, releases are necessary to maintain commercial hunting. We analysed economic parameters using data provided by 20 red-legged partridge hunting estates with different management and economic aims in central Spain. We calculated total revenues, total expenses, benefits and profitability of these estates and simulated results under two different scenarios (prices for buying farm-reared partridges being 15 % higher and prices for hunting in estates not using releases being 15 % higher) attempting to mimic the internalization of some ecological costs of farm-reared birds or possible rewards from using wild populations sustainably. Non-commercial estates (n = 5), as expected, just broke even, with almost no benefits. Benefits of intensive estates, where massive releases throughout the hunting season allow a much higher harvest, were on average an order of magnitude higher (20,404 ± 24,413 €/km², n = 8) than those of other commercial estates (1713 ± 1280 €/km², n = 7). Benefits of non-intensive commercial estates using releases were on average lower than those of commercial estates without releases. In fact, profitability of non-intensive commercial estates not using releases was similar to that of intensive estates. Any of the two price scenarios considered led to non-intensive commercial estates not using releases being the most profitable on average. Thus, efforts should be made to identify ways of improving economic profitability of non-intensive estates, which may be important for promoting hunting management styles that are ecologically more beneficial.     

When less can be better: How can we make genomic selection more cost-effective and accurate in barley?

Key message

We were able to obtain good prediction accuracy in genomic selection with ~?2000 GBS-derived SNPs. SNPs in genic regions did not improve prediction accuracy compared to SNPs in intergenic regions.

Abstract

Since genotyping can represent an important cost in genomic selection, it is important to minimize it without compromising the accuracy of predictions. The objectives of the present study were to explore how a decrease in the unit cost of genotyping impacted: (1) the number of single nucleotide polymorphism (SNP) markers; (2) the accuracy of the resulting genotypic data; (3) the extent of coverage on both physical and genetic maps; and (4) the prediction accuracy (PA) for six important traits in barley. Variations on the genotyping by sequencing protocol were used to generate 16 SNP sets ranging from ~?500 to ~?35,000 SNPs. The accuracy of SNP genotypes fluctuated between 95 and 99%. Marker distribution on the physical map was highly skewed toward the terminal regions, whereas a fairly uniform coverage of the genetic map was achieved with all but the smallest set of SNPs. We estimated the PA using three statistical models capturing (or not) the epistatic effect; the one modeling both additivity and epistasis was selected as the best model. The PA obtained with the different SNP sets was measured and found to remain stable, except with the smallest set, where a significant decrease was observed. Finally, we examined if the localization of SNP loci (genic vs. intergenic) affected the PA. No gain in PA was observed using SNPs located in genic regions. In summary, we found that there is considerable scope for decreasing the cost of genotyping in barley (to capture ~?2000 SNPs) without loss of PA.

     

Speciation with gene flow in a heterogeneous virtual world: can physical obstacles accelerate speciation?

The origin of species remains one of the most controversial and least understood topics in evolution. While it is being widely accepted that complete cessation of gene-flow between populations owing to long-lasting geographical barriers results in a steady, irreversible increase of divergence and eventually speciation, the extent to which various degrees of habitat heterogeneity influences speciation rates is less well understood. Here, we investigate how small, randomly distributed physical obstacles influence the distribution of populations and species, the level of population connectivity (e.g. gene flow), as well as the mode and tempo of speciation in a virtual ecosystem composed of prey and predator species. We adapted an existing individual-based platform, EcoSim, to allow fine tuning of the gene flow's level between populations by adding various numbers of obstacles in the world. The platform implements a simple food chain consisting of primary producers, herbivores (prey) and predators. It allows complex intra- and inter-specific interactions, based on individual evolving behavioural models, as well as complex predator-prey dynamics and coevolution in spatially homogenous and heterogeneous worlds. We observed a direct and continuous increase in the speed of evolution (e.g. the rate of speciation) with the increasing number of obstacles in the world. The spatial distribution of species was also more compact in the world with obstacles than in the world without obstacles. Our results suggest that environmental heterogeneity and other factors affecting demographic stochasticity can directly influence speciation and extinction rates.     

When can a clonal organism escape senescence?

Abstract Some clonal organisms may live for thousands of years and show no signs of senescence, while others consistently die after finite life spans. Using two models, we examined how stage-specific life-history rates of a clone's modules determine whether a genetic individual escapes senescence by replacing old modules with new ones. When the rates of clonal or sexual reproduction and survival of individual modules decline with age, clones are more likely to experience senescence. In addition, the models predict that there is a greater tendency to find senescence in terms of a decline in the rate of sexual reproduction with clone age than in terms of an increase in the probability of clone mortality, unless rates of sexual reproduction increase dramatically with module stage. Using a matrix model modified to represent the clonal lifestyle, we show how a trade-off between sexual and clonal reproduction could result in selection for or against clonal senescence. We also show that, in contrast to unitary organisms, the strength of selection on life-history traits can increase with the age of a clone even in a growing population, countering the evolution of senescence.     

Are microorganisms everywhere they can be?

Baas-Becking is famously attributed with the conjecture that ‘everything is everywhere, but the environment selects’. Although this aphorism is largely challenged by microbial biogeographical data, even weak versions of the claim leave unanswered the question about whether all environments that could theoretically support life contain life. In the last decade, the discovery of thermally sterilized habitable environments disconnected from inhabited regions, and habitats within organisms such as the sterile, but habitable human fetal gut, suggest the existence of a diversity of macroscopic habitable environments apparently devoid of actively metabolizing or reproducing life. Less clear is the status of such environments at the micron scale, for example, between colonies of organisms within rock interstices or on and within other substrates. I discuss recent evidence for these types of environments. These environments have practical uses in: (i) being negative controls for understanding the role of microbial processes in geochemical cycles and geological processes, (ii) yielding insights into the extent to which the biosphere extends into all spaces it theoretically can, (iii) suggesting caution in interpreting the results of life detection instrumentation, and (iv) being useful for establishing the conditions for the origin of life and its prevalence on other planetary bodies.     

How accurate can genetic predictions be?

ABSTRACT: BACKGROUND: Pre-symptomatic prediction of disease and drug response based on genetic testing is a critical component of personalized medicine. Previous work has demonstrated that the predictive capacity of genetic testing is constrained by the heritability and prevalence of the tested trait, although these constraints have only been approximated under the assumption of a normally distributed genetic risk distribution. RESULTS: Here, we mathematically derive the absolute limits that these factors impose on test accuracy in the absence of any distributional assumptions on risk. We present these limits in terms of the best-case receiver-operating characteristic (ROC) curve, consisting of the best-case test sensitivities and specificities, and the AUC (area under the curve) measure of accuracy. We apply our method to genetic prediction of type 2 diabetes and breast cancer, and we additionally show the best possible accuracy that can be obtained from integrated predictors, which can incorporate non-genetic features. CONCLUSIONS: Knowledge of such limits is valuable in understanding the implications of genetic testing even before additional associations are identified.     

The birds, the bees, and the virtual flowers: can pollinator behavior drive ecological speciation in flowering plants?

Biologists have long assumed that pollinator behavior is an important force in angiosperm speciation, yet there is surprisingly little direct evidence that floral preferences in pollinators can drive floral divergence and the evolution of reproductive (ethological) isolation between incipient plant species. In this study, we expose computer-generated plant populations with a wide variation in flower color to selection by live and virtual hummingbirds and bumblebees and track evolutionary changes in flower color over multiple generations. Flower color, which was derived from the known genetic architecture and phenotypic variance of naturally occurring plant species pollinated by both groups, evolved in simulations through a genetic algorithm in which pollinator preference determined changes in flower color between generations. The observed preferences of live hummingbirds and bumblebees were strong enough to cause adaptive divergence in flower color between plant populations but did not lead to ethological isolation. However, stronger preferences assigned to virtual pollinators in sympatric and allopatric scenarios rapidly produced ethological isolation. Pollinators can thus drive ecological speciation in flowering plants, but more rigorous and comprehensive behavioral studies are required to specify conditions that produce sufficient preference levels in pollinators.     

How common is ecological speciation in plant-feeding insects? A 'Higher' Nematinae perspective

Background  

Ecological speciation is a process in which a transiently resource-polymorphic species divides into two specialized sister lineages as a result of divergent selection pressures caused by the use of multiple niches or environments. Ecology-based speciation has been studied intensively in plant-feeding insects, in which both sympatric and allopatric shifts onto novel host plants could speed up diversification. However, while numerous examples of species pairs likely to have originated by resource shifts have been found, the overall importance of ecological speciation in relation to other, non-ecological speciation modes remains unknown. Here, we apply phylogenetic information on sawflies belonging to the 'Higher' Nematinae (Hymenoptera: Tenthredinidae) to infer the frequency of niche shifts in relation to speciation events.