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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.

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.

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.

Characterizing the genetic and behavioural consequences of contact between previously geographically isolated lineages provides insights into the mechanisms underlying diversification and ultimately speciation. The spring peeper (Pseudacris crucifer) is a widespread Nearctic chorus frog with six divergent mitochondrial DNA (mtDNA) lineages, many of which came into secondary contact during the Holocene. We examined genetics, morphology, advertisement calls and female preference for two lineages that began diverging in allopatry in the Pliocene and now overlap in southwestern Ontario, Canada. We found non-coincident clines in mtDNA and nuclear DNA, mirroring directionality of premating isolation barriers. We also found divergence in a range of traits between these two lineages, displacement in male call attributes and female preference for calls of their natal lineage in sympatry. Hybrids were morphologically distinct from both parental lineages, but hybrid male calls were acoustically intermediate. Female hybrids showed asymmetrical preference for Eastern male calls. These results considered together provide evidence of either unidirectional hybridization or selection against hybrids, potentially implying reproductive character displacement. Our work demonstrates the utility of integrated, multi-character approaches to understanding the processes of divergence and the nature of speciation. Genotypic_Acoustic_Morphological_Preference_Data_PseudacrisThis file contains 5 worksheets: worksheet 1 describes identifiers used throughout data set; worksheet 2 (Genotypes (G)) encompasses 14 columns of microsatellite and mtDNA data; worksheet 3 (Call (C)) encompasses 21 columns of mean acoustic data; worksheet 4 (Morphology (M)) encompasses 11 columns of mean morphological measurements; worksheet 5 (Female Preference (F)) encompasses 6 columns of phonotaxis experimental results. For more detail refer to Methods and Table 1.Stewart et al Heredity 2015 DRYAD.xlsx

This 2021 update was prompted by the discovery of an incorrect barcode data file for the MacGillivray's / Mourning Warbler GBS data. The files have now been completely re-processed, correcting the error. These updated versions of the original Dryad archive files are provided in this update: scripts: converting GBS reads to genotypes This text file ("warbler_genomics_processing_scripts_update2021.txt") contains scripts and notes for the steps used in converting raw Illumina GBS sequencing reads to individual genotypes (at both variant and invariant sites) across the genome. The resulting genotype files (in "012NA" format) were then used as input into R, for the rest of the analysis and production of figures. warbler_genomics_processing_scripts_update2021.txt custom R functions file This R file ("genomics_R_functions_V2.R") contains functions written by Darren Irwin originally for the analysis of Greenish Warbler GBS variation (in Irwin et al. 2016, Molecular Ecology) and modified more recently for the analysis of 3 North American warbler species groups (in Irwin et al. in review, Molecular Ecology). These functions are designed to work more broadly for any dataset in similar input format. To reproduce the analysis in the paper, the main R script file ("warbler_GBS_analysis_script_for_Dryad.R") should be run; it calls functions in the present file. genomics_R_functions_V2.R warbler GBS analysis R script This file ("warbler_GBS_analysis_script_2021_reanalysis.R") contains the main R scripts used to conduct the analysis and produce the figures. It uses as input the "012NA" files (and associated files) produced as described in the "warbler_genomics_processing_scripts.txt" file. Note that the metadata files "warbler.Fst_groups_14each.txt" (also contained in this Dryad package) is also needed. Also crucial is a file of R functions ("genomics_R_functions_V2.R") written especially for this analysis, but designed to work more generally; these functions are called by this script file. warbler_GBS_analysis_script_2021_reanalysis.R warbler.Fst_groups_14each_correct This file is required for conducting the 117-sample analysis (14 individuals per population, except 5 for goldmani) using the R script provided in this package. The file provides the names of each individual, the location code, the "group" (basically the specific or subspecific name) and "Fst_group" (the code used for defining groups in the Fst analysis, and for colouring the figures), and the "plot_order" (not used in the present paper). warbler.Fst_groups_14each_correct.txt warbler genotypes in "012NA" format This folder contains genotypic information used in the 117-sample analysis (14 individuals for each population, plus 5 for goldmani). For each chromosome, there is a file containing the genotypes (ending in "012NA"), a file containing the list of individuals (ending in "012.indv"), and a file containing the list of positions on the chromosome (ending in "012.pos"). For details of how these files were produced see the file "warbler_genomics_processing_scripts.txt", also provided in this Dryad package. These files are ready to be used for subsequent analysis and presentation in the R scripts supplied in this package. The metadata file ("warbler.Fst_groups_14each_correct.txt"; also in this package) is also needed in the R processing. warbler_GBS_14each_012NA_files_update2021.tar.gz SiteStats and WindowStats R files This folder contains files containing locus-based statistics ("SiteStats") and window-based statistics ("WindowStats") for each chromosome. These files can be produced by the R script (in this package), and they can also be used by that script (whether the script saves and/or loads SiteStats and WindowStats files can be adjusted in that script using the setting for "calculate_or_load_stats" and the related settings below that). Producing these files can take days of processing time; I have included them here so you can produce most of the figures in the paper, by running the R script below the heading "GENOME-WIDE plots". That script will call the appropriate files (as long as you have designated a path/folder structure that matches the R script). Separate WindowStats files are included for window sizes of 10000 (the main analysis in the paper) and 5000 (referred to briefly in the paper, with one figure in the supplement). SiteStats_and_WindowStats_files_update2021.tar.gz genotypes at SNPs only across the whole genome This folder contains genotypic information for variant sites only (no invariant sites) across the whole genome, among all individuals in the study. The folder contains a file containing the genotypes (ending in "012NA"), a file containing the list of individuals (ending in "012.indv"), and a file containing the list of positions on the chromosome (ending in "012.pos"). For details of how these files were produced see the file "warbler_genomics_processing_scripts.txt", also provided in this Dryad package. These files are ready to be used for subsequent analysis and presentation in the R scripts supplied in this package. The metadata file ("warbler.Fst_groups_14each_correct.txt"; also in this package) will be needed in the R processing. warbler_GBS_14each_SNPs_only_whole_genome_012NA_files.tar.gz Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., “islands of differentiation” in FST), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of genomic differentiation in three closely related pairs of New World warblers with the goal of evaluating support for the four models. Each pair (MacGillivray's/mourning warblers; Townsend's/black-throated green warblers; and Audubon's/myrtle warblers) consists of forms that were likely separated in western and eastern North American refugia during cycles of Pleistocene glaciations and have now come into contact in western Canada, where each forms a narrow hybrid zone. While there are a few differentiation peaks shared between the species pairs, substantial differences between pairs in which regions have high FST suggest differing selective forces and/or differing genomic responses to similar selective forces among the three pairs. Across most of the genome, levels of within-group nucleotide diversity (πWithin) are almost as large as levels of between-group nucleotide distance (πBetween) within each pair, suggesting recent common ancestry and/or gene flow. In all three pairs, a pattern of high‐FST regions having lower πBetween (compared to moderate‐FST regions) suggests that selective sweeps spread between geographically differentiated groups, followed by local differentiation. This “sweep-before-differentiation” model is consistent with signatures of gene flow within the yellow-rumped warbler species complex. These findings add to our growing understanding of speciation as a complex process that can involve phases of adaptive introgression among partially differentiated populations. Please see the 2018 paper and the 2021 Corrigendum, which together describes this in detail. Additional detail is provided in this file: warbler_genomics_processing_scripts_update2021.txt

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.

Two genetically distinct lineages of European green crabs (Carcinus maenas) were independently introduced to eastern North America, the first in the early 19th century and the second in the late 20th century. These lineages first came into secondary contact in southeastern Nova Scotia, Canada (NS), where they hybridized, producing latitudinal genetic clines. Previous studies have documented a persistent southward shift in the clines of different marker types, consistent with existing dispersal and recruitment pathways. We evaluated current clinal structure by quantifying the distribution of lineages and fine-scale hybridization patterns across the eastern North American range (25 locations, ~39-49°N) using informative single nucleotide polymorphisms (SNPs; n=96). In addition, temporal changes in the genetic clines were evaluated using mitochondrial DNA and microsatellite loci (n=9-11) over a 15-year period (2000-2015). Clinal structure was consistent with prior work demonstrating the existence of both northern and southern lineages with a hybrid zone occurring between southern New Brunswick (NB) and southern NS. Extensive later generation hybrids were detected in this region and in southeastern Newfoundland. Temporal genetic analysis confirmed the southward progression of clines over time; however, the rate of this progression was slower than predicted by forecasting models, and current clines for all marker types deviated significantly from these predictions. Our results suggest that neutral and selective processes contribute to cline dynamics, and ultimately, highlight how selection, hybridization, and dispersal can collectively influence invasion success. Genepop file 96 SNPGenepop file of all green crab samples genotyped at 96 informative single nucleotide polymorphisms (SNPs). Includes all individuals collected between 2011 and 2015 from eastern North America. Samples are combined by location (population).crab2015-2011-all-genepop96.txtMicrosatellite genotypes for green crabs in 2011Genepop file of microsatellite data (11 loci) for green crabs collected in 2011.Genepop_2011_micro_crabs.txt

A mechanistic understanding of community ecology requires tackling the nonadditive effects of multispecies interactions, a challenge that necessitates integration of ecological and molecular complexity-- namely moving beyond pairwise ecological interaction studies and the ‘gene at a time’ approach to mechanism. Here, we investigate the consequences of multispecies mutualisms for the structure and function of genome-wide coexpression networks for the first time, using the tractable and ecologically-important interaction between legume Medicago truncatula, rhizobia, and mycorrhizal fungi. First, we found that genes whose expression is affected nonadditively by multiple mutualists are more highly connected in gene networks than expected by chance and had 94% greater network centrality than genes showing additive effects, suggesting that nonadditive genes may be key players in the widespread transcriptomic responses to multispecies symbioses. Second, multispecies mutualisms substantially changed coexpression network structure of host plants and symbionts. Less than 50% of the plant and 10% of mycorrhizal fungi coexpression modules detected with rhizobia present were preserved in its absence, indicating that third-party mutualists can cause significant rewiring of plant and fungal molecular networks. Third, we identified unique sets of coexpressed genes that explain variation in plant performance only when multiple mutualists were present. Finally, an ‘across-symbiosis’ approach identified sets of coexpressed plant and mycorrhizal genes that were significantly associated with plant performance, were unique to the multiple mutualist context, and suggested coupled responses across the plant-mycorrhizal interaction to third-party mutualists. Taken together, these results show multispecies mutualism have substantial effects on the molecular interactions in host plants, microbes, and across symbiotic boundaries. Differential Coexpression ScriptThis script contains the use of previously normalized data to execute the DiffCoEx computational pipeline on an experiment with four treatment groups.differentialCoexpression.rNormalized Transformed Expression Count DataNormalized, transformed expression count data of Medicago truncatula and mycorrhizal fungi is given as an R data frame where the columns denote different genes and rows denote different samples. This data is used for downstream differential coexpression analyses.Expression_Data.zipNormalization and Transformation of Raw Count Data ScriptRaw count data is transformed and normalized with available R packages and RNA-Seq best practices.dataPrep.rRaw_Count_Data_Mycorrhizal_FungiRaw count data from HtSeq for mycorrhizal fungi reads are later transformed and normalized for use in differential coexpression analysis. 'R+' indicates that the sample was obtained from a plant grown in the presence of both mycorrhizal fungi and rhizobia. 'R-' indicates that the sample was obtained from a plant grown only in the presence of mycorrhizal fungi.Raw Count Data Medicago truncatulaRaw count data from HtSeq for Medicago truncatula reads are later transformed and normalized for use in differential coexpression analysis. 'M+R+' indicates that the sample was obtained from a plant grown in the presence of both mycorrhizal fungi and rhizobia. 'M+R-' indicates that the sample was obtained from a plant grown only in the presence of mycorrhizal fungi. 'M-R+' indicates that the sample was obtained from a plant grown only in the presence of rhizobia. 'M-R-' indicates that the sample was obtained from a plant grown in a sterile environment.Raw_Count_Data_Medicago_truncatula.zip