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

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

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

Sperm design and variation in the New World blackbirds (Icteridae)

Post-copulatory sexual selection (PCSS) is thought to be one of the evolutionary forces responsible for the rapid and divergent evolution of sperm design. However, whereas in some taxa particular sperm traits are positively associated with PCSS, in other taxa, these relationships are negative, and the causes of these different patterns across taxa are poorly understood. In a comparative study using New World blackbirds (Icteridae), we tested whether sperm design was influenced by the level of PCSS and found significant positive associations with the level of PCSS for all sperm components but head length. Additionally, whereas the absolute length of sperm components increased, their variation declined with the intensity of PCSS, indicating stabilizing selection around an optimal sperm design. Given the diversity of, and strong selection on, sperm design, it seems likely that sperm phenotype may influence sperm velocity within species. However, in contrast to other recent studies of passerine birds, but consistent with several other studies, we found no significant link between sperm design and velocity, using four different species that vary both in sperm design and PCSS. Potential reasons for this discrepancy between studies are discussed

Estimating the sustainability of towed fishing-gear impacts on seabed habitats: a simple quantitative risk assessment method applicable to data-limited fisheries

1. Impacts of bottom fishing, particularly trawling and dredging, on seabed (benthic) habitats are commonly perceived to pose serious environmental risks. Quantitative ecological risk assessment can be used to evaluate actual risks and to help guide the choice of management measures needed to meet sustainability objectives. 2. We develop and apply a quantitative method for assessing the risks to benthic habitats by towed bottom-fishing gears. The method is based on a simple equation for relative benthic status (RBS), derived by solving the logistic population growth equation for the equilibrium state. Estimating RBS requires only maps of fishing intensity and habitat type — and parameters for impact and recovery rates, which may be taken from meta-analyses of multiple experimental studies of towed-gear impacts. The aggregate status of habitats in an assessed region is indicated by the distribution of RBS values for the region. The application of RBS is illustrated for a tropical shrimp-trawl fishery. 3. The status of trawled habitats and their RBS value depend on impact rate (depletion per trawl), recovery rate and exposure to trawling. In the shrimp-trawl fishery region, gravel habitat was most sensitive, and though less exposed than sand or muddy-sand, was most affected overall (regional RBS=91% relative to un-trawled RBS=100%). Muddy-sand was less sensitive, and though relatively most exposed, was less affected overall (RBS=95%). Sand was most heavily trawled but least sensitive and least affected overall (RBS=98%). Region-wide, >94% of habitat area had >80% RBS because most trawling and impacts were confined to small areas. RBS was also applied to the region's benthic invertebrate communities with similar results. 4. Conclusions. Unlike qualitative or categorical trait-based risk assessments, the RBS method provides a quantitative estimate of status relative to an unimpacted baseline, with minimal requirements for input data. It could be applied to bottom-contact fisheries worldwide, including situations where detailed data on characteristics of seabed habitats, or the abundance of seabed fauna are not available. The approach supports assessment against sustainability criteria and evaluation of alternative management strategies (e.g. closed areas, effort management, gear modifications)

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

Effects of habitat and land use on breeding season density of male Asian Houbara Chlamydotis macqueenii

Landscape-scale habitat and land-use influences on Asian Houbara Chlamydotis macqueenii (IUCN Vulnerable) remain unstudied, while estimating numbers of this cryptic, low-density, over-hunted species is challenging. In spring 2013, male houbara were recorded at 231 point counts, conducted twice, across a gradient of sheep density and shrub assemblages within 14,300 km² of the Kyzylkum Desert, Uzbekistan. Four sets of models related male abundance to: (1) vegetation structure (shrub height and substrate); (2) shrub assemblage; (3) shrub species composition (multidimensional scaling); (4) remote-sensed derived land-cover (GLOBCOVER, 4 variables). Each set also incorporated measures of landscape rugosity and sheep density. For each set, multi-model inference was applied to generalised linear mixed models of visit-specific counts that included important detectability covariates and point ID as a random effect. Vegetation structure received strongest support, followed by shrub species composition and shrub assemblage, with weakest support for the GLOBCOVER model set. Male houbara numbers were greater with lower mean shrub height, more gravel and flatter surfaces, but were unaffected by sheep density. Male density (mean 0.14 km-2, 95% CI, 0.12‒0.15) estimated by distance analysis differed substantially among shrub assemblages, being highest in vegetation dominated by Salsola rigida (0.22 [CI, 0.20‒0.25]), high in areas of S. arbuscula and Astragalus (0.14 [CI, 0.13‒0.16] and 0.15 [CI, 0.14‒0.17] respectively), lower (0.09 [CI, 0.08‒0.10]) in Artemisia and lowest (0.04 [CI, 0.04‒0.05]) in Calligonum. The study area was estimated to hold 1,824 males (CI: 1,645‒2,030). The spatial distribution of relative male houbara abundance, predicted from vegetation structure models, had the strongest correspondence with observed numbers in both model-calibration and the subsequent year’s data. We found no effect of pastoralism on male distribution but potential effects on nesting females are unknown. Density differences among shrub communities suggest extrapolation to estimate country- or range-wide population size must take account of vegetation composition

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

Biogeographic distributions of neotropical trees reflect their directly measured drought tolerances

High levels of species diversity hamper current understanding of how tropical forests may respond to environmental change. In the tropics, water availability is a leading driver of the diversity and distribution of tree species, suggesting that many tropical taxa may be physiologically incapable of tolerating dry conditions, and that their distributions along moisture gradients can be used to predict their drought tolerance. While this hypothesis has been explored at local and regional scales, large continental-scale tests are lacking. We investigate whether the relationship between drought-induced mortality and distributions holds continentally by relating experimental and observational data of drought-induced mortality across the Neotropics to the large-scale bioclimatic distributions of 115 tree genera. Across the different experiments, genera affiliated to wetter climatic regimes show higher drought-induced mortality than dry-affiliated ones, even after controlling for phylogenetic relationships. This pattern is stronger for adult trees than for saplings or seedlings, suggesting that the environmental filters exerted by drought impact adult tree survival most strongly. Overall, our analysis of experimental, observational, and bioclimatic data across neotropical forests suggests that increasing moisture-stress is indeed likely to drive significant changes in floristic composition

War‐induced behavioral change in spotted hyena (Crocuta crocuta) populations in Tigray, Northern Ethiopia

In Tigray, northern Ethiopia, there is a long tradition of peaceful coexistence between spotted hyenas (Crocuta crocuta) and humans. While historically the coexistence has been relatively stable, we assessed the impact of the recent war in Tigray on this coexistence. We investigated the effects of war on the scavenging and hunting behavior of spotted hyenas, and the consequences for local people in Tigray. We compared current spotted hyena foraging at six battle sites with six control sites across Tigray using diet analysis, hyena abundance through playback experiments, and assessed human−wildlife interactions via semistructured interviews in 1200 households. Spotted hyena diets at both site types consisted exclusively of domestically derived prey; however, the composition of prey species differed significantly (χ2=64.03, df=6, p=0.001). Human hair was prevalent in hyena scats from battle sites but was absent in scats collected from the control sites. In total, 318 hyenas responded to 48 call stations, response rates were significantly higher at battle sites (x=36.7±9.7 SD) than at control sites (x=16.3±14.6 SD). There were several lines of evidence that human−wildlife interactions were more negative. Reported livestock predation was 18.85% higher at battle sites, with 78.5% of depredation events occurring during the war, compared to 6% pre-war and 15.5% post-war. We conclude that changes in hyena feeding behavior during the war and siege period can be linked to changes in the availability of scavengable food sources. These results yield insight not only into the consequences of war for the people of Tigray but also into how the many armed conflicts in regions with large scavenger/carnivore populations may have long-lasting impacts on human−wildlife conflict around the globe