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Studies of biodiversity-ecosystem function in treed ecosystems have generally focused on aboveground functions. The present study investigates inter-trophic links between tree diversity and soil microbial community function and composition.We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR), functional diversity (FD), community-weighted mean trait value (CWM) and tree identity. The site was a 4-yr-old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community-level physiological profiles (CLPP) and respiration were evaluated using phospholipid fatty acid (PLFA) analysis and the MicroRespTM system, respectively. The relationship between tree species richness and glucose induced respiration (GIR), basal respiration (BR), metabolic quotient (qCO2) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration (BR)), with higher biomass (glucose induced respiration (GIR)), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR. In general, the CWM of traits had stronger effects than did FD, suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD. Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR) and identity (species and functional identity – leaf habit) affected soil microbial community respiration, biomass and composition. For the first time, we identified functional traits related to life history strategy, as well as root traits that influence another trophic level, soil microbial community function, via effects on BR and GIR. Montreal_IDENT_2012_SMCThe data are associated to the publication "Do temperate tree species diversity and identity influence soil microbial community function and composition?" by Khlifa, Rim, Paquette, Alain, Messier, Christian, Reich, Peter, Munson, Alison. They report measurements of soil microbial community function (analysed using the MicroResp method) and structure (using the PLFA analysis). The data also report mineral soil properties (0-15 cm depth). The samples are from the IDENT experiment of Montreal (Quebec, Canada), and were collected and analysed in 2012. A "read me" file is incorporated in the data file.

Substantial research has shown that while some parasite infections can be fatal to hosts, most infections are sub-clinical and non-lethal. Such sub-clinical infections can nonetheless have negative consequences for the long-term fitness of the host such as reducing juvenile growth and the host’s ability to compete for food and mates. With such effects, infected individuals are expected to exhibit behavioural changes. Here we use a parasite removal experiment to quantify how gastrointestinal parasite infections affect the behaviour of vervet monkeys (Chlorocebus aethiops) at Lake Nabugabo, Uganda. Behavioural profiles and the structure of nearest neighbour relationships varied significantly. As predicted, after deworming the duration of the resting events decreased, which is consistent with the idea that parasite infections are energetically costly. In contrast to what was predicted, we could not reject the null hypothesis and we observed no change in either the frequency or duration of grooming, but we found that the duration of travel events increased. A network analysis revealed that after deworming, individuals tended to have more nearest neighbours and hence probably more frequent interactions, with this effect being particularly marked for juveniles. The heightened response by juveniles may indicate that they are avoiding infected individuals more than other age classes because it is too costly to move energy away from growth. We consider that populations with high parasite burden may have difficulties developing social networks and behaviours that could have cascading effects that impact the population in general. Nabugabo vervet observationsObservational data collected in the field at Lake Nabugabo, Uganda of Vervet monkeys (Chlorocebus aethiops) between June 2011 and April 2014. The data is stored created using excel and stored as a .xlsx. The column names are kept intuitive. Further codes used in the file can be found in the "Read Me" file.Nab_VT_Act_Master_forDryad.xlsx

Collections of cells called engrams are thought to represent memories. Although there has been progress in identifying and manipulating single engrams, little is known about how multiple engrams interact to influence memory. In lateral amygdala (LA), neurons with increased excitability during training outcompete their neighbors for allocation to an engram. We examined whether competition based on neuronal excitability also governs the interaction between engrams. Mice received two distinct fear conditioning events separated by different intervals. LA neuron excitability was optogenetically manipulated and revealed a transient competitive process that integrates memories for events occurring closely in time (coallocating overlapping populations of neurons to both engrams) and separates memories for events occurring at distal times (disallocating nonoverlapping populations to each engram). Rashid et al Science 2016- Data for Figs 1-4, S1-S9Excel file with all data presented in manuscript (each sheet corresponds to specific figures as indicated).Rashid et al Science 2016.xlsx

One of the most important drivers of local adaptation for forest trees is climate. Coupled to these patterns, however, are human-induced disturbances through habitat modification and pollution. The confounded effects of climate and disturbance have rarely been investigated with regard to selective pressure on forest trees. Here, we have developed and used a population genetic approach to search for signals of selection within a set of 36 candidate genes chosen for their putative effects on adaptation to climate and human-induced air pollution within five populations of red spruce (Picea rubens Sarg.), distributed across its natural range and air pollution gradient in eastern North America. Specifically, we used FST outlier and environmental correlation analyses to highlight a set of seven single nucleotide polymorphisms (SNPs) that were overly correlated with climate and levels of sulphate pollution after correcting for the confounding effects of population history. Use of three age cohorts within each population allowed the effects of climate and pollution to be separated temporally, as climate-related SNPs (n = 7) showed the strongest signals in the oldest cohort, while pollution-related SNPs (n = 3) showed the strongest signals in the youngest cohorts. These results highlight the usefulness of population genetic scans for the identification of putatively nonneutral evolution within genomes of nonmodel forest tree species, but also highlight the need for the development and application of robust methodologies to deal with the inherent multivariate nature of the genetic and ecological data used in these types of analyses. Bashalkhanov-Eckert-Rajora_Mol_Ecol_DATARed spruce genetic and climate dataBashalkhanov-Eckert-Rajora_genetic_analysesR Scripts for Genetic Data AnalysisBashalkhanov-Eckert-Rajora-climate_dataR Scripts for Climate Data Analysis

Spatial and temporal heterogeneity within landscapes influences the distribution and phenotypic diversity of individuals both within and across populations. Phenotype-habitat correlations arise either through phenotypes within an environment altering through the process of natural selection or plasticity, or phenotypes remaining constant but individuals altering their distribution across environments. The mechanisms of non-random movement and phenotype-dependent habitat choice may account for associations within highly heterogeneous systems, such as streams, where local adaptation may be negated, plasticity too costly and movement is particularly important. Despite growing attention, however, few empirical tests have yet to be conducted. Here we provide a test of phenotype-dependent habitat choice and ask: 1) if individuals collected from a single habitat type continue to select original habitat; 2) if decisions are phenotype-dependent and functionally related to habitat requirements; and 3) if phenotypic-sorting continues despite increasing population density. To do so we both conducted experimental trials manipulating the density of four stream-fish species collected from either a single riffle or pool and developed a game-theoretical model exploring the influence of individuals’ growth rate, sampling and competitive abilities as well as interference on distribution across two habitats as a function of density. Our experimental trials show individuals selecting original versus alternative habitats differed in their morphologies, that morphologies were functionally related to habitat-type swimming demands, and that phenotypic-sorting remained significant (although decreased) as density increased. According to our model this only occurs when phenotypes have contrasting habitat preferences and only one phenotype disperses (i.e. selects alternatives) in response to density pressures. This supports our explanation that empirical habitat selection was due to a combination of collecting a fraction of mobile individuals with different habitat preferences and the exclusion of individuals via scramble competition at increased densities. Phenotype-dependent habitat choice can thereby account for observed patterns of natural stream-fish distribution. DataJacobsonetal2017This file contains the density level, trial, selected habitat, partial warp and length and size variables for each of the individuals and species tested within artificial stream experiments.

Premise of the study: Agricultural practices routinely create opportunities for crops to hybridize with wild relatives, leading to crop gene introgression into wild genomes. Conservationists typically worry this introgression could lead to genetic homogenization of wild populations, over and above the central concern of transgene escape. Alternatively, viewing introgression as analogous to species invasion, we suggest that increased genetic diversity may likewise be an undesirable outcome. Methods: Here, we compare the sensitivity of conventional population genetic metrics with species diversity indices as indicators of the impact of gene flow on genetic diversity. We illustrate this novel approach using multilocus genotype data (12 allozyme loci) from 10 wild (Beta vulgaris subsp. maritima) and eight putative crop–wild hybrid beet populations (B. vulgaris subsp. vulgaris × B. vulgaris subsp. maritima) scattered throughout Europe. Results: Conventional population genetic metrics mostly failed to detect shifts in genetic composition of putative hybrid populations. By contrast, species diversity indices unambiguously revealed increased genetic diversity in putative hybrid populations. Discussion: We encourage other workers to explore the utility of our more sensitive approach for risk assessment prior to the release of transgenic crops, with a view toward widespread adoption of our method in studies aimed at detecting allelic invasion. Genotyped Beta vulgaris after Structure ClusteringThis file contains allozyme genotypes of Beta vulgaris individuals collected from cultivated (ssp. vulgaris), wild (ssp. maritima), and putative crop-wild hybrid populations in Europe.

Premise of the study: Polyploidization is a common and recurring phenomenon in plants and is often thought to be a mechanism of "instant speciation." Whether polyploidization is associated with the formation of new species ("cladogenesis") or simply occurs over time within a lineage ("anagenesis") has never, however, been assessed systematically. Methods: Here, we tested this hypothesis using phylogenetic and karyotypic information from 235 plant genera (mostly angiosperms). We first constructed a large database of combined sequence and chromosome number data sets using an automated procedure. We then applied likelihood models (ClaSSE) that estimate the degree of synchronization between polyploidization and speciation events in maximum likelihood and Bayesian frameworks. Key results: Our maximum likelihood analysis indicated that 35 genera supported a model that includes cladogenetic transitions over a model with only anagenetic transitions, whereas three genera supported a model that incorporates anagenetic transitions over one with only cladogenetic transitions. Furthermore, the Bayesian analysis supported a preponderance of cladogenetic change in four genera but did not support a preponderance of anagenetic change in any genus. Conclusions: Overall, these phylogenetic analyses provide the first broad confirmation that polyploidization is temporally associated with speciation events, suggesting that it is indeed a major speciation mechanism in plants, at least in some genera. PloiDBPhylogenetic trees inferred using MrBayes, ploidy estimates using ChromEvol, and TPL-based genus species diversity estimates for 223 genera.ploidb_dryad.tar.gz

Ecological speciation is often observed in phytophagous insects and their parasitoids due to divergent selection caused by host-associated or temporal differences. Most previous studies have utilized limited genetic markers or distantly related species to look for reproductive barriers of speciation. In our study we focus on closely related species of Lygus bugs and two sister species of Peristenus parasitoid wasps. Using mitochondrial DNA COI and genome wide SNPs generated using ddRADseq, we tested for potential effects of host-associated differentiation (HAD) or temporal isolation in this system. While three species of Lygus are clearly delineated with both COI and SNPs, no evidence of HAD or temporal differentiation was detected. Two Peristenus sister species were supported by both sets of markers and separated temporally with P. mellipes emerging early in June and attacking the first generation of Lygus, and P. howardi emerging later in August and attacking the second generation of their hosts. This is one of the few studies to examine closely related hosts and parasitoids to examine drivers of diversification. Given the results of this study, the Lygus-Peristenus system demonstrates temporal isolation as a potential barrier to reproductive isolation for parasitoids, which could indicate higher parasitoid diversity in regions of multivoltine hosts. This study also demonstrates that incorporating systematics improves studies of parasitoid speciation, particularly by obtaining accurate host records through rearing, carefully delimiting cryptic species, and examining population level differences with genomic scale data among closely related taxa. Zhang et al 2018 - Habitat or Temporal Isolation: Unravelling herbivore-parasitoid speciation patterns using double digest RADseq-VCF files for all raw SNP data sets -Input files for MrBayes (Nexus format), RAxML (PHYLIP format), STRUCTURE (.str format) -R scripts for AMOVA and ggtree.Zhang et al 2018.zip

Between 11 and 21 vertical CTD profiles were recorded in the top 300 m of the water column in five areas over the Chatham Rise, New Zealand in October and November 2018. Temperature, salinity, fluorescence, and dissolved oxygen concentrations were measured. The latter two were converted to final values using calibrations.