cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mp5rn5b
title: Habitat selection in transformed landscapes and the role of forest remnants and shade coffee in the conservation of resident birds

description: 1. Biodiversity conservation in transformed landscapes is becoming
 increasingly important. However, most assessments of the value of modified
 habitats rely heavily on species presence and/or abundance, masking
 ecological processes such as habitat selection and phenomena like
 ecological traps, which may render species persistence uncertain. High
 species richness has been documented in tropical agroforestry systems but
 comparisons with native habitat remnants generally lack detailed
 information on species demography and habitat use. 2. We generated a
 multi-species, multi-measure framework to evaluate the role of habitat
 selection in the adaptation of species to transformed landscapes, and
 demonstrate that its use could affect how we value the contribution
 different land uses make to biodiversity conservation. 3. We analyzed
 seven years of capture-mark-recapture and observation data for twelve
 species of resident birds present in native forest remnants and shade
 coffee plantations in a mega-diverse region. We assessed whether species
 behaved adaptively by evaluating the correlation between measures of
 habitat preference (occurrence, abundance, fidelity, inter-seasonal
 variance and age) and performance (body condition, muscle, primary molt,
 breeding and juveniles) in forest and coffee, and generated hypotheses
 about their role in species persistence. 4. We documented adaptive habitat
 selection for seven species, non-ideal selection for four, and maladaptive
 selection for one. While many species showed equal-preference and/or equal
 performance in many traits, in general we found more evidence for birds
 preferring and/or performing better in forest than coffee, although
 relationships between our indicators and population adaptation need to be
 studied further before our proposed framework can be applied to more
 species and landscapes. 5. While shade coffee can act as a
 biodiversity-friendly matrix providing complementary or supplementary
 habitat to a wide range of resident bird species, protecting remnants of
 native vegetation is still of paramount importance for biodiversity
 conservation in agricultural landscapes.
description: SanchezClavijo_etal2019_observation_historiesData for occupancy models (code in section 1.1.1 of supporting information part 2)SanchezClavijo_etal2019_capture_historiesData for population models (code in section 1.1.2 to 1.1.4 of supporting information part 2)SanchezClavijo_etal2019_individual_characteristicsData for generalized lineal models (code in section 1.1.5 to 1.2.5 of supporting information part 2)SanchezClavijo_etal2019_performance_metanalysisData for meta-analysis (code in section 2.2 of supporting information part 2)
DOI: 10.5061/dryad.55b2b15
title: Data from: Transcriptome profiling of maternal stress-induced wing dimorphism in pea aphids

description: Wing dimorphism, i.e., wingless and winged forms, can be induced by
 maternal stress signals and is an adaptive response of aphids to
 environmental changes. Here, we investigated the ecological and molecular
 effects of three kinds of stress, namely, crowding, predation, and aphid
 alarm pheromone, on wing dimorphism. These three stressors induced high
 proportion of up to 60% of winged morphs in offspring. Transcriptome
 analysis of stress-treated female aphids revealed different changes in
 maternal gene expression as induced by the three stressors. Crowding
 elicited widespread changes in the expression of genes involved in
 nutrient accumulation and energy mobilization. Distinct from crowding,
 predation caused dramatic expression changes in cuticle protein (CP)
 genes. Twenty-three CP genes that belong to CP RR2 subfamily and are
 highly expressed in legs and embryos were greatly repressed by the
 presence of ladybird. By contrast, application of alarm pheromone,
 E--farnesene, caused slight changes in gene expression. The three factors
 shared a responsive gene, cuticle protein 43. This study reveals the
 adaptive response of aphids to environmental stresses and provides a rich
 resource on genome-wide expression genes for exploring molecular
 mechanisms of ecological adaptation in aphids.
description: Supplementary
 Table
DOI: 10.34740/kaggle/dsv/14642560
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.p8350q3
title: The soil microbial community alters patterns of selection on flowering time and fitness‐related traits in Ipomoea purpurea

description: Premise of the study Plant flowering time plays an important role in plant
 fitness and thus evolutionary processes. Soil microbial communities are
 diverse and have a large impact, both positive and negative, on the host
 plant. However, owing to few available studies, how the soil microbial
 community may influence the evolutionary response of plant populations is
 not well understood. Here we sought to uncover if below-ground microbial
 communities act as an agent of selection on flowering and growth traits in
 the common morning glory, Ipomoea purpurea. Methods We performed
 a controlled greenhouse experiment in which genetic lines of I.
 purpurea were planted into either sterilized soils, or soils that
 were sterilized and re-inoculated with the microbial community from
 original field soil. This allowed us to directly test the influence of
 alterations to the microbial community on plant growth, flowering, and
 fitness, as well as assess patterns of selection in both soil microbial
 environments. Results We found that a more complex soil microbial
 community resulted in larger plants that produced more flowers. Selection
 strongly favored earlier flowering when plants were grown in the complex
 microbial environment than compared to sterilized soil. Additionally, we
 uncovered a pattern of negative correlational selection on growth rate and
 flowering time, indicating that selection favored different combinations
 of growth and flowering traits in the simplified versus complex soil
 community. Conclusions Together these results suggest the soil microbial
 community is a selective agent on flowering time and ultimately that soil
 microbial community influences important plant evolutionary processes.
description: CSV file formated ready to import into R for analysis. See readme
 for data details.
description: Plant growth, flowering, and fitness traits measured from
 <em>Ipomoea purpurea</em>, the common morning glory, grown in
 the greenhouse with experimental treatments altering the soil microbial
 community. Data has been cleaned and processed to reflect the published
 study.
DOI: 10.5061/dryad.596sn62
title: Data from: Duplication and diversification of trehalase confers evolutionary advantages on lepidopteran insects

description: Gene duplication provides a major source of new genes for evolutionary
 novelty and ecological adaptation. However, the maintenance of duplicated
 genes and their relevance to adaptive evolution has long been debated.
 Insect trehalase (Treh) plays key roles in energy metabolism, growth, and
 stress recovery. Here, we show that the duplication of Treh in Lepidoptera
 (butterflies and moths) is linked with their adaptation to various
 environmental stresses. Generally, two Treh genes are present in insects:
 Treh1 and Treh2. We report three distinct forms of Treh in lepidopteran
 insects, where Treh1 was duplicated into two gene clusters (Treh1a and
 Treh1b). These gene clusters differ in gene expression patterns, enzymatic
 properties, and subcellular localizations, suggesting that the enzymes
 probably underwent sub and/or neo-functionalization in the lepidopteran
 insects. Interestingly, selective pressure analysis provided significant
 evidence of positive selection on duplicate Treh1b gene in lepidopteran
 insect lineages. Most positively selected sites were located in the
 alpha-helical region, and several sites were close to the trehalose
 binding and catalytic sites. Subcellular adaptation of duplicate Treh1b
 driven by positive selection appears to have occurred as a result of
 selected changes in specific sequences, allowing for rapid reprogramming
 of duplicated Treh during evolution. Our results suggest that gene
 duplication of Treh and subsequent functional diversification could
 increase the survival rate of lepidopteran insects through various
 regulations of intracellular trehalose levels, facilitating their
 adaptation to diverse habitats. This study provides evidence regarding the
 mechanism by which gene family expansion can contribute to species
 adaptation through gene duplication and subsequent functional
 diversification.
description: Duplication and
 diversification of trehalase confers evolutionary advantages on
 lepidopteran insectsThe data file provides
 the raw Ct values for the qRT-PCR assay.Raw qPCR
 data.xlsx
DOI: 10.5061/dryad.7m5s110
title: Data from: Dive behaviour and foraging effort of female Cape fur seals Arctocephalus pusillus pusillus

description: While marine top predators can play a critical role in ecosystem structure
 and dynamics through their effects on prey populations, how they function
 is often not well understood. In southern Africa, the Cape fur seal
 (Arctocephalus pusillus pusillus) population constitutes the largest
 marine top predator biomass but little is known of its foraging ecology
 other than its diet and some preliminary dive records. Dive information
 was obtained from 32 adult females instrumented with dive recorders at the
 Kleinsee colony (29º34.17 S, 16 º59.80 E) in South Africa during
 2006–2008. Most dives were in the depth range of epipelagic prey species
 (&lt; 50 m deep) and at night, reflecting the reliance of Cape fur
 seals on small vertically migrating schooling prey. However, most females
 also performed benthic dives, which was prevalent in some individuals.
 Benthic diving was significantly associated with the frequency with which
 females exceeded their aerobic dive limit. The greater putative costs of
 benthic diving highlights the potential detrimental effects on Cape fur
 seals of environmental changes that may reduce the availability of
 epipelagic prey in the Benguela region of southern Africa.
description: Cape fur seal dive
 behaviour data, Kleinsee, South Africa, 2006-2008Excel workbook with 32
 spreadsheets, one spreadsheet for each study animal. The data is dive data
 for the first/only foraging trip of each animal. Data were collected
 during austral winter months of 2006, 2007, 2008. Data show the start and
 end date and time of foraging trip, the beginning and end times of dives
 and phases of dives, time spent during different phases, the distances and
 depths of dives and phases of dives, post-dive durations, dive shape and
 temperatures during dives.DataForSubmission.xlsx
DOI: 10.5061/dryad.m3r1r2t
title: Data from: Microbial functional diversity: from concepts to applications

description: Functional diversity is increasingly recognized by microbial ecologists as
 the essential link between biodiversity patterns and ecosystem
 functioning, determining the trophic relationships and interactions
 between microorganisms, their participation in biogeochemical cycles and
 their responses to environmental changes. Consequently, its definition and
 quantification have practical and theoretical implications. In this
 opinion paper, we present a synthesis on the concept of microbial
 functional diversity from its definition to its application. Initially, we
 revisit to the original definition of functional diversity, highlighting
 two fundamental aspects, the ecological unit under study and the
 functional traits used to characterize it. Then, we discuss how the
 particularities of the microbial world disallow the direct application of
 the concepts and tools developed for macroorganisms. Next, we provide a
 synthesis of the literature on the types of ecological units and
 functional traits available in microbial functional ecology. We also
 provide a list of more than 400 traits covering a wide array of
 environmentally relevant functions. Lastly, we provide examples of the use
 of functional diversity in microbial systems based on the different units
 and traits discussed herein. It is our hope that this paper will stimulate
 discussions and help the growing field of microbial functional ecology to
 realize a potential that thus far has only been attained in macrobial
 ecology.
description: geochip_data_tibetFunctional gene array data (Geochip 4). These data were originally generated in the frame of the publication: Yue, H., Wang, M., Wang, S., Gilbert, J. A., Sun, X., Wu, L., Yang, Y. (2015). The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands. ISME Journal, 9(9), 2012–2020. doi:10.1038/ismej.2015.19metadata_tibetMetadata describing the samples present in the data file "geochip_data_tibet.csv". Data originally generated in the publication: Yue, H., Wang, M., Wang, S., Gilbert, J. A., Sun, X., Wu, L., Yang, Y. (2015). The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands. ISME Journal, 9(9), 2012–2020. doi:10.1038/ismej.2015.19
DOI: 10.5061/dryad.pb21tm8
title: Data from: Taxonomic divergence and functional convergence in Iberian spider forest communities: insights from beta diversity partitioning

description: Aim The main aims were to determine: i) the relative contribution of
 species replacement and richness difference components to overall
 taxonomic (TDβ) and functional (FDβ) beta diversity of spider communities;
 ii) the degree to which TDβ and FDβ components can be explained by the
 environmental or geographic predictors; iii) whether FDβ components were
 lower than expected given the underlying TDβ variation. Location This
 study was carried out in 22 oak forest sites across the Iberian Peninsula.
 The area comprises two biogeographic regions, Eurosiberian (North) and
 Mediterranean (Centre and South). Methods Spiders were sampled using a
 standardized protocol. A species x traits matrix was constructed. Total
 taxonomic (TDβtotal) and total functional (FDβtotal) beta diversity were
 calculated, by pairwise comparisons, and partitioned into their
 replacement (βrepl) and richness difference (βrich) components. Mantel
 tests were used to relate taxonomic and functional dissimilarity with
 environmental and geographic distances. A spatial eigenfunction model was
 constructed and the variation of TDβ and FDβ explained by environment and
 geographic predictors was quantified. Null models were used to test if FDβ
 was higher or lower than expected given TDβ. Results βrepl was the
 dominant component contributing to 84.2% and 72.8% for TDβtotal and
 FDβtotal, respectively. TDβtotal and FDβtotal (and their replacement
 components) were higher between- than within-biogeographic regions.
 TDβtotal and TDβrepl were positively correlated with environmental and
 geographic distances, even when controlling for a biogeographic effect,
 but their functional counterparts were only correlated with environmental
 distance. Variation partitioning showed that pure environmental and
 spatially structured environmental effects had a small contribution to
 beta diversity, except for TDβrich. The observed slopes of the regressions
 of FDβtotal and FDβrepl in relation to environmental distance were slower
 than the null model expectations. Main conclusions Spider’ assemblages
 variation was mainly determined by the replacement, and not the net loss,
 of species and traits. TDβ was influenced by niche filtering and dispersal
 limitation, whereas FDβ was mainly generated by niche filtering. A high
 level of functional convergence among spider communities, despite the high
 taxonomic divergence, revealed the signal of replacement of species
 performing similar functions across sites.
description: Species distribution
 dataContains a table in csv
 format with species adundance distribution dataspecies_distr_data.csvSpecies trait dataContains a table in csv format with trait data for each speciesspecies_trait_data.csv
DOI: 10.5061/dryad.54gb2m9
title: Data from: Divergent selection and drift shape the genomes of two avian sister species spanning a saline-freshwater ecotone

description: The role of species divergence due to ecologically-based divergent
 selection – or ecological speciation – in generating and maintaining
 biodiversity is a central question in evolutionary biology. Comparison of
 the genomes of phylogenetically related taxa spanning a selective habitat
 gradient enables discovery of divergent signatures of selection and
 thereby provides valuable insight into the role of divergent ecological
 selection in speciation. Tidal marsh ecosystems provide tractable
 opportunities for studying organisms’ adaptations to selective pressures
 that underlie ecological divergence. Sharp environmental gradients across
 the saline-freshwater ecotone within tidal marshes present extreme
 adaptive challenges to terrestrial vertebrates. Here we sequence 20 whole
 genomes of two avian sister species endemic to tidal marshes – the
 Saltmarsh Sparrow (Ammodramus caudacutus) and Nelson’s Sparrow (A.
 nelsoni) – to evaluate the influence of selective and demographic
 processes in shaping genome-wide patterns of divergence. Genome-wide
 divergence between these two recently diverged sister species was notably
 high (genome-wide FST = 0.32). Against a background of high genome-wide
 divergence, regions of elevated divergence were widespread throughout the
 genome, as opposed to focused within islands of differentiation. These
 patterns may be the result of genetic drift resulting from past tidal
 march colonization events in conjunction with divergent selection to
 different environments. We identified several candidate genes that
 exhibited elevated divergence between Saltmarsh and Nelson’s sparrows,
 including genes linked to osmotic regulation, circadian rhythm, and
 plumage melanism – all putative candidates linked to adaptation to tidal
 marsh environments. These findings provide new insights into the roles of
 divergent selection and genetic drift in generating and maintaining
 biodiversity.
description: Saltmarsh and
 Nelson's sparrow autosomal SNP datasetGzipped VCF file
 containing the final SNP dataset (6,256,980 SNPs) used in the publication.
 The data results from whole genome resequencing of 10 saltmarsh and 10
 Nelson's sparrows, as described in the manuscript. The metadata for
 each individual can be found in Supplementary Table S1.ComparativeGenomics_Autosomal.vcf.recode.vcf.gzSaltmarsh sparrow reference genomeGZipped file containing the saltmarsh sparrow reference genome that was sequenced and assembled in this study.final.assembly.fasta.gzReference genome annotationsGzipped GFF file of the saltmarsh sparrow reference genome annotations.SALS.gff.gz
DOI: 10.5061/dryad.3sv28v7
title: Data from: Arm waving in stylophoran echinoderms: three-dimensional mobility analysis illuminates cornute locomotion

description: The locomotion strategies of fossil invertebrates are typically
 interpreted on the basis of morphological descriptions. However, it has
 been shown that homologous structures with disparate morphologies in
 extant invertebrates do not necessarily correlate with differences in
 their locomotory capability. Here, we present a new methodology for
 analysing locomotion in fossil invertebrates with a rigid skeleton through
 an investigation of a cornute stylophoran, an extinct fossil echinoderm
 with enigmatic morphology that has made its mode of locomotion difficult
 to reconstruct. We determined the range of motion of a stylophoran arm
 based on digitized three-dimensional morphology of an early Ordovician
 form, Phyllocystis crassimarginata. Our analysis showed that efficient
 arm-forward epifaunal locomotion based on dorsoventral movements, as
 previously hypothesized for cornute stylophorans, was not possible for
 this taxon; locomotion driven primarily by lateral movement of the
 proximal aulacophore was more likely. 3D digital modelling provides an
 objective and rigorous methodology for illuminating the movement
 capabilities and locomotion strategies of fossil invertebrates.
description: FSL712515 Range of motion model Micro-CT
 scan of Phyllocystis crassimarginata (FSL 712515). See Material and
 methods section of the main text for more information.
 FSL712515_ROM.mb micro-CT files: VG
 Studio Micro-CT scan of Phyllocystis crassimarginata
 (FSL 712515) (.vgl file for VG Studio). See Material and methods section
 of the main text for more information. VG Studio
 Files.zip micro-CT files: TIFF stack
 Micro-CT scan of Phyllocystis crassimarginata (FSL 712515)
 (reconstructed TIFF stack). See Material and methods section of the main
 text for more information. TIFF Stack.zip
DOI: 10.5061/dryad.31201jg
title: Data from: Functional richness shows spatial scale dependency in Pheidole ant assemblages from Neotropical savannas

description: There is a growing recognition that spatial scale is important for
 understanding ecological processes shaping community membership, but
 empirical evidence on this topic is still scarce. Ecological processes
 such as environmental filtering can decrease functional differences among
 species and promote functional clustering of species assemblages, whereas
 interspecific competition can do the opposite. These different ecological
 processes are expected to take place at different spatial scales, with
 competition being more likely at finer scales and environmental filtering
 most likely at coarser scales. We used a comprehensive dataset on species
 assemblages of a dominant ant genus, Pheidole, in the Cerrado (savanna)
 biodiversity hotspot to ask how functional richness relate to species
 richness gradients and whether such relationships vary across spatial
 scales. Functional richness of Pheidole assemblages decreased with
 increasing species richness, but such relationship did not vary across
 different spatial scales. Species were more functionally dissimilar at
 finer spatial scales, and functional richness increased less than expected
 with increasing species richness. Our results indicate a tighter packing
 of the functional volume as richness increases and point out to a primary
 role for environmental filtering in shaping membership of Pheidole
 assemblages in Neotropical savannas.
description: dataThe csv file contains 11
 columns, each of which is explained below: 1. Scale = factor with 3 levels
 representing the spatial scale of plot, transect, or site 2. Site = factor
 with 29 levels representing each sampling site in the Cerrado 3. Transect
 = factor with multiple levels representing the three transects of each
 site 4. Plot = factor with multiple levels representing the 10 plots of
 each transect 5. Longitude = longitude of the transects in decimal
 degrees, datum WGS84 (available only for sites and transects) 6. Latitude
 = latitude of the transects in decimal degrees, datum WGS84 (available
 only for sites and transects) 7. Total_richness = total ant richness
 including all ant genera (available only for sites) 8. Pheidole_richness =
 species richness of Pheidole ants in each assemblage 9. FR = functional
 richness of ant assemblages 10. SES_FR_z = standardized effect size (SES)
 of the FR of each ant assemblage 11. SES_FR_p = p-value associated with
 the SES FR valueR
 scriptR script for the
 analysis performed in the manuscript.R_script.RShapefile of the Cerrado domainShapefile provided only for illustrative purposes. It represents the Cerrado domain in South America, and it was created by overlapping the distribution of 1454 plant species typical form the Cerrado. Such plant maps represent the limits of the watersheds in which any given plant species was recorded, based on knowledge of various specialists.shapefile.rar