cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t3f1tg0
title: Data from: Contributions toward understanding the biodiversity of Passiflora in North America: updates and a new combination from the Baja California Peninsula, Mexico and vicinity

description: The Baja California Peninsula and surrounding landmasses harbor an
 abundant flora in an otherwise harsh and arid environment. Of the many
 plant groups native to this peninsular and insular region, passionflowers
 (Passiflora, Passifloraceae) are represented by a handful of taxa that all
 belong to a single lineage within the genus (section Dysosmia). Despite
 centuries of exploration and floristic research in the area, basic
 questions remain regarding this group—particularly the taxonomic status
 among the Passiflora arida complex. Using an extensive sampling of
 herbarium specimens and iNaturalist observations, the claims of endemism,
 habitat characteristics, and taxon boundaries were investigated.
 Peninsular endemism was confirmed for only one of the native Passiflora
 taxa (P. fruticosa), with an additional taxon (P. palmeri) considered
 near-endemic. Soil and climatic data revealed significant distinctions
 between the habitats of many of the native taxa as well as within the P.
 arida complex, corresponding mostly to precipitation and temperature
 variables. Geometric morphometric analyses showed little success in
 separating taxa based on leaf shape, indicating this line of evidence may
 not be a good indicator of taxon identity in this group of plants. Based
 on ecological differences and discrete macro- and micromorphological
 features, a varietal name is here synonymized and a new combination is
 proposed: Passiflora pentaschista.
description: Environmental
 DataRaw climatic (WorldClim)
 and soil (World Harmonized Soil Index) data used in the
 study.JSE-2017-12-115_EnvData.xlsMorphometric Analysis CodeR code for the leaf geometric morphometric analyses used in the study.JSE-2017-12-115_MorphoCode.RMorphometrics DataUnadjusted leaf geometric morphometrics data used in the study.JSE-2017-12-115_MorphoData.xls
DOI: 10.5061/dryad.rd1df0c
title: Data from: Two additional species of Gymnopus (Eugarics, Basidiomycotina)

description: For more than a decade, a combination of molecular phylogenetic analyses
 and morphological characterization have led to a renovation of the
 Omphalotaceae, especially of Gymnopus sensu lato. Numerous new genera have
 been proposed, but Gymnopus sensu stricto has also seen an accretion of
 species and species complexes. In this manuscript, two species are added
 to Gymnopus sensu stricto within Section Androsacei.
description: Gymnopus neobrevipes and
 related taxa ITS sequencesAligned Fungal ITS
 sequences for two new taxa within Gymnopus and PhyML
 trees
DOI: 10.5061/dryad.0506g
title: Data from: The genetic architecture of hybrid incompatibilities and their effect on barriers to introgression in secondary contact

description: Genetic incompatibilities are an important component of reproductive
 isolation. Although theoretical studies have addressed their evolution,
 little is known about their maintenance when challenged by potentially
 high migration rates in secondary contact. Whereas theory predicts that
 recombination can erode barriers, many empirical systems have been found
 to retain species-specific differences despite substantial gene flow. By
 simulating whole genomes in individuals of hybridizing species, we find
 that the genetic architecture of two contrasting models of epistatic
 hybrid incompatibilities and the context of hybridization can
 substantially affect species integrity and genomic heterogeneity. In line
 with theory, our results show that inter-genomic incompatibilities break
 down rapidly by recombination but can maintain genome-wide differentiation
 under very limited conditions. By contrast, intra-genomic interactions
 that arise from genetic pathways can maintain species-specific differences
 even with high migration rates and gene flow, while introgression at large
 parts of the genome can simultaneously remain extensive, consistent with
 empirical observations. We discuss the importance of intra-genomic
 interactions in speciation and consider how this form of epistatic fitness
 variation is implicated and supported by other theoretical and empirical
 studies. We further address the relevance of replicates and knowledge of
 context when investigating the genomics of speciation.
description: Source code package for
 simulation software dfuseContains C source code
 files: main_dfuse.c, func_dfuse.c, head_dfuse.h, COPYING, Makefile;
 documentation file: notes.pdf; folder with example input files:
 inputfilesdfuse.tgzExample commands to run simulations for each Figure in the articleColumn 1, Figure number; column 2, Figure subpart; column 3, architecture of selection; column 4, example command to run simulation to generate data presented in that FigureexampleCommands.csvAll input files used for simulations presented in the articleFiles to specify deme settings: demefile; epistatic selection: epifile; single-locus selection: selfile; environmental settings: envifileinputfilesPaper.tgzScripts to recreate simulation results shown in Figures 2-4 in the articlePerl and R scripts to run simulation software and to create Figures with resultsscripts.tgz
DOI: 10.5061/dryad.s16s3
title: Data from: Noise affects the shape of female preference functions for acoustic signals

description: The shape of female mate preference functions influences the speed and
 direction of sexual signal evolution. However, the expression of female
 preferences is modulated by interactions between environmental conditions
 and the female's sensory processing system. Noise is an especially
 relevant environmental condition because it interferes directly with the
 neural processing of signals. Although noise is therefore likely a
 significant force in the evolution of communication systems, little is
 known about its effects on preference function shape. In the grasshopper
 Chorthippus biguttulus, female preferences for male calling song
 characteristics are likely to be affected by noise because its auditory
 system is sensitive to fine temporal details of songs. We measured female
 preference functions for variation in male song characteristics in several
 levels of masking noise and found strong effects of noise on preference
 function shape. The overall responsiveness to signals in noise generally
 decreased. Preference strength increased for some signal characteristics
 and decreased for others, largely corresponding to expectations based on
 neurophysiological studies of acoustic signal processing. These results
 suggest that different signal characteristics will be favored under
 different noise conditions, and thus that signal evolution may proceed
 differently depending on the extent and temporal patterning of
 environmental noise.
description: Experiment_1_DataData from Experiment 1 - Preference functions measured for varied onset accentuation. Corresponds to figure 2Experiment1_Fig2_OnsetAccentuation.txtExperiment_2_DataRaw data from Experiment 2 - Preference functions measured for varied pause durations. Corresponds to Figure 3 in text.Experiment2_Fig3_PauseDuration.txtExperiment_3_DataData from Experiment 3 - preference functions measured for varied offset amplitudes. Corresponds to Figure 4 in text.Experiment3_Fig4_OffsetAmplitude.txtExperiment_4_DataData from Experiment 4 - preference functions measured for varied gap durations. Corresponds to Figure 5 in text.Experiment4_Fig5_GapDuration.txt
DOI: 10.5061/dryad.76f45
title: Data from: The extent and genetic basis of phenotypic divergence in life history traits in Mimulus guttatus

description: Differential natural selection acting on populations in contrasting
 environments often results in adaptive divergence in multivariate
 phenotypes. Multivariate trait divergence across populations could be
 caused by selection on pleiotropic alleles or through many independent
 loci with trait-specific effects. Here, we assess patterns of association
 between a suite of traits contributing to life history divergence in the
 common monkeyflower, Mimulus guttatus, and examine the genetic
 architecture underlying these correlations. A common garden survey of 74
 populations representing annual and perennial strategies from across the
 native range revealed strong correlations between vegetative and
 reproductive traits. To determine whether these multitrait patterns arise
 from pleiotropic or independent loci, we mapped QTLs using an approach
 combining high-throughput sequencing with bulk segregant analysis on a
 cross between populations with divergent life histories. We find extensive
 pleiotropy for QTLs related to flowering time and stolon production, a key
 feature of the perennial strategy. Candidate genes related to axillary
 meristem development co-localize with the QTLs in a manner consistent with
 either pleiotropic or independent QTL effects. Further, these results are
 analogous to previous work showing pleiotropy-mediated genetic
 correlations within a single population of M. guttatus experiencing
 heterogeneous selection. Our findings of strong multivariate trait
 associations and pleiotropic QTLs suggest that patterns of genetic
 variation may determine the trajectory of adaptive divergence.
description: Phenotypic
 dataMeasurements of
 phenotypic data for wild populations grown in a
 greenhousetraits_pops.xlsxPhenotypic data for F2sFlowering time and stolon number for F2 mapping populationDUN_IM_F2.xlsxGenotypes for F2sGenotype for single marker analysis for 384 F2 individualsF2_markers.xlsx
DOI: 10.5061/dryad.1q34p
title: Data from: Spatial patterns of AFLP diversity in Bulbophyllum occultum (Orchidaceae) indicate long-term refugial isolation in Madagascar and long-distance colonization effects in La Réunion

description: Bulbophyllum occultum, an epiphytic orchid mainly distributed in the
 rainforests of (north)eastern Madagascar and La Réunion, represents an
 interesting model case for testing the effects of anthropogenic vs
 historical (e.g., climate induced) habitat isolation and long-distance
 colonization on the genetic structure of plant species with disjunct
 distributions in the Madagascan region. To this aim, we surveyed amplified
 fragment length polymorphisms (AFLPs) across 13 populations in Madagascar
 and nine in La Réunion (206 individuals in total). We found overall high
 levels of population subdivision (ΦPT=0.387) and low within-population
 diversity (HE, range: 0.026–0.124), indicating non-equilibrium conditions
 in a mainly selfing species. There was no impact of recent deforestation
 (Madagascar) or habitat disturbance (La Réunion) detectable on AFLP
 diversity. K-means clustering and BARRIER analyses identified multiple
 gene pools and several genetic breaks, both within and among islands.
 Inter-island levels of population genetic diversity and subdivision were
 similar, whereby inter-individual divergence in flower colour explained a
 significant part of gene pool divergence in La Réunion. Our results
 suggest that (i) B. occultum persisted across multiple isolated
 (‘refugial’) regions along the eastern rainforest corridor of Madagascar
 over recent climatic cycles and (ii) populations in La Réunion arose from
 either single or few independent introductions from Madagascar. High
 selfing rates and sufficient time for genetic drift likely promoted
 unexpectedly high population genetic and phenotypic (flower colour)
 differentiation in La Réunion. Overall, this study highlights a strong
 imprint of history on the genetic structure of a low-gene-dispersing
 epiphytic orchid from the Madagascan region.
description: Bulbophyllum occultum,
 AFLP-matrixB_occultum_AFLP.xls
DOI: 10.5061/dryad.1339
title: Data from: Introgression from modern hybrid varieties into landrace populations of maize (Zea mays ssp. mays L.) in central Italy

description: Landraces are domesticated local plant varieties that did not experienced
 a deliberate and intensive selection during a formal breeding programme.
 In Europe, maize landraces are still cultivated, particularly in marginal
 areas where traditional farming is often practised. Here, we have studied
 the evolution of flint maize landraces from central Italy over 50 years of
 on-farm cultivation, when dent hybrid varieties were introduced and their
 use was widespread. We have compared an 'old' collection,
 obtained during the 1950s, before the introduction of hybrids, and a
 recent collection of maize landraces. For comparison, a sample of maize
 landraces from north Italy, and of improved germplasm, including hybrids
 and inbred lines were also used. A total of 296 genotypes were analysed
 using 21 microsatellites. Our results show that the maize landraces
 collected in the last 5-10 years have evolved directly from the flint
 landrace gene pool cultivated in central Italy before the introduction of
 modern hybrids. The population structure, diversity and linkage
 disequilibrium analyses indicate a significant amount of introgression
 from hybrid varieties into the recent landrace populations. No evidence of
 genetic erosion of the maize landraces was seen, suggesting that in-situ
 conservation of landraces is an efficient strategy for preserving genetic
 diversity. Finally, the level of introgression detected was very variable
 among recent landraces, with most of them showing a low level of
 introgression; this suggests that co-existence between different types of
 agriculture is possible, with the adoption of correct practices that are
 aimed at avoiding introgression from undesired genetic sources.
description: SSR data for maize
 landraces from Central ItalyDatafile_Bitocchietal2009.xls
DOI: 10.5061/dryad.jq16r
title: Data from: Preference evaluation of ground beef by untrained subjects with three levels of finely textured beef

description: After receiving bad publicity in 2012 and being removed from many ground
 beef products, finely textured beef (referred to as 'pink slime'
 by some) is making a comeback. Some of its proponents argue that consumers
 prefer ground beef containing finely textured beef, but no objective
 scientific party has tested this claim—that is the purpose of the present
 study. Over 200 untrained subjects participated in a sensory analysis in
 which they tasted one ground beef sample with no finely textured beef,
 another with 15% finely textured beef (by weight), and another with more
 than 15%. Beef with 15% finely textured beef has an improved juiciness (p
 &lt; 0.01) and tenderness (p &lt; 0.01) quality. However, subjects
 rate the flavor-liking and overall likeability the same regardless of the
 finely textured beef content. Moreover, when the three beef types are
 consumed as part of a slider (small hamburger), subjects are indifferent
 to the level of finely textured beef.
description: Preference
 dataContains all the
 original data and transformed data used in a preference experiment for
 ground beef with and without finely textured beef.Dryad Data
 Store.xlsx
DOI: 10.5061/dryad.d5s4g
title: Data from: Relationships between forest cover and fish diversity in the Amazon River floodplain

description: 1.Habitat degradation leads to biodiversity loss and concomitant changes
 in ecosystem processes. Tropical river floodplains are highly threatened
 by land cover changes and support high biodiversity and important
 ecosystems services, but the extent to which changes in floodplain land
 cover affect fish biodiversity remains unknown. 2.We combined fish and
 environmental data collected in situ and satellite-mapped landscape
 features to evaluate how fish species with different ecological strategies
 and assemblage structures respond to deforestation in floodplains of the
 Amazon River. We surveyed 462 floodplain habitats distributed along a
 gradient of land cover, from largely forested to severely deforested.
 Rather than analyze only taxonomic metrics, we employed an integrative
 approach that simultaneously considers different aspects of fish
 biodiversity (i.e., beta diversity and taxonomic and functional assemblage
 structure) to facilitate mechanistic interpretations of the influence of
 land cover. 3.Spatial patterns of fish biodiversity in tropical floodplain
 rivers were strongly associated with forest cover as well as local
 environmental conditions linked to landscape gradients. Several species
 and functional groups defined by life history, feeding,
 swimming/microhabitat-use strategies were positively associated with
 forest cover. Other species, including some that would usually be
 considered habitat generalists and species directly dependent on
 autochthonous resources (e.g., planktivores), were most common in areas
 dominated by herbaceous vegetation or open-water habitats associated with
 the opposite extreme of the forest cover gradient. Beta-diversity and the
 degree of uniqueness of species combinations within habitats were also
 positively associated with forest cover. 4.Synthesis and applications. Our
 results, demonstrating that spatial patterns of fish biodiversity are
 associated with forest cover, indicate that deforestation of floodplains
 of the Amazon River results in spatial homogenization of fish assemblages
 and reduced functional diversity at both local and regional scales.
 Floodplains worldwide have undergone major land cover changes, with forest
 loss projected to increase during the next decades. Conserving fish
 diversity in these ecosystems requires protecting mosaics of both aquatic
 habitats and floodplain vegetation, with sufficient forest cover being
 critically important.
description: Arantes et al 2017
 dataExcel file containing
 450 × 60 site-by-species matrix and geographic coordinates, land cover and
 environmental data for the same sites (see Arantes et al. JAE for
 details).
DOI: 10.18739/a2vh5cm13
title: Wetland greenhouse gas response, biomass, and plant height to experimental warming, flooding, and herbivory, Yukon-Kuskokwim Delta (Western Alaska, USA) (2024)

description: This dataset was created to understand greenhouse gas responses (carbon dioxide and methane), plant community biomass, and three dominant plant species height (Carex rariflora, Carex lyngbyei, and Salix fuscescens) to warming, flooding, and herbivory in the Yukon-Kuskokwim (Y-K) Delta (western Alaska, USA). We conducted a two-year field experiment in which we passively increased temperatures, simulated periodic tidal flooding at two intensity levels (low and high), and applied an herbivory treatment (grazing, fecal addition, and trampling) during the 2023 and 2024 summer growing season; however, only the 2024 data are presented. Our treatments reflect changes expected in the Y-K Delta in the next 10-20 years. We conducted the experiment in two wetlands (lowland and upland wetland) with different elevations and flooding histories: a wet sedge-shrub meadow and a transitional wet community between the meadow and tundra. Greenhouse gas fluxes were taken once a week in the summer using static chambers for a total of 9 measurements. We characterized aboveground plant-community structure using the point intercept frequency methodology (PIM). We clumped vascular plant species into five broad plant functional groups: graminoids, deciduous and evergreen shrubs, forbs, and standing-dead graminoids. When measuring plant height, we chose the same five intercepts for each species on the PIM gridded frame and selected the closest individual.
DOI: 10.5061/dryad.483hr
title: Data from: Preadult life history variation determines adult transcriptome expression

description: Preadult determinants of adult fitness and behavior have been documented
 in a variety of organisms with complex life cycles, but little is known
 about expression patterns of genes underlying these adult traits. We
 explored the effects of differences in egg to adult development time on
 adult transcriptome and cuticular hydrocarbon variation in order to
 understand the nature of the genetic correlation between preadult
 development time and premating isolation between populations of Drosophila
 mojavensis reared in different host cactus environments. Transcriptome
 variation was analyzed separately in flies reared on each host and
 revealed that hundreds of genes in adults were differentially expressed
 (FDR P &lt; 0.05) due to development time differences. For flies
 reared on pitaya agria cactus, longer preadult development times caused
 increased expression of genes in adults enriched for ribosome production,
 protein metabolism, chromatin remodeling, and regulation of alternate
 splicing and transcription. Baja California flies reared on organ pipe
 cactus showed fewer differentially expressed genes in adults due to longer
 preadult development time, but these were enriched for ATP synthesis and
 the TCA cycle. Mainland flies reared on organ pipe cactus with shorter
 development times showed increased transcription of genes enriched for
 mitochondria and energy production, protein synthesis, and glucose
 metabolism: adults with longer development times had increased expression
 of genes enriched for adult life span, cuticle proteins and ion binding,
 although most differentially expressed genes were unannotated. Differences
 due to population, sex, mating status, and their interactions were also
 assessed. Adult cuticular hydrocarbon profiles also showed shifts due to
 egg to adult development time, and were influenced by population and
 mating status. These results help to explain why preadult life history
 variation determines subsequent expression of the adult transcriptome
 along with traits involved with reproductive isolation and revealed
 previously undocumented connections between genetic and environmental
 influences over the entire life cycle in this desert insect.
description: Etges_etal_2015_MEC_CHCdataCuticular hydrocarbon amounts for male and female Drosophila mojavensis reared on fermenting agria (Stenocereus gummosus) or organ pipe (S. thurberi) cactus tissues. Samples are based on mature adults grouped by day of egg to adult development time. Two populations were studied, LB, from Las Bocas, Sonora, and PP, from Punta Prieta, Baja California. Hydrocarbon types and chainlengths are described in Etges and Jackson (2001).