Predicting species abundance distributions by simultaneously using number and biomass as units of measurement

The universal observation that some species in an ecological community are common, but many more are rare, is neatly encapsulated in a species abundance distribution (SAD)1. However, the shape of the distribution can depend on the currency used to measure abundance 2. Here we show how the SADs for numerical abundance and biomass are related and how this relationship can be used to predict the form of the SAD. When plotted in log numerical abundance, log biomass space, species points lie within an approximately triangular area the limits of which are set by body size range, and the upper limit of abundance in both metrics. Under the simplifying, but reasonable, assumption that the observed scatter of species within this region is random, the shape of the SAD is immediately derived from simple geometrical considerations. For the SAD of numerical abundance this is a power curve. The biomass SAD can be either a power curve or, more frequently, a unimodal curve, which can approximate a log normal. This log triangular random placement model serves as a null hypothesis against which actual communities can be compared. Data from two intensively surveyed local communities indicate that it can give a good approximation, with species scattered within a triangle. Further, we can predict the consequences, for the SAD, of size-selective sampling protocols. We argue that mechanistic models of SADs must be able to account for the relative abundance of species in alternative currencies. Moreover, this approach will shed light on niche packing and may have application in environmental monitoring

The important challenge of quantifying tropical diversity

The tropics are the repository of much of the world’s biodiversity, yet are undersampled relative to temperate regions. To help fill this knowledge gap, a paper in BMC Biology explores diversity patterns in tropical African plants, as revealed by the RAINBIO database. The paper documents spatial variation in diversity and data coverage, but also highlights the challenges faced in quantifying diversity patterns using data collated from a range of sources including herbaria. See research article: http://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0356-8.Publisher PDFPeer reviewe

The guppy sex chromosome system and the sexually antagonistic polymorphism hypothesis for y chromosome recombination suppression

Sex chromosomes regularly evolve suppressed recombination, distinguishing them from other chromosomes, and the reason for this has been debated for many years. It is now clear that non-recombining sex-linked regions have arisen in different ways in different organisms. A major hypothesis is that a sex-determining gene arises on a chromosome and that sexually antagonistic (SA) selection (sometimes called intra-locus sexual conflict) acting at a linked gene has led to the evolution of recombination suppression in the region, to reduce the frequency of low fitness recombinant genotypes produced. The sex chromosome system of the guppy (Poecilia reticulata) is often cited as supporting this hypothesis because SA selection has been demonstrated to act on male coloration in natural populations of this fish, and probably contributes to maintaining polymorphisms for the genetic factors involved. I review classical genetic and new molecular genetic results from the guppy, and other fish, including approaches for identifying the genome regions carrying sex-determining loci, and suggest that the guppy may exemplify a recently proposed route to sex chromosome evolution

Prevalence of multimodal species abundance distributions is linked to spatial and taxonomic breadth

We thank the University of St Andrews MHD Cluster and the Bioinformatics Unit (Wellcome Trust ISSF grant 105621/Z/14/Z). L.H.A. was supported by Fundação para a Ciência e Tecnologia, Portugal (POPH/FSE SFRH/BD/90469/2012). A.E.M. acknowledges the ERC (BioTIME 250189). M.D. acknowledges funding from the Marine Alliance for Science and Technology Scotland (MASTS), funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.Aim. Species abundance distributions (SADs) are a synthetic measure of biodiversity and community structure. Although typically described by unimodal logseries or lognormal distributions, empirical SADs can also exhibit multiple modes. However, we do not know how prevalent multimodality is, nor do we have an understanding of the factors leading to this pattern. Here we quantify the prevalence of multimodality in SADs across a wide range of taxa, habitats and spatial extents. Location. Global. Methods. We used the second-order Akaike information criterion for small sample sizes (AICc) and likelihood ratio tests (LRTs) to test whether models with more than one mode accurately describe the empirical abundance frequency distributions of the underlying communities. We analysed 117 empirical datasets from intensely sampled communities, including taxa ranging from birds, plants, fish and invertebrates, from terrestrial, marine and freshwater habitats. Results. We find evidence for multimodality in 14.5% of the SADs when using AICc and LRT. This is a conservative estimate, as AICc alone estimates a prevalence of multimodality of 22%. We additionally show that the pattern is more common in data encompassing broader spatial scales and greater taxonomic breadth, suggesting that multimodality increases with ecological heterogeneity. Main conclusions. We suggest that higher levels of ecological heterogeneity, underpinned by larger spatial extent and higher taxonomic breadth, can yield multimodal SADs. Our analysis shows that multimodality occurs with a prevalence that warrants its systematic consideration when assessing SAD shape and emphasizes the need for macroecological theories to include multimodality in the range of SADs they predict.PostprintPeer reviewe

Balancing the dilution and oddity effects: Decisions depend on body size

Background Grouping behaviour, common across the animal kingdom, is known to reduce an individual's risk of predation; particularly through dilution of individual risk and predator confusion (predator inability to single out an individual for attack). Theory predicts greater risk of predation to individuals more conspicuous to predators by difference in appearance from the group (the ‘oddity’ effect). Thus, animals should choose group mates close in appearance to themselves (eg. similar size), whilst also choosing a large group. Methodology and Principal Findings We used the Trinidadian guppy (Poecilia reticulata), a well known model species of group-living freshwater fish, in a series of binary choice trials investigating the outcome of conflict between preferences for large and phenotypically matched groups along a predation risk gradient. We found body-size dependent differences in the resultant social decisions. Large fish preferred shoaling with size-matched individuals, while small fish demonstrated no preference. There was a trend towards reduced preferences for the matched shoal under increased predation risk. Small fish were more active than large fish, moving between shoals more frequently. Activity levels increased as predation risk decreased. We found no effect of unmatched shoal size on preferences or activity. Conclusions and Significance Our results suggest that predation risk and individual body size act together to influence shoaling decisions. Oddity was more important for large than small fish, reducing in importance at higher predation risks. Dilution was potentially of limited importance at these shoal sizes. Activity levels may relate to how much sampling of each shoal was needed by the test fish during decision making. Predation pressure may select for better decision makers to survive to larger size, or that older, larger fish have learned to make shoaling decisions more efficiently, and this, combined with their size relative to shoal-mates, and attractiveness as prey items influences shoaling decisions

Predation pressure shapes brain anatomy in the wild

The predation pressure data were collected by AEM and AED as part of an ERC-funded project (BioTIME 250189), AEM was supported by the Royal Society, AK and NK were supported by the Knut and Alice Wallenberg Foundation (KAW2013.0072 to NK).There is remarkable diversity in brain anatomy among vertebrates and evidence is accumulating that predatory interactions are crucially important for this diversity. To test this hypothesis, we collected female guppies (Poecilia reticulata) from 16 wild populations and related their brain anatomy to several aspects of predation pressure in this ecosystem, such as the biomass of the four major predators of guppies (one prawn and three fish species), and predator diversity (number of predatory fish species in each site). We found that populations from localities with higher prawn biomass had relatively larger telencephalon size as well as larger brains. Optic tectum size was positively associated with one of the fish predator’s biomass and with overall predator diversity. However, both olfactory bulb and hypothalamus size were negatively associated with the biomass of another of the fish predators. Hence, while fish predator occurrence is associated with variation in brain anatomy, prawn occurrence is associated with variation in brain size. Our results suggest that cognitive challenges posed by local differences in predator communities may lead to changes in prey brain anatomy in the wild.Publisher PDFPeer reviewe

Sex-Specific Differences in Shoaling Affect Parasite Transmission in Guppies

Background: Individuals have to trade-off the costs and benefits of group membership during shoaling behaviour. Shoaling can increase the risk of parasite transmission, but this cost has rarely been quantified experimentally. Guppies (Poecilia reticulata) are a model system for behavioural studies, and they are commonly infected by gyrodactylid parasites, notorious fish pathogens that are directly transmitted between guppy hosts. Methodology/Principal Findings:Parasite transmission in single sex shoals of male and female guppies were observed using an experimental infection of Gyrodactylus turnbulli. Parasite transmission was affected by sex-specific differences in host behaviour, and significantly more parasites were transmitted when fish had more frequent and more prolonged contact with each other. Females shoaled significantly more than males and had a four times higher risk to contract an infection. Conclusions/Significance: Intersexual differences in host behaviours such as shoaling are driven by differences in natural and sexual selection experienced by both sexes. Here we show that the potential benefits of an increased shoaling tendency are traded off against increased risks of contracting an infectious parasite in a group-living species

The impact of resource dependence of the mechanisms of life on the spatial population dynamics of an in silico microbial community

Biodiversity has a critical impact on ecosystem functionality and stability, and thus the current biodiversity crisis has motivated many studies of the mechanisms that sustain biodiversity, a notable example being non-transitive or cyclic competition. We therefore extend existing microscopic models of communities with cyclic competition by incorporating resource dependence in demographic processes, characteristics of natural systems often oversimplified or overlooked by modellers. The spatially explicit nature of our individual-based model of three interacting species results in the formation of stable spatial structures, which have significant effects on community functioning, in agreement with experimental observations of pattern formation in microbial communities. Published by AIP Publishing

Experimentally testing and assessing the predictive power of species assembly rules for tropical canopy ants.

Understanding how species assemble into communities is a key goal in ecology. However, assembly rules are rarely tested experimentally, and their ability to shape real communities is poorly known. We surveyed a diverse community of epiphyte-dwelling ants and found that similar-sized species co-occurred less often than expected. Laboratory experiments demonstrated that invasion was discouraged by the presence of similarly sized resident species. The size difference for which invasion was less likely was the same as that for which wild species exhibited reduced co-occurrence. Finally we explored whether our experimentally derived assembly rules could simulate realistic communities. Communities simulated using size-based species assembly exhibited diversities closer to wild communities than those simulated using size-independent assembly, with results being sensitive to the combination of rules employed. Hence, species segregation in the wild can be driven by competitive species assembly, and this process is sufficient to generate observed species abundance distributions for tropical epiphyte-dwelling ants.TMF was funded by the UK Natural Environment Research Council, the project “Biodiversity of Forest Ecosystems” CZ.1.07/2.3.00/20.0064 co-financed by the European Social Fund and the state budget of the Czech Republic, an Australian Research Council Discovery Grant (DP140101541), Yayasan Sime Darby, and the Czech Science Foundation (Reg, nos. 14-32302S,14-04258S).This is the final published version. It first appeared at http://onlinelibrary.wiley.com/doi/10.1111/ele.12403/abstract

Predation risk and abiotic habitat parameters affect personality traits in extremophile populations of a neotropical fish (<i style="box-sizing: border-box;">Poecilia vivipara</i>)

Understanding whether and how ambient ecological conditions affect the distribution of personality types within and among populations lies at the heart of research on animal personality. Several studies have focussed on only one agent of divergent selection (or driver of plastic changes in behavior), considering either predation risk or a single abiotic ecological factor. Here, we investigated how an array of abiotic and biotic environmental factors simultaneously shape population differences in boldness, activity in an open‐field test, and sociability/shoaling in the livebearing fish Poecilia vivipara from six ecologically different lagoons in southeastern Brazil. We evaluated the relative contributions of variation in predation risk, water transparency/visibility, salinity (ranging from oligo‐ to hypersaline), and dissolved oxygen. We also investigated the role played by environmental factors for the emergence, strength, and direction of behavioral correlations. Water transparency explained most of the behavioral variation, whereby fish from lagoons with low water transparency were significantly shyer, less active, and shoaled less than fish living under clear water conditions. When we tested additional wild‐caught fish from the same lagoons after acclimating them to homogeneous laboratory conditions, population differences were largely absent, pointing toward behavioral plasticity as a mechanism underlying the observed behavioral differences. Furthermore, we found correlations between personality traits (behavioral syndromes) to vary substantially in strength and direction among populations, with no obvious associations with ecological factors (including predation risk). Altogether, our results suggest that various habitat parameters simultaneously shape the distribution of personality types, with abiotic factors playing a vital (as yet underestimated) role. Furthermore, while predation is often thought to lead to the emergence of behavioral syndromes, our data do not support this assumption