Effects of climate, species interactions, and dispersal on decadal colonization and extinction rates of Iberian tree species

We studied the relative importance of climate, abundance of potentially competing species, and dispersal in explaining local colonization and extinction rates of tree species throughout mainland Spain. We used a Bayesian framework to parameterize a patch occupancy model to 23 species censused in 46,596 permanent plots in a 1 × 1 km grid across most Spanish forests. For most species, dispersal was the single best predictor of colonization, whereas climate and dispersal were equally important as predictors of extinction. Precipitation was positively correlated with the colonization rate of 12 out of 13 deciduous broad-leaved species, and negatively correlated with the extinction rate of nine of them. In contrast, precipitation equally decreased colonization and extinction of five out of eight of needle-leaved species (Juniperus and Pinus spp.). There was, however, marked variation among species in the magnitude of these effects, with some species exhibiting contrasting patterns for the colonization and the extinction process. Abundance of competing tree species (= summed plot basal area) was consistently correlated with decreased colonization of all needle-leaved species, and it increased the extinction rate of 6 out of 8 of these species. It had, nonetheless, weak facilitative effect on some broad-leaved species by promoting colonization (3 of 13 species) and decreasing extinction (7 of 13 species). With local colonization and extinction data, non-equilibrial and dynamic species distribution modelling can be improved by incorporating measures of biotic interactions and dispersal effects, along with traditional climate variables.Ministerio de Economía y CompetitividadComunidad de Madri

Effects of climate, species interactions, and dispersal on decadal colonization and extinction rates of Iberian tree species

We studied the relative importance of climate, abundance of potentially competing species, and dispersal in explaining local colonization and extinction rates of tree species throughout mainland Spain. We used a Bayesian framework to parameterize a patch occupancy model to 23 species censused in 46,596 permanent plots in a 1 × 1 km grid across most Spanish forests. For most species, dispersal was the single best predictor of colonization, whereas climate and dispersal were equally important as predictors of extinction. Precipitation was positively correlated with the colonization rate of 12 out of 13 deciduous broad-leaved species, and negatively correlated with the extinction rate of nine of them. In contrast, precipitation equally decreased colonization and extinction of five out of eight of needle-leaved species (Juniperus and Pinus spp.). There was, however, marked variation among species in the magnitude of these effects, with some species exhibiting contrasting patterns for the colonization and the extinction process. Abundance of competing tree species (= summed plot basal area) was consistently correlated with decreased colonization of all needle-leaved species, and it increased the extinction rate of 6 out of 8 of these species. It had, nonetheless, weak facilitative effect on some broad-leaved species by promoting colonization (3 of 13 species) and decreasing extinction (7 of 13 species). With local colonization and extinction data, non-equilibrial and dynamic species distribution modelling can be improved by incorporating measures of biotic interactions and dispersal effects, along with traditional climate variables.Ministerio de Economía y CompetitividadComunidad de Madri

Co-assortment in integron-associated gene cassette assemblages in environmental DNA samples

<p>Abstract</p> <p>Background</p> <p>It has been shown that integron-associated gene cassettes exist largely in tandem arrays of variable size, ranging from antibiotic resistance arrays of three to five cassettes up to arrays of more than 100 cassettes associated with the vibrios. Further, the ecology of the integron/gene cassette system has been investigated by showing that very many different cassettes are present in even small environmental samples. In this study, we seek to extend the ecological perspective on the integron/gene cassette system by investigating the way in which this diverse cassette metagenome is apportioned amongst prokaryote lineages in a natural environment.</p> <p>Results</p> <p>We used a combination of PCR-based techniques applied to environmental DNA samples and ecological analytical techniques to establish co-assortment within cassette populations, then establishing the relationship between this co-assortment and genomic structures. We then assessed the distribution of gene cassettes within the environment and found that the majority of gene cassettes existed in large co-assorting groups.</p> <p>Conclusions</p> <p>Our results suggested that the gene cassette diversity of a relatively pristine sampling environment was structured into co-assorting groups, predominantly containing large numbers of cassettes per group. These co-assorting groups consisted of different gene cassettes in stoichiometric relationship. Conservatively, we then attributed co-assorting cassettes to the gene cassette complements of single prokaryote lineages and by implication, to large integron-associated arrays. The prevalence of large arrays in the environment raises new questions about the assembly, maintenance and utility of large cassette arrays in prokaryote populations.</p

The bacterial community associated with adult vine weevil (Otiorhynchus sulcatus) in UK populations growing on strawberry is dominated by Candidatus Nardonella

Otiorhynchus sulcatus (Fabricius) (Coleoptera: Curculionidae), commonly known as black vine weevil or simply vine weevil, is an important pest of soft fruit and ornamental crops. This species is endemic to temperate areas of Europe but has spread to many other areas over the last century, including North America and Australasia. The ability of vine weevils to adapt to such different environments is difficult to reconcile with the parthenogenetic reproduction strategy, which is likely to underpin a low genetic diversity. It is therefore tempting to hypothesize that weevil adaptation to different environments is mediated, at least partly, by the microbial communities inhabiting these insects. As a first step towards testing this hypothesis we characterized the composition of the bacterial microbiota in weevils from populations feeding on strawberry plants across four geographically separate locations in the UK. We performed 16S rRNA gene Illumina amplicon sequencing, generating 2 882 853 high‐quality reads. Ecological indices, namely Chao1 and Shannon, revealed that the populations used for this study harboured a low diversity and an uneven bacterial microbiota. Furthermore, β‐diversity analysis failed to identify a clear association between microbiota composition and location. Notably, a single operational taxonomic unit phylogenetically related to Candidatus Nardonella accounted for 81% of the total sequencing reads for all tested insects. Our results indicate that vine weevil bacterial microbiota resembles that of other insects as it has low diversity and it is dominated by few taxa. A prediction of this observation is that location per se may not be a determinant of the microbiota inhabiting weevil populations. Rather, other or additional selective pressures, such as the plant species used as a food source, ultimately shape the weevil bacterial microbiota. Our results will serve as a reference framework to investigate other or additional hypotheses aimed at elucidating vine weevil adaptation to its environment

Species Richness and Range Size of the Terrestrial Mammals of the World: Biological Signal within Mathematical Constraints

We explore global spatial diversity patterns for terrestrial mammals using as a tool range-diversity plots. These plots display simultaneously information about the number of species in localities and their spatial covariance in composition. These are highly informative, as we show by linking range-diversity plots with maps and by highlighting the correspondences between well defined regions of the plots with geographical regions or with taxonomic groups. Range-diversity plots are mathematically constrained by the lines of maximum and minimum mean covariance in species composition. We show how regions in the range-diversity plot corresponding to the line of maximum covariance correspond to large continental masses, and regions near the lower limit of the range-diversity plot correspond to archipelagos and mountain ranges. We show how curves of constant covariance correspond to nested faunas. Finally, we show that the observed distribution of the covariance range has significantly longer tails than random, with clear geographic correspondences. At the scale of our data we found that range-diversity plots reveal biodiversity patterns that cannot be replicated by null models, and correspond to conspicuous terrain features and taxonomic groupings

Manipulation of feeding regime alters sexual dimorphism for lifespan and reduces sexual conflict in Drosophila melanogaster

Sexual dimorphism for lifespan (SDL) is widespread, but poorly understood. A leading hypothesis, which we test here, is that strong SDL can reduce sexual conflict, by allowing each sex to maximise its sex-specific fitness. We used replicated experimental evolution lines of the fruit fly, Drosophila melanogaster, which had been maintained for over 360 generations on either unpredictable ‘Random’ or predictable ‘Regular’ feeding regimes. This evolutionary manipulation of feeding regime led to robust, enhanced SDL in Random over control, Regular lines. Enhanced SDL was associated with a significant increase in the fitness of focal males, tested with wild type females. This was due to sex-specific changes to male life history, manifested as increased early reproductive output and reduced survival. In contrast, focal female fitness, tested with wild type males, did not differ across regimes. Hence increased SDL was associated with a reduction in sexual conflict, which increased male fitness and maintained fitness in females. Differences in SDL were not associated with developmental time or developmental survival. Overall, the results showed that the expression of enhanced SDL, resulting from experimental evolution of feeding regimes, was associated with male-specific changes in life history, leading to increased fitness and reduced sexual conflict

Protection of cells from salinity stress by extracellular polymeric substances in diatom biofilms.

Diatom biofilms are abundant in the marine environment. It is assumed (but untested) that extracellular polymeric substances (EPS), produced by diatoms, enable cells to cope with fluctuating salinity. To determine the protective role of EPS, Cylindrotheca closterium was grown in xanthan gum at salinities of 35, 50, 70 and 90 ppt. A xanthan matrix significantly increased cell viability (determined by SYTOX-Green), growth rate and population density by up to 300, 2,300 and 200%, respectively. Diatoms grown in 0.75% w/v xanthan, subjected to acute salinity shock treatments (at salinities 17.5, 50, 70 and 90 ppt) maintained photosynthetic capacity, Fq'/Fm', within 4% of pre-shock values, whereas Fq'/Fm' in cells grown without xanthan declined by up to 64% with hypersaline shock. Biofilms that developed in xanthan at standard salinity helped cells to maintain function during salinity shock. These results provide evidence of the benefits of living in an EPS matrix for biofilm diatoms

What is the price of using the Price equation in ecology?

The Dialogue series is intended to promote critical thinking and the expression of contrasting or even opposing viewpoints on important ecological topics. Here, seven researchers debate the use of the Price equation, a framework that has long been used in evolution to analyze temporal changes in the frequency of traits and alleles. This Dialogue describes different philosophical and mathematical perspectives on the application of the Price equation to ecological questions such as the relationship between biodiversity and ecosystem functioning (BEF). The hope is that the broader scientific community will benefit from these contrasting viewpoints

Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ("Hill diversities"), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.Comment: To be published in The ISME Journal. Main text: 16 pages, 5 figures. Supplement: 16 pages, 4 figure