cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c186k
title: Data from: Land-use type and intensity differentially filter traits in above- and belowground arthropod communities

description: 1. Along with the global decline of species richness goes a loss of
 ecological traits. Associated biotic homogenization of animal communities
 and narrowing of trait diversity threaten ecosystem functioning and human
 well-being. High management intensity is regarded as an important
 ecological filter, eliminating species that lack suitable adaptations.
 Belowground arthropods are assumed to be less sensitive to such effects
 than aboveground arthropods. 2. Here, we compared the impact of management
 intensity between (grassland vs. forest) and within land-use types (local
 management intensity) on the trait diversity and composition in below- and
 aboveground arthropod communities. 3. We used data on 722 arthropod
 species living above ground (Auchenorrhyncha and Heteroptera), primarily
 in soil (Chilopoda and Oribatida) or at the interface (Araneae and
 Carabidae). 4. Our results show that trait diversity of arthropod
 communities is not primarily reduced by intense local land use, but is
 rather affected by differences between land-use types. Communities of
 Auchenorrhyncha and Chilopoda had significantly lower trait diversity in
 grassland habitats as compared to forests. Carabidae showed the opposite
 pattern with higher trait diversity in grasslands. Grasslands had a lower
 proportion of large Auchenorrhyncha and Carabidae individuals, whereas
 Chilopoda and Heteroptera individuals were larger in grasslands. Body size
 decreased with land-use intensity across taxa, but only in grasslands. The
 proportion of individuals with low mobility declined with land-use
 intensity in Araneae and Auchenorrhyncha, but increased in Chilopoda and
 grassland Heteroptera. The proportion of carnivorous individuals increased
 with land-use intensity in Heteroptera in forests and in Oribatida and
 Carabidae in grasslands. 5. Our results suggest that gradients in
 management intensity across land-use types will not generally reduce trait
 diversity in multiple taxa, but will exert strong trait filtering within
 individual taxa. The observed patterns for trait filtering in individual
 taxa are not related to major classifications into above- and belowground
 species. Instead, ecologically different taxa resembled each other in
 their trait diversity and compositional responses to land-use differences.
 These previously undescribed patterns offer an opportunity to develop
 management strategies for the conservation of trait diversity across
 taxonomic groups in permanent grassland and forest habitats.
description: Percent_Dominance_CommunitiesThe percentage dominance of species in each taxon per site.Traits_CommunitiesBinary coding of traits from Table 1 for all speciesFactors_CovariablesFactors and co-variables for all sites used in models.ProportionsArcSin transformed proportional data for traits.
DOI: 10.5061/dryad.h32m962j
title: Data from: DNA variation in the phenotypically-diverse brown alga Saccharina japonica

description: BACKGROUND: Saccharina japonica (Areschoug) Lane, Mayes, Druehl et
 Saunders is an economically important and highly morphologically variable
 brown alga inhabiting the northwest Pacific region. On the basis of
 nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data,
 we have analyzed the genetic composition of typical Saccharina japonica
 (TYP) and its two common morphological varieties, known as the “longipes”
 (LON) and “shallow-water” (SHA) forms seeking to clarify their taxonomical
 status and to evaluate the possibility of cryptic species within S.
 japonica. RESULTS: The data show that the TYP and LON forms are very
 similar genetically in spite of drastic differences in morphology, life
 history traits, and ecological preferences. Both, however, are genetically
 quite different from the SHA form. The two Saccharina lineages are
 distinguished by 109 fixed single nucleotide differences as well as by
 seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset
 that includes three gene regions). The GenBank database reveals a close
 affinity of the TYP and LON forms to S. japonica and the SHA form to S.
 cichorioides. The three gene markers used in the present work have
 different sensitivity for the algae species identification. The COI gene
 is the most discriminant gene marker. However, the 5’-COI “barcoding”
 region (~ 650 bp) is not satisfactory and even misleading for
 identification purposes, at least in the case of algae species that might
 have experienced historical hybridization events. CONCLUSION: Taking into
 account the potential roles of phenotypic plasticity in evolution, we
 conclude that the TYP and LON forms represent examples of algae phenotypic
 diversification that enables successful adaptation to contrasting shallow-
 and deep-water marine environments, while the SHA form is very similar to
 S. cichorioides and should be considered a different species. Practical
 applications for algal management and conservation are shortly considered.
description: CONCATENATE_rbcLS_COI_ITS_for_DRYADThe data represent the alignment of rbcLS, COI, and ITS in 29 algae samples.Concatenate_NJ_tree_Saccharina_rbcLS_COI_ITSThe tree shows relationships between morphological forms of Saccharina japonica.
DOI: 10.5061/dryad.gm29rj2f
title: Data from: Genetic and phenotypic population divergence on a microgeographic scale in brown trout

description: Salmonid populations of many rivers are rapidly declining. One possible
 explanation is that habitat fragmentation increases genetic drift and
 reduces the populations’ potential to adapt to changing environmental
 conditions. We measured the genetic and eco-morphological diversity of
 brown trout (Salmo trutta) in a Swiss stream system, using multivariate
 statistics and Bayesian clustering. We found large genetic and phenotypic
 variation within only 40 km of stream length. Eighty-eight percent of all
 pairwise FST comparisons and 50% of the population comparisons in body
 shape were significant. High success rates of population assignment tests
 confirmed the distinctiveness of populations in both genotype and
 phenotype. Spatial analysis revealed that divergence increased with
 waterway distance, the number of weirs, and stretches of poor habitat
 between sampling locations, but effects of isolation-by-distance and
 habitat fragmentation could not be fully disentangled. Stocking intensity
 varied between streams but did not appear to erode genetic diversity
 within populations. A lack of association between phenotypic and genetic
 divergence points to a role of local adaptation or phenotypically plastic
 responses to habitat heterogeneity. Indeed, body shape could be largely
 explained by topographic stream slope, and variation in overall phenotype
 matched the flow regimes of the respective habitats.
description: Stelkens et al. geo
 morpho dataData file containing raw
 coordinates of 13 geometric morphometric landmarks from 580 brown trout
 specimens and the first 3 PC scores from principal component analysis. ID
 = individual identity; Pop ID = poplation identityStelkens et al,
 microsatellite dataData file containing raw
 allele sizes from 11 microsatellite markers of 590 Salmo trutta specimens.
 ID = individual ID. Pop ID = population identity
DOI: 10.5061/dryad.391dj
title: Data from: Evolution and maintenance of haploid-diploid life cycles in natural populations: the case of the marine brown alga Ectocarpus

description: The evolutionary stability of haploid-diploid life cycles is still
 controversial. Mathematical models indicate that niche differences between
 ploidy phases may be a necessary condition for the evolution and
 maintenance of these life cycles. Nevertheless, experimental support for
 this prediction remains elusive. In the present work, we explored this
 hypothesis in natural populations of the brown alga Ectocarpus. Consistent
 with the life cycle described in culture, E. crouaniorum in NW France and
 E. siliculosus in SW Italy exhibited an alternation between haploid
 gametophytes and diploid sporophytes. Our field data invalidated, however,
 the long-standing view of an isomorphic alternation of generations.
 Gametophytes and sporophytes displayed marked differences in size and,
 conforming to theoretical predictions, occupied different spatio-temporal
 niches. Gametophytes were found almost exclusively on the alga Scytosiphon
 lomentaria during spring while sporophytes were present year-round on
 abiotic substrata. Paradoxically, E. siliculosus in NW France exhibited
 similar habitat usage despite the absence of alternation of ploidy phases.
 Diploid sporophytes grew both epilithically and epiphytically, and this
 mainly-asexual population gained the same ecological advantage postulated
 for haploid-diploid populations. Consequently, an ecological
 interpretation of the niche differences between haploid and diploid
 individuals does not seem to satisfactorily explain the evolution of the
 Ectocarpus life cycle.
description: Dataset Couceiro et al.
 2015
DOI: 10.15468/dl.gvbn4h
title: Occurrence Download

description: A dataset containing 2036 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
 },
 {
 "and" : [
 "InstitutionCode is one of (MSB)",
 "TaxonKey is one of (Lithobates pipiens [GBIF Backbone Taxonomy])"
 ]
 }
 ]
}

 The dataset includes 2036 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000617-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4ff1t
title: Data from: Genetic constraints predict evolutionary divergence in Dalechampia blossoms

description: If genetic constraints are important, then rates and direction of
 evolution should be related to trait evolvability. Here we use recently
 developed measures of evolvability to test the genetic constraint
 hypothesis with quantitative genetic data on floral morphology from the
 Neotropical vine Dalechampia scandens (Euphorbiaceae). These measures were
 compared against rates of evolution and patterns of divergence among 24
 populations in two species in the D. scandens species complex. We found
 clear evidence for genetic constraints, particularly among traits that
 were tightly phenotypically integrated. This relationship between
 evolvability and evolutionary divergence is puzzling, because the
 estimated evolvabilities seem too large to constitute real constraints. We
 suggest that this paradox can be explained by a combination of weak
 stabilizing selection around moving adaptive optima and small realized
 evolvabilities relative to the observed additive genetic variance.
description: Morphological
 measurements D. scandens Tulum diallelTulumDiallel.csvMorphological measurements D. scandens Tovar diallelTovarDiallel.csvPedigree D. scandens Tulum diallelTulumDiallelPedigree.csvPedigree D. scandens Tovar diallelTovarDiallelPedigree.csvMorphological measurements D. scandens populationsPopulations.csvPhylogeny large-glanded populationsphyloLargeGlanded.nexPhylogeny small-glanded populationsphyloSmallGlanded.nexReadme
DOI: 10.5061/dryad.1303
title: Data from: Phenotypic correlates of Clock gene variation in a wild blue tit population: evidence for a role in seasonal timing of reproduction

description: The timing of reproduction in birds varies considerably within populations
 and is often under strong natural selection. Individual timing within
 years is dependent on a range of environmental factors in addition to
 having an additive genetic basis. In vertebrates, an increasing amount is
 known about the molecular basis for variation in biological timing. The
 Clock gene includes a variable poly-glutamine (poly-Q) repeat influencing
 behaviour and physiology. Recent work in birds, fish and insects has
 demonstrated associations between Clock genotype and latitude across
 populations, which match latitudinal variation in breeding time. In this
 study, we investigated the phenotypic correlates of variation in Clock
 genotype within a single blue tit Cyanistes caeruleus population over two
 successive breeding seasons. In females, but not in males, we observed a
 general trend for birds with fewer poly-Q repeats to breed earlier in the
 season. Incubation duration was shorter in both females and males with
 fewer repeats at the polymorphic Clock locus. Poly-Q Clock
 allele-frequency was homogenously distributed within the study population
 and did not exhibit any consistent environment-related variation. We
 further tested for effects of Clock genotype on reproductive success and
 survival, and found that females with fewer poly-Q repeats produced a
 higher number of fledged offspring. Our results therefore suggest that (i)
 selection in females, but not in males, for fewer poly-Q repeats may be
 operating, (ii) the across-population associations in timing of breeding
 involving this locus might be linked to variation within populations, and
 (iii) the Clock gene might be involved in local adaptation to seasonal
 environments.
description: Clock genotype for blue
 tit breeding population 2006-2007The file contains
 genotyping data and relevant covariates for the blue tit population
 breeding in Wytham woods 2006 and 2007.Dryad_MolEcol_BT-clock.xls
DOI: 10.5061/dryad.s0s60
title: Data from: Genetic basis of octanoic acid resistance in Drosophila sechellia: functional analysis of a fine-mapped region

description: Drosophila sechellia is a species of fruit fly endemic to the Seychelles
 islands. Unlike its generalist sister species, D. sechellia has evolved to
 be a specialist on the host plant Morinda citrifolia. This specialization
 is interesting because the plant's fruit contains secondary defense
 compounds, primarily octanoic acid (OA), that are lethal to most other
 Drosophilids. Although ecological and behavioral adaptations to this toxic
 fruit are known, the genetic basis for evolutionary changes in OA
 resistance are not. Prior work showed that a genomic region on chromosome
 3R containing 18 genes has the greatest contribution to differences in OA
 resistance between D. sechellia and D. simulans. To determine which
 gene(s) in this region might be involved in the evolutionary change in OA
 resistance, we knocked-down expression of each gene in this region in D.
 melanogaster with RNA interference (RNAi) (i) ubiquitously throughout
 development, (ii) during only the adult stage, and (iii) within specific
 tissues. We identified three neighboring genes in the Osiris family,
 Osiris 6 (Osi6), Osi7, and Osi8, that lead to decreased OA resistance when
 ubiquitously knocked-down. Tissue specific RNAi, however, showed that
 decreasing expression of Osi6 and Osi7 specifically in the fat body and/or
 salivary glands increased OA resistance. Gene expression analyses of Osi6
 and Osi7 revealed that while standing levels of expression are higher in
 D. sechellia, Osi6 expression is significantly downregulated in salivary
 glands in response to OA exposure, suggesting that evolved tissue-specific
 environmental plasticity of Osi6 expression may be responsible for OA
 resistance in D. sechellia.
description: MEC_qRT-PCR_RawDataQuantitative real time PCR data for Osiris 6 (Osi6), Osi7 and Osi8 and the housekeeping gene aTub84B in whole adult and dissected adult tissues (INT = intestine, SG = salivary gland, FB = Fat body, NS = Nervous system) from Drosophila species with and without exposure to octanoic acid (OA vs control = no OA).Drosophila survival data in response to octanoic acid exposureSurvival data in response to octanoic acid (OA) exposure of Drosophila adult flies. The sample type is indicated as to whether it is from different species (D. sechellia (sec), D. simulans (sim), D. mauritiana (mau), or D. melanogaster RNAi lines (gene targeted named), GAL4 lines, RNAiXGAL4 (ubiquitous (ActinGAL4), stage specific (Geneswitch-Tub5) or tissue specific (Bloomington stock number provided) knockdown) cross progeny and sibling controls and mutant lines are indicated. Flies were separated based in sex (1 = male, 0 = female), presence of CyO balancer (0 = CyO, 1 = wildtype) chromosome, and the number of individuals surviving at 12 time points (every 5 minutes for 1 hour) was determined in vials containing N flies per vial and vial number and date of each experiment are indicated.OA_data_Coolon_2016.xlsx
DOI: 10.5061/dryad.ht554
title: Data from: Small founding number and low genetic diversity in an introduced species exhibiting limited invasion success (speckled dace, Rhinichthys osculus)

description: Molecular evaluations of successful invaders are common, however studies
 of introduced species that have had limited invasion success, or have died
 out completely, are rare. We studied an introduced population of speckled
 dace (Rhinichthys osculus) from northern California, USA that has rapidly
 increased in abundance but remained restricted to a 25-km stretch of river
 since its introduction in the mid-1980s. Field and laboratory analyses
 indicate that invasion success of speckled dace is constrained by the
 combined effects of multiple predators. The role of bottleneck effects
 associated with the introduction has not been studied. We assayed
 variation in seven microsatellite loci and one mitochondrial DNA gene in
 the introduced population and nine putative source populations to identify
 the source population and evaluate bottleneck effects. The Trinity River
 system was supported as the source owing to its genetic similarity and
 geographic proximity to the introduced population. Consistent with a
 bottleneck, the introduced population exhibited reduced allelic and
 haplotype richness in comparison to source populations. Estimates of the
 genetically effective number of individuals founding the introduced
 population using nuclear coalescent analyses and a mitochondrial
 simulation procedure were highly concordant in suggesting that the initial
 colonizing group was comprised of about 10 individuals. A bottleneck
 effect in an exotic species exhibiting limited invasion success has rarely
 been documented and thus introduction of speckled dace represents an
 important model system for future investigation. Establishing a
 relationship between genetic diversity and factors limiting invasion
 success in this system (e.g., predator avoidance) will help determine the
 extent to which genetic diversity loss has constrained invasion success in
 speckled dace.
description: mtDNAMitochondrial DNA data
 in FASTA format. Genotypes can be linked to specimens using information
 contained in README file.usat.genepop_2digitMicrosatellite data in GENEPOP format (2 digit). Genotypes can be linked to specimens using information contained in README file.
DOI: 10.5061/dryad.gp384
title: Data from: Colour ornamentation in the blue tit: quantitative genetic (co)variances across sexes

description: Although secondary sexual traits are commonly more developed in males than
 females, in many animal species females also display elaborate ornaments
 or weaponry. Indirect selection on correlated traits in males and/or
 direct sexual or social selection in females are hypothesized to drive the
 evolution and maintenance of female ornaments. Yet, the relative roles of
 these evolutionary processes remain unidentified, because little is known
 about the genetic correlation that might exist between the ornaments of
 both sexes, and few estimates of sex-specific autosomal or sex-linked
 genetic variances are available. In this study, we used two wild blue tit
 populations with 9 years of measurements on two colour ornaments: one
 structurally based (blue crown) and one carotenoid based (yellow chest).
 We found significant autosomal heritability for the chromatic part of the
 structurally based colouration in both sexes, whereas carotenoid chroma
 was heritable only in males, and the achromatic part of both colour
 patches was mostly non heritable. Power limitations, which are probably
 common among most data sets collected so far in wild populations,
 prevented estimation of sex-linked genetic variance. Bivariate analyses
 revealed very strong cross-sex genetic correlations in all heritable
 traits, although the strength of these correlations was not related to the
 level of sexual dimorphism. In total, our results suggest that males and
 females share a majority of their genetic variation underlying colour
 ornamentation, and hence the evolution of these sex-specific traits may
 depend greatly on correlated responses to selection in the opposite sex.
description: PhenotypesPhenotypic measures of colour in male and female blue tits from three different populations between 2005 and 2013Pedigree_corsicaPedigree of corsican blue tits used in the analysis.Pedigree_mainlandPedigree of mainland blue tits used in the quantitative genetic analysis.
DOI: 10.5061/dryad.653
title: Data from: Mining the Mammalian Genome for Artiodactyl Systematics

description: A total of 7806 nucleotide positions derived from one mitochondrial and
 eight nuclear DNA segments were used to provide a robust phylogeny for
 members of the order Artiodactyla. Twenty-four artiodactyl and two
 cetacean species were included and the horse, order Perissodactyla, was
 used as the outgroup. Limited rate heterogeneity was observed among the
 nuclear genes. The partition homogeneity tests indicated no conflicting
 signal among the nuclear gene fragments and the sequence data were
 analyzed together and as separate loci. Analyses based on the individual
 nuclear DNA fragments, and 34 unique indels, all produced phylogenies
 largely congruent with the topology from the combined data set. In sharp
 contrast to the nuclear DNA data, the mtDNA cytochrome b sequence data
 showed high levels of homoplasy, failed to produce a robust phylogeny, and
 were remarkably sensitive to taxon sampling. The nuclear DNA data clearly
 support the paraphyletic nature of the Artiodactyla. Additionally, the
 family Suidae is diphyletic and the non-ruminating pigs and peccaries
 (Suiformes) were the most basal cetartiodactyl group. The morphologically
 derived Ruminantia was always monophyletic and within this group all taxa
 with paired bony structures on their skulls clustered together. The
 nuclear DNA data suggested that the Antilocaprinae comprise a unique
 evolutionary lineage, the Cervidae and Bovidae are sister taxa while the
 Giraffidae is more primitive.
description: Matthee et al Data
 SetMatthee.nexus