Phylogeny and ecological processes influence grass coexistence at different spatial scales within the steppe biome

Phylogenetic analyses are essential for disentangling how environmental filtering and competition determine species coexistence across spatial scales. Inner Mongolia steppe has strong environmental gradients, but how the phylogenetic relatedness of co-occurring species and phylogenetic signals of functional traits change across spatial scales remains unclear. We investigated the phylogenetic structure of grass assemblages along environmental gradients from regional to local scales, and measured functional traits within assemblages. We compared phylogenetic signals of plant traits between the same numbers of species randomly selected from the regional pool and species observed at the local scale, did phylogenetic principal component analysis to infer the main factors driving species coexistence, and examined the key plant trait–environment relationships across the phylogeny to reveal ecological adaptation mechanisms. Regionally, grass species were phylogenetically clustered with contrasting climate preferences. With decreasing spatial scales, species richness declined, changing from phylogenetically clustered to overdispersed, and phylogenetic signals of plant traits became weaker. At the local scale, grass assemblages were structured by soil water content and neighbor density, and the trait–environment relationships were less clear than those at the regional scale. This study demonstrated that at smaller scales, co-occurring grass species in the steppe tended to be more phylogenetically overdispersed, and that phylogenetic signals of plant functional traits became weaker with increasing abiotic and biotic interactions. Our findings contributed evidence for understanding species coexistence and maintenance at scales spanning regional to local communities in the East Asia steppe biome

Effects of density, species interactions, and environmental stochasticity on the dynamics of British bird communities

Our knowledge of the factors affecting species abundances is mainly based on time-series analyses of a few well-studied species at single or few localities, but we know little about whether results from such analyses can be extrapolated to the community level. We apply a joint species distribution model to long-term time-series data on British bird communities to examine the relative contribution of intra- and interspecific density dependence at different spatial scales, as well as the influence of environmental stochasticity, to spatiotemporal interspecific variation in abundance. Intraspecific density dependence has the major structuring effect on these bird communities. In addition, environmental fluctuations affect spatiotemporal differences in abundance. In contrast, species interactions had a minor impact on variation in abundance. Thus, important drivers of single-species dynamics are also strongly affecting dynamics of communities in time and space.Peer reviewe

Oligotyping : differentiating between closely related microbial taxa using 16S rRNA gene data

© The Authors. Methods in Ecology and Evolution © 2013 British Ecological Society.. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Methods in Ecology and Evolution 4 (2013): 1111–1119, doi:10.1111/2041-210X.12114.Bacteria comprise the most diverse domain of life on Earth, where they occupy nearly every possible ecological niche and play key roles in biological and chemical processes. Studying the composition and ecology of bacterial ecosystems and understanding their function are of prime importance. High-throughput sequencing technologies enable nearly comprehensive descriptions of bacterial diversity through 16S ribosomal RNA gene amplicons. Analyses of these communities generally rely upon taxonomic assignments through reference data bases or clustering approaches using de facto sequence similarity thresholds to identify operational taxonomic units. However, these methods often fail to resolve ecologically meaningful differences between closely related organisms in complex microbial data sets. In this paper, we describe oligotyping, a novel supervised computational method that allows researchers to investigate the diversity of closely related but distinct bacterial organisms in final operational taxonomic units identified in environmental data sets through 16S ribosomal RNA gene data by the canonical approaches. Our analysis of two data sets from two different environments demonstrates the capacity of oligotyping at discriminating distinct microbial populations of ecological importance. Oligotyping can resolve the distribution of closely related organisms across environments and unveil previously overlooked ecological patterns for microbial communities. The URL http://oligotyping.org offers an open-source software pipeline for oligotyping.This work was supported by the National Institutes of Health [1UH2DK083993 to M.L.S.] and the Alfred P. Sloan Foundation

The Epidemiological Framework for Biological Invasions (EFBI): An interdisciplinary foundation for the assessment of biosecurity threats

Emerging microparasite (e.g. viruses, bacteria, protozoa and fungi) epidemics and the introduction of non-native pests and weeds are major biosecurity threats worldwide. The likelihood of these threats is often estimated from probabilities of their entry, establishment, spread and ease of prevention. If ecosystems are considered equivalent to hosts, then compartment disease models should provide a useful framework for understanding the processes that underpin non-native species invasions. To enable greater cross-fertilisation between these two disciplines, the Epidemiological Framework for Biological Invasions (EFBI) is developed that classifies ecosystems in relation to their invasion status: Susceptible, Exposed, Infectious and Resistant. These states are linked by transitions relating to transmission, latency and recovery. This viewpoint differs markedly from the species-centric approaches often applied to non-native species. It allows generalisations from epidemiology, such as the force of infection, the basic reproductive ratio R0, super-spreaders, herd immunity, cordon sanitaire and ring vaccination, to be discussed in the novel context of non-native species and helps identify important gaps in the study of biological invasions. The EFBI approach highlights several limitations inherent in current approaches to the study of biological invasions including: (i) the variance in non-native abundance across ecosystems is rarely reported; (ii) field data rarely (if ever) distinguish source from sink ecosystems; (iii) estimates of the susceptibility of ecosystems to invasion seldom account for differences in exposure to non-native species; and (iv) assessments of ecosystem susceptibility often confuse the processes that underpin patterns of spread within -and between- ecosystems. Using the invasion of lakes as a model, the EFBI approach is shown to present a new biosecurity perspective that takes account of ecosystem status and complements demographic models to deliver clearer insights into the dynamics of biological invasions at the landscape scale. It will help to identify whether management of the susceptibility of ecosystems, of the number of vectors, or of the diversity of pathways (for movement between ecosystems) is the best way of limiting or reversing the population growth of a non-native species. The framework can be adapted to incorporate increasing levels of complexity and realism and to provide insights into how to monitor, map and manage biological invasions more effectively

Tree diversity and liana infestation predict acoustic diversity in logged tropical forests

Logged tropical forests can retain a great deal of biodiversity, but there is substantial variation in the type and severity of habitat degradation caused by logging. Logging-induced habitat degradation can vary significantly at fine spatial scales, with differing effects on plant communities and the growth of lianas, which are woody, climbing vines that proliferate in degraded forests and infest trees by climbing onto them and competing for above and below ground resources. The impacts of such fine-scale variation in habitat structure on faunal diversity is relatively poorly known. We recorded soundscapes and variation in local-scale habitat structure in selectively logged and old-growth primary forests in Malaysian Borneo to examine how changes to logged forest structure predict variation in acoustic diversity indices that are known to correlate with biodiversity indices. We show that acoustic indices relating to higher soundscape diversity increase with liana prevalence but decline with tree species richness and are unaffected by the liana load of adult trees. Our results suggest that acoustic data represent a simple, practicable measure for detecting fine-scale patterns of biodiversity response to post-logging habitat structure. Our findings also suggest that retaining many trees lightly infested by lianas in logged forests is the optimal outcome for biodiversity. This emphasises the need for forest restoration that retains some climbers, rather than blanket-cutting of all stems in projects seeking to return post-logging forest communities towards their primary forest state

Shedding light on the ‘dark side’ of phylogenetic comparative methods

ORCID: 0000-0003-4919-8655© 2016 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. The attached file is the published version of the article

Are evolutionary transitions in sexual size dimorphism related to sex determination in reptiles?

Sex determination systems are highly variable in vertebrates, although neither the causes nor the implications of this diversity are fully understood. Theory suggests that sex determination is expected to relate to sexual size dimorphism, because environmental sex determination promotes sex-specific developmental bias in embryonic growth rates. Furthermore, selection for larger size in one sex or the other has been proposed to drive the evolution of different genetic sex determination systems. Here, we investigate whether sex determination systems relate to adult sexual size dimorphism, using 250 species of reptiles (Squamata, Testudines and Crocodylia) representing 26 families. Using phylogenetically informed analyses, we find that sexual size dimorphism is associated with sex determination: species with TSDIa sex determination (i.e. in which the proportion of female offspring increases with incubation temperature) have more female-biased size dimorphism than species with TSDII (i.e. species in which males are produced at mid temperatures). We also found a trend that species with TSD ancestors had more male-biased size dimorphism in XY sex chromosome systems than in ZW sex chromosome systems. Taken together, our results support the prediction that sexual size dimorphism is linked to sex-dependent developmental variations caused by environmental factors and also by sex chromosomes. Since the extent of size dimorphism is related to various behavioural, ecological and life-history differences between sexes, our results imply profound impacts of sex determination systems for vertebrate diversity

By hook or by crook? Morphometry, competition and cooperation in rodent sperm

Background Sperm design varies enormously across species and sperm competition is thought to be a major factor influencing this variation. However, the functional significance of many sperm traits is still poorly understood. The sperm of most murid rodents are characterised by an apical hook of the sperm head that varies markedly in extent across species. In the European woodmouse Apodemus sylvaticus (Muridae), the highly reflected apical hook of sperm is used to form sperm groups, or “trains,” which exhibited increased swimming velocity and thrusting force compared to individual sperm. Methodology/Principal Findings Here we use a comparative study of murine rodent sperm and demonstrate that the apical hook and sperm cooperation are likely to be general adaptations to sperm competition in rodents. We found that species with relatively larger testes, and therefore more intense sperm competition, have a longer, more reflected apical sperm hook. In addition, we show that sperm groups also occur in rodents other than the European woodmouse. Conclusions Our results suggest that in rodents sperm cooperation is more widespread than assumed so far and highlight the importance of diploid versus haploid selection in the evolution of sperm design and function

Evolution of reproductive modes in sharks and rays

The ecological and life history drivers of the diversification of reproductive modes in early vertebrates are not fully understood. Sharks, rays and chimaeras (group Chondrichthyes) have an unusually diverse variety of reproductive modes and are thus an ideal group to test the factors driving the evolution of reproductive complexity. Here, using 960 species representing all major Chondrichthyes taxa, we reconstruct the evolution of their reproduction modes and investigate the ecological and life history predictors of reproduction. We show that the ancestral Chondrichthyes state was egg-laying and find multiple independent transitions between egg-laying and live-bearing via an intermediate state of yolk-only live-bearing. Using phylogenetically informed analysis, we also show that live-bearing species have larger body size and larger offspring than egg-laying species. In addition, live-bearing species are distributed over shallow to intermediate depths, while egg-layers are typically found in deeper waters. This suggests that live-bearing is more closely associated with pelagic, rather than demersal habitats. Taken together, using a basal vertebrate group as a model, we demonstrat how reproductive mode co-evolves with environmental conditions and life-history traits

Climate warming, marine protected areas and the ocean-scale integrity of coral reef ecosystems

Coral reefs have emerged as one of the ecosystems most vulnerable to climate variation and change. While the contribution of a warming climate to the loss of live coral cover has been well documented across large spatial and temporal scales, the associated effects on fish have not. Here, we respond to recent and repeated calls to assess the importance of local management in conserving coral reefs in the context of global climate change. Such information is important, as coral reef fish assemblages are the most species dense vertebrate communities on earth, contributing critical ecosystem functions and providing crucial ecosystem services to human societies in tropical countries. Our assessment of the impacts of the 1998 mass bleaching event on coral cover, reef structural complexity, and reef associated fishes spans 7 countries, 66 sites and 26 degrees of latitude in the Indian Ocean. Using Bayesian meta-analysis we show that changes in the size structure, diversity and trophic composition of the reef fish community have followed coral declines. Although the ocean scale integrity of these coral reef ecosystems has been lost, it is positive to see the effects are spatially variable at multiple scales, with impacts and vulnerability affected by geography but not management regime. Existing no-take marine protected areas still support high biomass of fish, however they had no positive affect on the ecosystem response to large-scale disturbance. This suggests a need for future conservation and management efforts to identify and protect regional refugia, which should be integrated into existing management frameworks and combined with policies to improve system-wide resilience to climate variation and change