cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vd8b0
title: Data from: Genetic variation and seasonal migratory connectivity in Wilson’s warblers (Wilsonia pusilla): species-level differences in nuclear DNA between western and eastern populations

description: There is growing interest in understanding patterns of seasonal migratory
 connectivity between breeding and wintering sites, both because
 differences in migratory behavior can be associated with population
 differentiation and because knowledge of migratory connectivity is
 essential for understanding the ecology, evolution, and conservation of
 migratory species. We present the first broad survey of geographic
 variation in the nuclear genome of breeding and wintering Wilson’s
 warblers (Wilsonia pusilla), which have previously served as a research
 system for the study of whether genetic markers and isotopes can reveal
 patterns of migratory connectivity. Using 153 samples surveyed at up to
 257 variable amplified fragment length polymorphism (AFLP) markers, we
 show that Wilson’s warblers consist of highly distinct western and eastern
 breeding groups, with all winter samples grouping with the western
 breeding group. Within the west there is weak geographic differentiation,
 at a level insufficient for use in assignment of wintering samples to
 specific areas. The distinctiveness of western and eastern genetic groups,
 with no known intermediates, strongly suggests that these two groups are
 cryptic species. Analysis of mitochondrial cytochrome b sequence variation
 shows that the estimated coalescence time between western and eastern
 clades is roughly 2.3 million years ago, a surprisingly old time of
 divergence that is more typical of distinct species than of subspecies.
 Given their morphological similarity but strong genetic differences,
 western and eastern Wilson’s warblers present a likely case of association
 between divergence in migratory behavior and the process of speciation.
description: WIWA_6combo_AFLPdata_IrwinIrwinSmithWIWA_2combo_AFLPdata_IrwinIrwinSmith
DOI: 10.5061/dryad.1fj40
title: Data from: Genetic differentiation and regional adaptation among seed origins used for grassland restoration: lessons from a multispecies transplant experiment

description: One of the key questions in ecosystem restoration is the choice of seed
 material for restoring plant communities. More and more scientists and
 practitioners are currently advocating the use of regional seed sources,
 based on the argument that plants are often adapted to local or regional
 environmental conditions, and thus, regional seed sources should provide
 the best restoration success. However, there is still substantial debate
 about this approach, partly because of a lack of solid empirical data. We
 conducted a multispecies transplant experiment in which we compared the
 performance of eight seed origins of seven plant species frequently used
 in grassland restoration in four common gardens across Germany. We found
 that, on average, plants of regional origins produced 10% more
 inflorescences and 7% more biomass than those of foreign origins. There
 were substantial differences among species in the strength of these
 effects, but in the majority of the study species fitness decreased with
 increasing geographical distance of seed origins or with increasing
 climatic differences between plant origins and experimental sites. In
 addition to these effects on plant fitness, increasing geographical or
 climatic distances of origin were often also correlated with increasing
 differences in plant phenology. Since phenology is important for biotic
 interactions, especially with pollinators and seed predators, using
 foreign seed sources may have cascading effects on local ecosystems.
 Synthesis and applications. Genetic differentiation is widespread in
 grassland species and often shows the patterns of regional adaptation. Our
 study thus supports the use of regional seed sources in restoration.
 Moreover, using non-regional seed sources in grassland restoration may not
 only decrease the performance of plants, but it will likely also affect
 their biotic interactions.
description: Regional adaptation
 phenotype dataData on seven species,
 eight origins, grown in four common gardens (detailed description in the
 connected publication).all_data_dryad.txt
DOI: 10.5061/dryad.4qk2k11
title: Data from: Testing and interpreting the shared space-environment fraction in variation partitioning analyses of ecological data

description: Variation partitioning analyses combined with spatial predictors (Moran’s
 eigenvector maps, MEM) are commonly used in ecology to test the fractions
 of species abundance variation purely explained by environment and space.
 However, while these pure fractions can be tested using a classical
 residuals permutation procedure, no specific method has been developed to
 test the shared space-environment fraction (SSEF). Yet, the SSEF is
 expected to encompass a major driver of community assembly, that is, an
 induced spatial dependence effect (ISD; i.e. the reflection of a spatially
 structured habitat filter on a species distribution). A reliable test of
 this fraction is therefore crucial to properly test the presence of an ISD
 on ecological data. To bridge the gap, we propose to test the SSEF through
 spatially-constrained null models: torus-translations, and Moran spectral
 randomisations. We investigated the type I error rate and statistical
 power of our method based on two real environmental datasets and
 simulations of tree distributions. Ten types of tree distribution
 displaying contrasted aggregation properties were simulated, and their
 abundances were sampled in 153 regularly-distributed 20 × 20 m quadrats.
 The SSEF was tested for 1000 simulated tree distributions either unrelated
 to the environment, or filtered by environmental variables displaying
 contrasting spatial structures. The method proposed provided a correct
 type I error rate (&lt; 0.05). The statistical power was high
 (&gt; 0.9) when abundances were filtered by an environmental variable
 structured at broad scale. However, the spatial resolution allowed by the
 sampling design limited the power of the method when using a fine-scale
 filtering variable. This highlighted that an ISD can be properly detected
 providing that the spatial pattern of the filtering process is correctly
 captured by the sampling design of the study. An R function to apply the
 SSEF testing method is provided and detailed in a tutorial.
description: Table S1. Standardised
 values of the eight environmental variables used in our
 simulations.The file contains
 standardised values of each environmental variable used in our
 simulations. Standardisation was performed by centering values by their
 mean and dividing them by their standard deviation.Table
 S1.xlsx
DOI: 10.5061/dryad.1222
title: Data from: Body size evolution in mammals: complexity in tempo and mode

description: Body size correlates with virtually every aspect of species' biology,
 so understanding the tempo and mode of its evolution is of key importance
 in macroecology and macroevolution. Here we use body-mass data from 3473
 of 4510 extant mammalian species and an almost complete species-level
 phylogeny to determine the best model of log(body-mass) evolution across
 all mammals, split taxonomically and spatially. An early-burst model fits
 better across all mammals than models based on either Brownian motion or
 an Ornstein-Uhlenbeck process, suggesting that mammals experienced a burst
 of morphological evolution relatively early in their history followed by
 slower change subsequently. We also use spatial models to investigate
 rates of body-mass evolution within ecoregions. These models show that
 around 50% of the variation in rate can be explained by just a few
 predictors. High estimated rates are associated with cold, low lying,
 species-poor, high energy, mainland ecoregions. We conclude that the
 evolution of mammalian body size has been influenced by a complex
 interplay among geography, climate and history.
description: DataAmNat51264.txtTab delimited text file - see ReadMe.txt for details
DOI: 10.5061/dryad.5s3kt727
title: Data from: Boechera, a model system for ecological genomics

description: The selection and development of a study system for evolutionary and
 ecological functional genomics (EEFG) depends on a variety of factors.
 Here we present the genus Boechera as an exemplary system with which to
 address ecological and evolutionary questions. Our focus on Boechera is
 based on several characteristics: 1) native populations in undisturbed
 habitats where current environments reflect historical conditions over
 several thousand years; 2) functional genomics benefitting from its close
 relationship to Arabidopsis thaliana; 3) inbreeding tolerance enabling
 development of recombinant inbred lines, near-isogenic lines, and
 positional cloning; 4) interspecific crosses permitting mapping for
 genetic analysis of speciation; 5) apomixis (asexual reproduction by
 seeds) in a genetically tractable diploid; and 6) broad geographic
 distribution in North America, permitting ecological genetics for a large
 research community. These characteristics, along with the current
 sequencing of three Boechera species by the Joint Genome Institute,
 position Boechera as a rapidly advancing system for EEFG studies.
description: AlignmentsThe original alignments of the 84 orthologous genes in fasta format. Notice that gaps and continuous un-gapped regions less than 20 bp long were removed before phylogenetic trees reconstruction. Refer to the original article for detailed methods.GenBank_accessionGenBank accession numbers of the corresponding genes for Boechera stricta
DOI: 10.5061/dryad.js480
title: Data from: Sex and genotype effects on nutrient-dependent fitness landscapes in Drosophila melanogaster

description: The sexes perform different reproductive roles and have evolved sometimes
 strikingly different phenotypes. One focal point of adaptive divergence
 occurs in the context of diet and metabolism, and males and females of a
 range of species have been shown to require different nutrients to
 maximize their fitness. Biochemical analyses in Drosophila melanogaster
 have confirmed that dimorphism in dietary requirements is associated with
 molecular sex differences in metabolite titres. In addition, they also
 showed significant within-sex genetic variation in the metabolome. To date
 however, it is unknown whether this metabolic variation translates into
 differences in reproductive fitness. The answer to this question is
 crucial to establish whether genetic variation is selectively neutral or
 indicative of constraints on sex-specific physiological adaptation and
 optimization. Here we assay genetic variation in consumption and metabolic
 fitness effects by screening male and female fitness of thirty D.
 melanogaster genotypes across four protein-to-carbohydrate ratios. In
 addition to confirming sexual dimorphism in consumption and fitness, we
 find significant genetic variation in male and female dietary
 requirements. Importantly, these differences are not explained by feeding
 responses and probably reflect metabolic variation that, in turn, suggests
 the presence of genetic constraints on metabolic dimorphism.
description: Diet consumption and
 fitnessData to plot heat maps.
 Contains consumption and fitness data.dietfitness.csv
DOI: 10.5061/dryad.7q7m6
title: Data from: Sexual selection on cuticular hydrocarbons of male sagebrush crickets in the wild

description: Cuticular hydrocarbons (CHCs) play an essential role in mate recognition
 in insects but the form and intensity of sexual selection on CHCs has only
 been evaluated in a handful of studies, and never in a natural population.
 We quantified sexual selection operating on CHCs in a wild population of
 sagebrush crickets, a species in which nuptial feeding by females imposes
 an unambiguous phenotypic marker on males. Multivariate selection analysis
 revealed a saddle-shaped fitness surface, suggesting a complex interplay
 between the total abundance of CHCs and specific CHC combinations in their
 influence on female choice. The fitness surface resulting from two axes of
 disruptive selection reflected a trade-off between short- and long-chained
 CHCs, suggesting that males may be sacrificing some level of desiccation
 resistance in favour of increased attractiveness. There was a significant
 correlation between male body size and total CHC abundance, suggesting
 that male CHCs provide females with a reliable cue for maximizing benefits
 obtained from males. Notwithstanding the conspicuousness of males’
 acoustic signals, our results suggest that selection imposed on males via
 female mating preferences may be far more complex than previously
 appreciated and operating in multiple sensory modalities.
description: Steiger et al 2013 Proc
 R Soc Sagebrush DataThis is a Microsoft
 Excel spreadsheet containing the data for Steiger et al (2013) Sexual
 selection on cuticular hydrocarbons of male sagebrush crickets in the
 wild. Column headings are either self explanatory or further details are
 at the bottom of the table. Data contained in columns D to AY represents
 area for CHC peaks 1-48 expressed in proportional values after dividing by
 a pentadecane standard.
DOI: 10.5061/dryad.gv506
title: Data from: Estimating dark diversity and species pools: an empirical assessment of two methods

description: 1. Species absent from a community, but with the potential to establish
 (dark diversity) are an important, yet rarely considered, component of
 habitat specific species pools. However, quantifying this component
 remains a challenge as dark diversity cannot be observed directly, and
 must be estimated. Here, we empirically test whether species ecological
 requirements or species co-occurrences provide accurate estimates of dark
 diversity. 2. We used two spatially nested independent datasets, one
 comprising 3033 samples of coastal grassland vegetation plots of 4m2 and
 200m2 from Scotland, UK and another comprising 780 samples of forest
 vegetation plots of 30m2 and 500m2 from Switzerland. Dark diversity for
 each of the smaller scaled plots was estimated through investigating the
 degree of 1) similarity in ecological requirements (measured as Ellenberg
 values) and 2) co-occurrence likelihood of all species observed. Estimates
 were validated through comparing estimates with observed species at the
 larger spatial scale. Estimates were further validated using observations
 from all larger-scale plots surrounding a focal small-scale plot within a
 2km (Scottish grassland) and 10km (Swiss forest) radius. 3. The
 co-occurrence method was shown to be more accurate and resulted in far
 fewer negative mismatches (i.e. species observed but not predicted), and
 higher proportions of observed and predicted species, relative to the
 Ellenberg approach. Of the species observed in the large-scale samples,
 18% were estimated as part of the smaller-scale dark diversity via the
 co-occurrence approach relative to 8% for the Ellenberg method for both
 the Scottish and Swiss data respectively. These values increased to 67%
 & 60% and 32% & 35% respectively across all observations
 within a 2km (Scottish grasslands) and 10km (Swiss forests) radius. 4. The
 study demonstrates that dark diversity for a community can be successfully
 estimated using readily available data, through exploring species
 co-occurrence patterns. This work substantiates that; habitat-specific
 species pools, can be accurately quantified and should prove valuable for
 understanding underlying community processes and improving our knowledge
 of the mechanisms governing species co-existence.
description: SG_Nested_DataHistoric dataset of Scottish coastal grasslands, derived from the Scottish Coastal Survey (1975–1977); For details see: Shaw, M.W., Hewett, D.G. & Pizzey, J.M. (1983). Scottish coastal survey. Institute of Terrestrial Ecology. Bangor Research Station, Bangor, Gwynedd. The dataset is nested: i.e. records of plant species with taken following a hierarchical sampling design, measuring nested community compositions at 4m2 and 200m2. The uploaded dataset comprises species information (recorded as octets) on 3033 nested samples.Lewis,R.SG_Nest.RData
DOI: 10.5061/dryad.37354
title: Data from: Genetic consequences of selection cutting on sugar maple (Acer saccharum Marshall)

description: Selection cutting is a treatment that emulates tree-by-tree replacement
 for forests with uneven-age structures. It creates small openings in large
 areas and often generates a more homogenous forest structure (fewer large
 leaving trees and defective trees) that differs from old-growth forest. In
 this study, we evaluated whether this type of harvesting has an impact on
 genetic diversity of sugar maple (Acer saccharum Marshall). Genetic
 diversity among seedlings, saplings and mature trees was compared between
 selection cut and old-growth forest stands in Québec, Canada. We found
 higher observed heterozygosity and a lower inbreeding coefficient in
 mature trees than in younger regeneration cohorts of both forest types. We
 detected a recent bottleneck in all stands undergoing selection cutting.
 Other genetic indices of diversity (allelic richness, observed and
 expected heterozygosity and rare alleles) were similar between forest
 types. We concluded that the effect of selection cutting on the genetic
 diversity of sugar maple was recent and no evidence of genetic erosion was
 detectable in Québec stands after one harvest. However, the cumulative
 effect of recurring applications of selection cutting in bottlenecked
 stands could lead to fixation of deleterious alleles, and this highlights
 the need for adopting better forest management practices.
description: Graignic-EvolAppli-Dryad-2016-04-14-18ssr-360ind-SelectionCuttingData of microsatellite genotypes using 18 ssr for 360 individuals. Each individual is associated with stand code (3 OG: old growth and 3 SC: selection cutting) and cohort (mature, sapling and seedling sugar maple)Graignic-EvolAppli-Dryad-2016-04-12-18ssr-Coupe-360ind.xls
DOI: 10.5061/dryad.808g7
title: Data from: Competition-driven build-up of habitat isolation and selection favouring dispersal modification in a young avian hybrid zone

description: Competition-driven evolution of habitat isolation is an important
 mechanism of ecological speciation but empirical support for this process
 is often indirect. We examined how an on-going displacement of pied
 flycatchers from their preferred breeding habitat by collared flycatchers
 in a young secondary contact zone is associated with (a) access to an
 important food resource (caterpillar larvae), (b) immigration of pied
 flycatchers in relation to habitat quality, and (c) the risk of
 hybridization in relation to habitat quality. Over the past 12 years, the
 estimated access to caterpillar larvae biomass in the habitat surrounding
 the nests of pied flycatchers has decreased by a fifth due to shifted
 establishment possibilities, especially for immigrants. However, breeding
 in the high quality habitat has become associated with such a high risk of
 hybridization for pied flycatchers that overall selection currently favors
 pied flycatchers that were forced to immigrate into the poorer habitats
 (despite lower access to preferred food items). Our results show that
 competition-driven habitat segregation can lead to fast habitat isolation,
 which per se caused an opportunity for selection to act in favor of future
 “voluntarily” altered immigration patterns and possibly strengthened
 habitat isolation through reinforcement.
description: Table 1
 dataTable 2
 dataTable 3
 dataTable 4
 data
DOI: 10.5061/dryad.gt57f
title: Data from: Joint effects of habitat, zooplankton, host stage structure and diversity on amphibian chytrid

description: Why does the severity of parasite infection differ dramatically across
 habitats? This question remains challenging to answer because multiple
 correlated pathways drive disease. Here, we examined habitat–disease links
 through direct effects on parasites and indirect effects on parasite
 predators (zooplankton), host diversity and key life stages of hosts. We
 used a case study of amphibian hosts and the chytrid fungus,
 Batrachochytrium dendrobatidis, in a set of permanent and ephemeral alpine
 ponds. A field experiment showed that ultraviolet radiation (UVR) killed
 the free-living infectious stage of the parasite. Yet, permanent ponds
 with more UVR exposure had higher infection prevalence. Two
 habitat-related indirect effects worked together to counteract parasite
 losses from UVR: (i) UVR reduced the density of parasite predators and
 (ii) permanent sites fostered multi-season host larvae that fuelled
 parasite production. Host diversity was unlinked to hydroperiod or UVR but
 counteracted parasite gains; sites with higher diversity of host species
 had lower prevalence of infection. Thus, while habitat structure explained
 considerable variation in infection prevalence through two indirect
 pathways, it could not account for everything. This study demonstrates the
 importance of creating mechanistic, food web-based links between multiple
 habitat dimensions and disease.
description: Hite_MS_ChytridThese are the mean data used for analyses and figures in the main manuscript as well as the supplementary materialsHite et al. Chytrid_field_incubationThis file contains data used in the in-situ experiment to test the effects of incident UVR exposure on Bd zoospore survival.Chytrid_Field_Incubation.xlsHite_et_al_Dryad_uploadThis file contains all of the data used in the paper and electronic supplementary material (Figs. 1-6 and Table S1, Fig. S1).Partition_Variation_3D_v3_focal_hostThis file contains the Matlab code for the regression-based partition of variation used in the ESM.Pond_Data_3D_focal_hostsThese data are used in the Matlab file "Partition_Variation_3D_v3_focal_host.m"Partition_Variation_3DThe file contains the Matlab code for the regression-based partition of variance presented in the main text (Figure 6).Pond_Data_3DDate for the Matlab code to generate Figure 6.Pond_Data_3D_newtsData for the regression-based variation partition that substitutes overall host diversity for the frequency of the introduced newt.