cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.780hc
title: Data from: Plant–soil feedbacks promote negative frequency dependence in the coexistence of two aridland grasses

description: Understanding the mechanisms of species coexistence is key to predicting
 patterns of species diversity. Historically, the ecological paradigm has
 been that species coexist by partitioning resources: as a species
 increases in abundance, self-limitation kicks in, because species-specific
 resources decline. However, determining coexistence mechanisms has been a
 particular puzzle for sedentary organisms with high overlap in their
 resource requirements, such as plants. Recent evidence suggests that
 plant-associated microbes could generate the stabilizing self-limitation
 (negative frequency dependence) that is required for species coexistence.
 Here, we test the key assumption that plant–microbe feedbacks cause such
 self-limitation. We used competition experiments and modelling to evaluate
 how two common groups of soil microbes (rhizospheric microbes and
 biological soil crusts) influenced the self-limitation of two competing
 desert grass species. Negative feedbacks between the dominant plant
 competitor and its rhizospheric microbes magnified self-limitation,
 whereas beneficial interactions between both plant species and biological
 soil crusts partly counteracted this stabilizing effect. Plant–microbe
 interactions have received relatively little attention as drivers of
 vegetation dynamics in dry land ecosystems. Our results suggest that
 microbial mechanisms can contribute to patterns of plant coexistence in
 arid grasslands.
description: Aboveground biomass data
 for B. eriopodaAboveground biomass (g)
 for B. eriopoda in every experimental pot where individuals existed at the
 end of the experiment. See ReadMe file for variable
 definitions.BOER.abv.csvAboveground biomass data for B. gracilisAboveground biomass (g) for B. gracilis in every experimental pot where individuals existed at the end of the experiment. See ReadMe file for variable definitions.BOGR.abv.csv
DOI: 10.5061/dryad.r0mg6
title: Data from: Genetic accommodation in the wild: evolution of gene expression plasticity during character displacement

description: Ecological character displacement is considered crucial in promoting
 diversification, yet relatively little is known of its underlying
 mechanisms. We examined whether evolutionary shifts in gene expression
 plasticity (‘genetic accommodation’) mediate character displacement in
 spadefoot toads. Where Spea bombifrons and S. multiplicata occur
 separately in allopatry (the ancestral condition), each produces
 alternative, diet-induced, larval ecomorphs: omnivores, which eat
 detritus, and carnivores, which specialize on shrimp. By contrast, where
 these two species occur together in sympatry (the derived condition),
 selection to minimize competition for detritus has caused S. bombifrons to
 become nearly fixed for producing only carnivores, suggesting that
 character displacement might have arisen through an extreme form of
 genetic accommodation (‘genetic assimilation’) in which plasticity is
 lost. Here, we asked if we could infer a signature of this process in
 regulatory changes of specific genes. In particular, we investigated
 whether genes that are normally expressed more highly in one morph
 (‘biased’ genes) have evolved reduced plasticity in expression levels
 among S. bombifrons from sympatry compared to S. bombifrons from
 allopatry. We reared individuals from sympatry vs. allopatry on detritus
 vs. shrimp and measured the reaction norms of nine biased genes. Although
 different genes displayed different patterns of gene regulatory evolution,
 the combined gene expression profiles revealed that sympatric individuals
 had indeed lost the diet-induced gene expression plasticity present in
 allopatric individuals. Our data therefore provide one of the few examples
 from natural populations in which genetic accommodation/assimilation can
 be traced to regulatory changes of specific genes. Such genetic
 accommodation might mediate character displacement in many systems.
description: Levis et al.
 data
DOI: 10.5061/dryad.3ck64027
title: Data from: Genetic and phenotypic variation in juvenile development in relation to temperature and developmental pathway in a geometrid moth

description: Life histories show genetic population-level variation due to spatial
 variation in selection pressures. Phenotypic plasticity in life histories
 is also common, facilitating fine-tuning of the phenotype in relation to
 the prevailing selection regime. In multivoltine (≥ 2 generations / year)
 insects, individuals following alternative developmental pathways
 (diapause / direct development) experience different selection regimes. We
 studied the genetic and phenotypic components of juvenile development in
 Cabera exanthemata (Lepidoptera: Geometridae) in a factorial split-brood
 experiment. F2 offspring of individuals originating from populations in
 northern and central Finland were divided among manipulations defined by
 temperature (14ºC / 20ºC) and day length (24h / 15h). Short day length
 invariably induced diapause, whereas continuous light almost invariably
 induced direct development in both regions, although northern populations
 are strictly univoltine in the wild. Individuals from northern Finland had
 higher growth rates, shorter development times and higher pupal masses
 than individuals from central Finland across the conditions, indicating
 genetic differences between regions. Individuals that developed directly
 into adults tended to have higher growth rates, shorter development times
 and higher pupal masses than those entering diapause, indicating
 phenotypic plasticity. Temperature-induced plasticity was substantial;
 growth rate was much higher, development time much shorter and pupal mass
 higher at 20ºC than at 14ºC. The degree of plasticity in relation to
 developmental pathway was pronounced at 20ºC in growth rate and
 development time and at 14ºC in pupal mass, emphasizing
 multidimensionality of reaction norms. The observed genetic variation and
 developmental plasticity seem adaptive in relation to time-stress due to
 seasonality.
description: Kivelä et al.
 2012_JEB_datadata
 file
DOI: 10.5061/dryad.rd78f
title: Data from: Strong inbreeding depression in two Scandinavian populations of the self-incompatible perennial herb Arabidopsis lyrata

description: Inbreeding depression is a key factor influencing mating system evolution
 in plants, but current understanding of its relationship with selfing rate
 is limited by a sampling bias with few estimates for self-incompatible
 species. We quantified inbreeding depression (δ) over two growing seasons
 in two populations of the self-incompatible perennial herb Arabidopsis
 lyrata ssp. petraea in Scandinavia. Inbreeding depression was strong and
 of similar magnitude in both populations. Inbreeding depression for
 overall fitness across two seasons (the product of number of seeds,
 offspring viability, and offspring biomass) was 81% and 78% in the two
 populations. Chlorophyll deficiency accounted for 81% of seedling
 mortality in the selfing treatment, and was not observed among offspring
 resulting from outcrossing. The strong reduction in both early viability
 and late quantitative traits suggests that inbreeding depression is due to
 deleterious alleles of both large and small effect, and that both
 populations experience strong selection against the loss of
 self-incompatibility. A review of available estimates suggested that
 inbreeding depression tends to be stronger in self-incompatible than in
 self-compatible highly outcrossing species, implying that undersampling of
 self-incompatible taxa may bias estimates of the relationship between
 mating system and inbreeding depression.
description: Family
 meansMaternal family means of
 fitness components and total fitness, which are used to calculate
 treatment means and estimates of inbreeding depression presented in Table
 1 and Figs. 1 and 2. Variable names are explained in the
 file.
DOI: 10.5061/dryad.mb4g0
title: Data from: Is a larger refuge always better? Dispersal and dose in pesticide resistance evolution

description: The evolution of resistance against pesticides is an important problem of
 modern agriculture. The high-dose/refuge strategy, which divides the
 landscape into treated and non-treated (refuge) patches, has proven
 effective at delaying resistance evolution. However, theoretical
 understanding is still incomplete, especially for combinations of limited
 dispersal and partially recessive resistance. We reformulate a two-patch
 model based on the Comins model and derive a simple quadratic
 approximation to analyze the effects of limited dispersal, refuge size and
 dominance for high efficacy treatments on the rate of evolution. When a
 small but substantial number of heterozygotes can survive in the treated
 patch, a larger refuge always reduces the rate of resistance evolution.
 However, when dominance is small enough, the evolutionary dynamics in the
 refuge population, which is indirectly driven by migrants from the treated
 patch, mainly describes the resistance evolution in the landscape. In this
 case, for small refuges, increasing the refuge size will increase the rate
 of resistance evolution. Our analysis distils major driving forces from
 the model, and can provide a framework for understanding directional
 selection in source-sink environments.
description: R script to compute
 modelsmodel.R implements the
 simple Comins model (eq.1) and our approximation (eq.5). The code
 generates all plots in the main text and the supplemental
 information.model.R
DOI: 10.5061/dryad.g8c91
title: Data from: Time to extinction in deteriorating environments

description: Habitat degradation and destruction are the predominant drivers of
 population extinction, but there is little theory to guide the analysis of
 population viability in deteriorating environments. To address this gap,
 we investigated extinction times in time-varying, demographically
 stochastic versions of the logistic model for population dynamics. A
 property of these models is the “extinction delay,” a quantitative measure
 of the time lag in extinction created by species-specific extinction debt.
 For completeness, three models were constructed to represent the different
 demographic routes by which deterioration may affect population dynamics.
 Numerical analysis for two notional life histories indicated that the
 demographic response to environmental deterioration had a large effect on
 extinction delay, but a third analysis showed that the trajectory of the
 decline in carrying capacity ultimately characterized its magnitude. A
 concave decline in carrying capacity produced a large extinction delay
 while a small delay occurred with a convex decline. Furthermore, our
 results explore the non-monotonicity of extinction debt with respect to
 the speed of deterioration. A peak is present at low levels of
 deterioration, and the height of the peak and the asymptote of delay are
 affected by both life history parameterizations and the rate of change of
 the carrying capacity. The results suggest that population viability
 analyses must consider not only environmental deterioration, but also the
 effects of deterioration on the trajectory of the decline in carrying
 capacity.
description: Time to extinction in
 deteriorating environments dataThe data file contains
 the code for the three models described in the article Time to extinction
 in deteriorating environments. These models were solved using the
 adaptivetau package in R. Additionally, the file contains the data and
 code for the five figures in the publication.
DOI: 10.5061/dryad.5863d
title: Data from: Microhaplotypes provide increased power from short-read DNA sequences for relationship inference

description: The accelerating rate at which DNA sequence data is now generated by
 high-throughput sequencing instruments provides both opportunities and
 challenges for population genetic and ecological investigations of animals
 and plants. We show here how the common practice of calling genotypes from
 a single SNP per sequenced region ignores substantial additional
 information in the phased short-read sequences that are provided by
 high-throughput sequencing instruments. We target sequenced regions with
 multiple SNPs in kelp rockfish (Sebastes atrovirens) to determine
 “microhaplotypes” and then call these microhaplotypes as alleles at each
 locus. We then demonstrate how these multi-allelic marker data from 96
 such loci dramatically increase power for relationship inference. The
 microhaplotype approach decreases false positive rates by several orders
 of magnitude, relative to calling bi-allelic SNPs, for two challenging
 analytical procedures, full sibling and single parent-offspring pair
 identification. The advent of phased short-read DNA sequence data, in
 conjunction with emerging analytical tools for their analysis, promises to
 improve efficiency by reducing the number of loci necessary for a
 particular level of statistical confidence, thereby lowering the cost of
 data collection and reducing the degree of physical linkage amongst
 markers used for relationship estimation. Such advances will facilitate
 collaborative research and management for migratory and other widespread
 species.
description: Panel 1: vcf for 96
 microhaplotypesVariant call format file
 for 96 of the 192 microhaplotypes described in Baetscher et
 al.satro144_panel1_flashed_noMNP_noComplex.vcfPanel 2: vcf for 96 microhaplotypesVariant call format file for 96 of the 192 microhaplotypes described in Baetscher et al.satro96_panel2_run2_flashed_noMNP_noComplex.vcfPanel 1: BAM filesBAM files for 144 kelp rockfish with 96 microhaplotypesPanel1_bam_files.zipPanel 2: BAM filesBAM files for 96 kelp rockfish with 96 microhaplotypesPanel2_bam_files.zipDescription of statistical analysesR Notebook describing all statistical analyses in Baetscher et al.R_Notebook_Statistical_BaetscherEtAl.zipConsensus sequencesFASTA file with consensus sequences for all 192 targeted amplicons192_loci_kelpRF_consensus.fastaPrimer sequencesPrimer sequences for 192 targeted regions.Primers_kelpRF_192_loci.xlsxGenotype fileGenotypes and associated read depths for 144 kelp rockfish at 165 microhaplotypesGenotypes_144kelpRF.csv
DOI: 10.5061/dryad.vj12j
title: Data from: Cannibalism and intraguild predation community dynamics: coexistence, competitive exclusion and the loss of alternative stable states

description: Predators often exert strong top-down regulation of prey, but in many
 systems, juvenile predators must compete with their future prey for a
 shared resource. In such life-history intraguild predation (LHIGP)
 systems, prey can therefore also regulate the recruitment and thus
 population dynamics of their predator via competition. Theory predicts
 that such stage-structured systems exhibit a wide range of dynamics
 including alternative stable states. Here we show that cannibalism is an
 exceedingly common interaction within natural LHIGP systems that
 determines what coexistence states are possible. Using a modeling approach
 that simulates a range of ontogenetic niche shift scenarios along a
 productivity gradient, we demonstrate that only if the predator is
 competitively dominant can cannibalism promote coexistence by allowing
 prey to persist. If the prey is competitively dominant, cannibalism
 instead results in competitive exclusion of the predator and the loss of
 potential alternative stable states. Further, predator exclusion occurs at
 low cannibalistic preference relative to empirical estimates and is
 consistent across LHIGP systems in which the predator undergoes a complete
 diet shift or diet broadening over ontogeny. Given that prey is frequently
 competitively dominant in natural systems, our results demonstrate that
 even weak cannibalism can inhibit predator persistence, prompting
 exploration of mechanisms that reconcile theory with the common occurrence
 of such interactions in nature.
description: Model_implementationMATCONT model implementationCannibalistic_preference_estimatesCannibalistic preference estimates from the literature used in generating figure 2.
DOI: 10.5061/dryad.d4k51
title: Data from: Plant traits and plant biogeography control the biotic resistance provided by generalist herbivores

description: Globalization and climate change trigger species invasions and range
 shifts, which reshuffle communities at an exceptional rate and expose
 plant migrants to unfamiliar herbivores. Dominant hypotheses to predict
 plant success are based on evolutionary novelty: either herbivores are
 maladapted to consume novel plants (enemy release hypothesis), or novel
 plants are maladapted to deter herbivores (biotic resistance hypothesis).
 Since novelty can work both ways, it fails to consistently predict when
 herbivores will consume novel over non-novel plants. Surprisingly, the
 value of using plant traits to predict herbivore consumption of novel
 plants remains largely unexplored. We hypothesized that (i) plant traits
 explain generalist herbivore consumption rates of novel and non-novel
 plants, and (ii) any effect of novelty will be grounded in consistent
 trait differences between native and novel plants. Lastly, we expected to
 find (iii) differences in plant traits and plant consumption rates across
 latitude. To test these hypotheses, we measured the consumption rate of
 plant species for a tropical and a temperate generalist herbivore in
 controlled feeding trials by offering them a large variety of 40 plant
 species from different geographical origins. Therefore, whether a plant
 was novel depended on the herbivore used, allowing us to disentangle plant
 identity from plant novelty. We also measured plant chemical traits and
 determined whether traits, geographical origin or novelty best explained
 herbivore consumption rates. Both generalist herbivores consumed more of
 plants with a high nitrogen-to-phenolic compounds ratio, irrespective of
 the plant's novelty to the herbivore. A pattern of increasing
 plant's nitrogen-to-phenolics ratio with latitude could explain why
 both the tropical and temperate herbivore consumed more of plants from
 temperate regions. Plant novelty and its geographical origin no longer
 explained consumption rates once differences in nitrogen-to-phenolic
 compounds ratio were taken into account. We show that differences in plant
 traits along a latitudinal cline determine herbivore consumption rates,
 irrespective of whether plants are novel or familiar. Therefore, we
 propose that integrating evolutionary novelty theory with plant traits and
 biogeography will increase our understanding of the consequences of plant
 species migration beyond biogeographical barriers.
description: Phylogenetic tree of
 aquatic plant speciesThe phylogenetic tree
 used for the phylogenetic data analyses: to calculate the phylogenetic
 signal (Blomberg's K) and to perform PGLS (phylogenetic generalised
 least squares). The method of how this tree was constructed is described
 in the manuscript.FE-2016-00091-Data-phylogenetic-treePlant species, traits and herbivore consumption ratesPlant species, traits and herbivore consumption rates.FE-2016-00091-Data-plant-traits-and-consumption.xlsx
DOI: 10.5061/dryad.4s5r7
title: Data from: Mating system of Caiman yacare (Reptilia Alligatoridae) described from microsatellite genotypes

description: The yacare caiman (Caiman yacare) is a reptile from South America and 1 of
 the 2 crocodilian species present in Argentina. The degradation of their
 natural habitat and strong hunting pressure led to a sharp numerical
 decline of wild populations. Nowadays, C. yacare is included in Appendix
 II of CITES, and ranching practices in some areas in Argentina are helping
 hatching success. In this context, it is important to better understand
 the population structure and mating system of the species. To do this, we
 amplified 10 microsatellite markers (SSRs) in 148 individuals of 13 C.
 yacare nests. All of the markers were polymorphic with 2–12 alleles per
 locus, with allelic sizes ranging between 154 and 400 bp and medium levels
 of polymorphism (H o = 0.152–0.551 and H e = 0.221–0.621). We were able to
 determine the maternal genotype in 9 out of 13 nests. In 6 of them we
 found more than 1 paternal genotype, with a maximum of 3 fathers for a
 single nest. This study is the first to provide evidence of multiple
 paternity behavior. These findings will be useful to improve management
 and conservation strategies for the species.
description: Data
 AvailabilitySampling locations and
 microsatellite genotypes: Dryad
DOI: 10.5061/dryad.k94h8
title: Data from: The faces of Bacidia schweinitzii: molecular and morphological data reveal three new species including a widespread sorediate morph

description: Bacidia schweinitzii is a common crustose lichen that is widespread in
 eastern North America. It is comprised of three distinct morphotypes
 differing in apothecial pigmentation. Here we show that molecular data
 from the mtSSU region affirms the distinctiveness of these morphotypes,
 prompting the recognition of three species: B. schweinitzii s.str., B.
 ekmaniana sp. nov. and B. purpurans sp. nov. We also show that a common
 sorediate crustose lichen, sympatric with B. schweinitzii, represents a
 monophyletic lineage whose relationship with B. schweinitzii s.str. could
 not be resolved with certainty using analyses of ITS and mtSSU sequence
 data. We recognize this sorediate lineage as a distinct species, B.
 sorediata sp. nov. All four taxa are described, illustrated and mapped.
description: data_packetThis is a compressed zip folder that contains the input files and alignments for molecular phylogenetic analyses performed for the study. These include:1) alignment of nrITS (NEXUS); 2) alignment of nrITS used for distance metrics (NEXUS); 3, alignments of mtSSU used in maximum likelihood (ML; PHYLIP) and Bayesian inference (BI; NEXUS); and 4) alignments of mtSSU+nrITS (standard in NEXUSA format with excluded regions) used in partitioned ML (PHYLIP, together with partition input file for RAxML) and partitioned BI (NEXUS).
DOI: 10.5061/dryad.2p75f
title: Data from: Evolution of defense against depletion of local food resources in a mechanistic foraging model

description: Abstract Models of resource defense are usually based on the assumption
 that individuals fight over the possession of discrete food items. In many
 territorial species however conflicts occur over access to an area in
 space that contains resources rather than the resources themselves. We
 investigate under which conditions defense against depletion of local
 resources instead of single resource items can evolve from a
 non-aggressive ancestral population using a spatially explicit mechanistic
 model with resource dynamics and individual movement. We find that in
 general details of the model assumptions have a great influence on the
 costs and benefits of different behavior in the model. For patchy
 resources defense evolves if fighting costs are very high or if
 individuals can not avoid conflicts. If resources are distributed
 uniformly defense appears only if individuals can make their behavior
 dependent on distance to their opponent. Introducing role asymmetries
 during conflicts in general increases the frequency of contests but
 reduces the probability that they escalate. If losers of a fight control
 how far they run aggressiveness disappears or is greatly reduced for
 patchy resources but increases significantly for uniform resource
 distribution. Our results show how defense of space and territoriality
 could evolve even if resources are neither discrete nor clumped. The fact
 that seemingly minor differences in how individuals make decisions during
 encounters lead to huge differences in model outcome highlights the need
 for more mechanistic models of animal conflicts.
description: simulation source
 filesComplete C++ sources for
 the simulation program described in the article.src.zip