The effect of immigration on the adaptation of microbial communities to warming

Theory predicts that immigration can either enhance or impair the rate at which species and whole communities adapt to environmental change, depending on the traits of genotypes and species in the source pool relative to local conditions. These responses in turn will determine how well whole communities function in changing environments. We tested the effects of immigration and experimental warming on microbial communities during an 81 day field experiment. The effects of immigration depended on the warming treatment. In warmed communities immigration was detrimental to community growth whereas in ambient communities it was beneficial. This result is explained if colonists came from a local species pool pre-adapted to ambient conditions. Loss of metabolic diversity, however, was buffered by immigration in both environments. Communities showed increasing local adaptation to temperature conditions during the experiment and this was independent of whether or not they received immigration. Genotypes that comprised the communities were not locally adapted, however, indicating that community local adaptation can be independent of adaptation of component genotypes. Our results are consistent with a greater role for species interactions rather than adaptation of constituent species in determining local adaptation of whole communities, and confirm that immigration can either enhance or impair community responses to environmental change depending on the environmental context

A rapid and scalable method for multilocus species delimitation using Bayesian model comparison and rooted triplets

Multilocus sequence data provide far greater power to resolve species limits than the single locus data typically used for broad surveys of clades. However, current statistical methods based on a multispecies coalescent framework are computationally demanding, because of the number of possible delimitations that must be compared and time-consuming likelihood calculations. New methods are therefore needed to open up the power of multilocus approaches to larger systematic surveys. Here, we present a rapid and scalable method that introduces two new innovations. First, the method reduces the complexity of likelihood calculations by decomposing the tree into rooted triplets. The distribution of topologies for a triplet across multiple loci has a uniform trinomial distribution when the 3 individuals belong to the same species, but a skewed distribution if they belong to separate species with a form that is specified by the multispecies coalescent. A Bayesian model comparison framework was developed and the best delimitation found by comparing the product of posterior probabilities of all triplets. The second innovation is a new dynamic programming algorithm for finding the optimum delimitation from all those compatible with a guide tree by successively analyzing subtrees defined by each node. This algorithm removes the need for heuristic searches used by current methods, and guarantees that the best solution is found and potentially could be used in other systematic applications. We assessed the performance of the method with simulated, published and newly generated data. Analyses of simulated data demonstrate that the combined method has favourable statistical properties and scalability with increasing sample sizes. Analyses of empirical data from both eukaryotes and prokaryotes demonstrate its potential for delimiting species in real cases

Cross-contamination explains "inter- and intraspecific horizontal genetic transfers" between asexual bdelloid rotifers

A few metazoan lineages are thought to have persisted for millions of years without sexual reproduction. If so, they would offer important clues to the evolutionary paradox of sex itself [1, 2]. Most "ancient asexuals" are subject to ongoing doubt because extant populations continue to invest 17 in males [3–9]. However, males are famously unknown in bdelloid rotifers, a class of microscopic invertebrates comprising hundreds of species [10–12]. Bdelloid genomes have acquired an unusually high proportion of genes from non-metazoans via horizontal transfer [13–17]. This well-substantiated finding has invited speculation [13] that homologous horizontal transfer between bdelloid individuals also may occur, perhaps even "replacing" sex [14]. In 2016, Current Biology published an Article claiming to supply evidence for this idea. Debortoli et al. [18] sampled rotifers from natural populations and sequenced one mitochondrial and four nuclear loci. Species assignments were incongruent among loci for several samples, which was interpreted as evidence of "interspecific horizontal genetic transfers". Here, we use sequencing chromatograms supplied by the authors to demonstrate that samples treated as individuals actually contained two or more highly divergent mitoc hondrial and ribosomal sequences, revealing cross-contamination with DNA from multiple animals of different species. Other chromatograms indicate contamination with DNA from conspecific animals, explaining genetic and genomic evidence for "intraspecific horizontal exchanges" reported in the same study. Given the clear evidence of contamination, the data and findings of Debortoli et al. [18] provide no reliable support for their conclusions that DNA is transferred horizontally between or within bdelloid species

Community composition drives siderophore dynamics in multispecies bacterial communities

Background Intraspecific public goods are commonly shared within microbial populations, where the benefits of public goods are largely limited to closely related conspecifics. One example is the production of iron-scavenging siderophores that deliver iron to cells via specific cell envelope receptor and transport systems. Intraspecific social exploitation of siderophore producers is common, since non-producers avoid the costs of production but retain the cell envelope machinery for siderophore uptake. However, little is known about how interactions between species (i.e., interspecific interactions) can shape intraspecific public goods exploitation. Here, we predicted that strong competition for iron between species in diverse communities will increase costs of siderophore cooperation, and hence drive intraspecific exploitation. We examined how increasing microbial community species diversity shapes intraspecific social dynamics by monitoring the growth of siderophore producers and non-producers of the plant-growth promoting bacterium Pseudomonas fluorescens, embedded within tree-hole microbial communities ranging from 2 to 15 species. Results We find, contrary to our prediction, that siderophore production is favoured at higher levels of community species richness, driven by increased likelihood of encountering key species that reduce the growth of siderophore non-producing (but not producing) strains of P. fluorescens. Conclusions Our results suggest that maintaining a diverse soil microbiota could partly contribute to the maintenance of siderophore production in natural communities

Convergent evolution of an ant-plant mutualism across plant families, continents and time

Questions: How often has dispersal of seeds by ants evolved in monocots and is the timing of origins associated with changes in the ant community or instead with the rise of forests? Are patterns in the origin of elaiosomes (the trait associated with the dispersal of seeds by ants) through time similar to those for the origins of fleshy fruits? Data studied: We estimate the timing of the origin of elaiosomes and fleshy fruits respectivelyby mapping seed morphology onto a recent phylogeny based on ndhF sequence data forthe monocots (Givnish et al., 2005). For comparison, we use fossil data on ant relativeabundance through time and phylogenetic data for the timing of the origin of seed-dispersing ant lineages. Search method: We mapped origins of both elaiosomes and fleshy fruits onto the phylogenyusing parsimony in the program Mesquite (Maddison and Maddison, 2005). We analysed therelationship between ant relative abundances, the number of origins of seed-dispersing ants, and the rate of origination of elaiosomes using randomization-based Monte Carlo regression in the program R (Cliff and Ord, 1981). Using the program Discrete (Pagel, 2006), we test whether fleshy fruits or elaiosomes and shaded forest understoreys show correlated evolution.Conclusions: Morphological features for the dispersal of seeds by ants (myrmecochory) have evolved at least twenty times within the monocots. Origins of myrmecochory are not associated with the rise of forests during the Cretaceous or with subsequent transitions of plant lineages into closed canopy habitats, nor are they contemporaneous with the origins of fleshy fruits. Instead, the origins of myrmecochory are closely associated with the rise in relative abundanceof ants (proportion of all individual insects in fossils) towards the end of the Eocene and more recently

A database of whole-body action videos for the study of action, emotion, and untrustworthiness

We present a database of high-definition (HD) videos for the study of traits inferred from whole-body actions. Twenty-nine actors (19 female) were filmed performing different actions—walking, picking up a box, putting down a box, jumping, sitting down, and standing and acting—while conveying different traits, including four emotions (anger, fear, happiness, sadness), untrustworthiness, and neutral, where no specific trait was conveyed. For the actions conveying the four emotions and untrustworthiness, the actions were filmed multiple times, with the actor conveying the traits with different levels of intensity. In total, we made 2,783 action videos (in both two-dimensional and three-dimensional format), each lasting 7 s with a frame rate of 50 fps. All videos were filmed in a green-screen studio in order to isolate the action information from all contextual detail and to provide a flexible stimulus set for future use. In order to validate the traits conveyed by each action, we asked participants to rate each of the actions corresponding to the trait that the actor portrayed in the two-dimensional videos. To provide a useful database of stimuli of multiple actions conveying multiple traits, each video name contains information on the gender of the actor, the action executed, the trait conveyed, and the rating of its perceived intensity. All videos can be downloaded free at the following address: http://www-users.york.ac.uk/~neb506/databases.html. We discuss potential uses for the database in the analysis of the perception of whole-body actions

Parastatal development - institutional strengthening

When the World Bank financed BKS technical assistance team arrived at the Water and Sewerage Authority of Lesotho (WASA) in 1994 it was evident that the organisation was facing three main obstacles to the sustainability of the organisation: • absence of a proper planning function; • financial frailty; and • limited institutional capacity. This paper illustrates the problems, discusses how solutions have been approached and the extent to which strategies have been successful

Hydrologic data for the Idaho National Engineering Laboratory site, Idaho

The Idaho Chemical Processing Plant (ICPP) discharges low-level waste and chemical waste directly to the Snake River Plain aquifer through a 600-foot (180 meter) disposal well. Most of the radioactivity is removed by distillation and ion exchange prior to being discharged into the well. During 1971 to 1973, the well was used to dispose of 404 curies of radioactivity, of which 389 curies were tritium (96 percent). The average yearly discharge was about 300 million gallons (1.1 x 10$sup 9$ liters). The distribution of waste products in the Snake River Plain aquifer covers about 15 square miles (30 square kilometers). Since disposal began in 1952, the wastes have migrated about 5 miles (8 kilometers) downgradient from discharge points. The perched ground-water body contains tritium, chromium-51, cobalt-60, and strontium-90. Radionuclides are subject to radioactive decay, sorption, and dilution by dispersion in the aquifer. Chemical wastes are subject to sorption and dilution by dispersion. Waste plumes south of the ICPP containing tritium, sodium, and chloride have been mapped and all cover a similar area. The plumes follow generally southerly flow lines and are widely dispersed in the aquifer. The waste plume of strontium-90 covers a much smaller area of the aquifer, about 1.5 square miles (4 square kilometers). Based on the relatively small size of the plume, it would appear that the strontium-90 is sorbed from solution as it moves through the Snake River Plain aquifer. (auth