cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.xuqs4f
title: Occurrence Download

description: A dataset listing the 864 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Flora y epífitas presentes en el proyecto Minera de Cobre Quebradona, municipio de Jericó"
 ]
}

 The dataset's 864 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000998-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8np44
title: Data from: Post-dispersal seed recovery by animals: is it a plant- or an animal-driven process?

description: The ability of animals to find and consume hoarded seeds (i.e. seed
 recovery) is a key stage within the seed dispersal process. However, the
 ecology of seed recovery is still poorly understood. Here, we analyze the
 factors controlling seed recovery by scatter-hoarding rodents in an
 oak-dominated temperate forest. We examined the relative importance of
 intrinsic seed traits (i.e. plant-driven) and extrinsic seed factors (i.e.
 animal-driven) on the probability of seed recovery. We found that seed
 recovery is mainly driven by extrinsic seed factors, mostly related to
 animal behavior (pilfering frequency, microsite preference, predation
 risk, burial depth and cache size). Important intrinsic traits such as
 seed size, seed quality and seed-drop timing were, on average, of lower
 significance in the probability of seed recovery (2.8-times less important
 than extrinsic factors); only seed quality was an important intrinsic
 trait. On the other hand, larger and nutritionally more valuable seeds
 showed a removal–recovery tradeoff as they enhance seed removal and
 hoarding (increasing dispersal quality) but also favour seed recovery
 (increasing predation). We find that other mechanisms beyond seed traits
 (e.g. masting) are needed to decrease seed recovery and, thus, increase
 seed survival. We conclude that, as seed recovery is mostly driven by
 animal behavioural factors, it substantially differs from other previous
 stages of the seed dispersal process that are more dependent on seed
 traits. We argue that seed recovery needs further attention to advance our
 understanding of the ecology of seed dispersal and the role of secondary
 dispersers as a selective force for seeds.
description: Perea_2015_Oikos_Seed_Recovery_rodentsRaw data on the recovery of seeds (acorns of Quercus pyrenaica) by rodents (Apodemus sylvaticus) after having been dispersed by the same rodent species
DOI: 10.5061/dryad.5s500
title: Data from: New information on Titanichthys (Placodermi: Arthrodira) from the Cleveland shale (upper devonian) of Ohio, USA

description: The placoderm (Titanichthys) from the Late Devonian (Famennian) is based
 on incomplete and fragmentary specimens that have hindered understanding
 of its overall anatomy and phylogenetic relationships. A new, nearly
 complete, articulated specimen from the Upper Devonian Cleveland Shale
 provides new information about the previously undescribed rostral,
 postmarginal, postsuborbital, submarginal, posterior superognathal plates,
 and the nasal capsule. A revised diagnosis is provided for the genus.
 Three new diagnostic characters are identified including a transversely
 elliptical rostral plate that does not contact adjacent plates, a reduced
 posterior superognathal, and a median dorsal plate that inserts into the
 posterior dorsal lateral plate. The first comprehensive phylogenetic
 analysis of (Titanichthys) indicates that the genus is a basal
 aspinothoracid arthrodire closely related to the enigmatic taxa
 (Bungartius) and (Tafilalichthys).
description: Boyle&Ryan2016_Appendix 1_PhylogeneticMatrixPhylogenetic matrix of 73 brachythoracid taxa with 121 characters used in Boyle & Ryan 2016.Appendix 1.xlsxBoyle&Ryan2016_Appendix 2_CharacterChangesChanges to phylogenetic character codings in Boyle & Ryan 2016 relative to those reported in Zhu et al. 2013 or Rucklin et al. 2015.Appendix 2.docx
DOI: 10.5061/dryad.ts705
title: Data from: Effects of increased flight on the energetics and life history of the butterfly Speyeria mormonia

description: Movement uses resources that may otherwise be allocated to somatic
 maintenance or reproduction. How does increased energy expenditure affect
 resource allocation? Using the butterfly Speyeria mormonia, we tested
 whether experimentally increased flight affects fecundity, lifespan or
 flight capacity. We measured body mass (storage), resting metabolic rate
 and lifespan (repair and maintenance), flight metabolic rate (flight
 capacity), egg number and composition (reproduction), and food intake
 across the adult lifespan. The flight treatment did not affect body mass
 or lifespan. Food intake increased sufficiently to offset the increased
 energy expenditure. Total egg number did not change, but flown females had
 higher early-life fecundity and higher egg dry mass than control females.
 Egg dry mass decreased with age in both treatments. Egg protein,
 triglyceride or glycogen content did not change with flight or age, but
 some components tracked egg dry mass. Flight elevated resting metabolic
 rate, indicating increased maintenance costs. Flight metabolism decreased
 with age, with a steeper slope for flown females. This may reflect
 accelerated metabolic senescence from detrimental effects of flight. These
 effects of a drawdown of nutrients via flight contrast with studies
 restricting adult nutrient input. There, fecundity was reduced, but flight
 capacity and lifespan were unchanged. The current study showed that when
 food resources were abundant, wing-monomorphic butterflies living in a
 continuous meadow landscape resisted flight-induced stress, exhibiting no
 evidence of a flight-fecundity or flight-longevity trade-off. Instead,
 flight changed the dynamics of energy use and reproduction as butterflies
 adopted a faster lifestyle in early life. High investment in early
 reproduction may have positive fitness effects in the wild, as long as
 food is available. Our results help to predict the effect of stressful
 conditions on the life history of insects living in a changing world.
description: Repeated measures data
 accompanying the paper: Effects of Increased Flight on the Energetics and
 Life History of the Butterfly Speyeria mormoniaData are in microsoft
 excel .xlsx format. Descriptions of each data type, including units, are
 in "comments" associated with the headers on each data column on
 each page. Data were collected on the butterfly Speyeria mormonia, derived
 from a population in Gunnison County, Colorado, USA and raised in
 captivity at Stanford University.Niitepõld & Boggs PLOS One
 dataset.xlsx
DOI: 10.5061/dryad.mm155
title: Data from: Are adaptive loci transferable across genomes of related species? Outlier and environmental association analyses in Alpine Brassicaceae species

description: Local adaptation is one possible response of organisms to survive in a
 changing environment. However, the genetic basis of adaptation is not well
 understood, especially in nonmodel species. To infer recurrent patterns of
 local adaptation, we investigated whether the same putative adaptive loci
 reoccur in related species. We performed genome scans using amplified
 fragment length polymorphism (AFLP) markers on populations of five Alpine
 Brassicaceae species sampled across a wide range of environmental
 conditions. To identify markers potentially under directional selection,
 we performed outlier and environmental association analyses using a set of
 topo-climatic variables available as GIS layers. Several AFLP loci showed
 signatures of adaptation, of which one, found in Cardamine resedifolia
 (Cre_P1_212.5), was associated with precipitation. We
 sequence-characterized this candidate locus and genotyped single
 nucleotide polymorphisms (SNPs) found within this locus for all species.
 Testing for environmental associations of SNPs revealed the same
 association of this locus in Arabis alpina but not in other study species.
 Cumulative statistical evidence indicates that locus Cre_P1_212.5 is
 environmentally relevant or is linked to a gene under selection in our
 study range. Furthermore, the locus shows an association to the same
 potentially selective factor in at least one other related species. These
 findings help to identify trends in plant adaptation in Alpine ecosystems
 in response to particular environmental parameters.
description: Zulliger_etal_MolEcol2013Data described in the ReadMe file included in the zip archive
DOI: 10.5061/dryad.rv5mg
title: Data from: Reproductive sharing in relation to group and colony-level attributes in a cooperative breeding fish

description: The degree to which group members share reproduction is dictated by both
 within-group (e.g. group size and composition) and between-group (e.g.
 density and position of neighbours) characteristics. While many studies
 have investigated reproductive patterns within social groups, few have
 simultaneously explored how within-group and between-group social
 structure influence these patterns. Here, we investigated how group size
 and composition, along with territory density and location within the
 colony, influenced parentage in 36 wild groups of a colonial,
 cooperatively breeding fish Neolamprologus pulcher. Dominant males sired
 76% of offspring in their group, whereas dominant females mothered 82% of
 offspring in their group. Subordinate reproduction was frequent, occurring
 in 47% of sampled groups. Subordinate males gained more paternity in
 groups located in high-density areas and in groups with many subordinate
 males. Dominant males and females in large groups and in groups with many
 reproductively mature subordinates had higher rates of parentage loss, but
 only at the colony edge. Our study provides, to our knowledge, the first
 comprehensive quantification of reproductive sharing among groups of wild
 N. pulcher, a model species for the study of cooperation and social
 behaviour. Further, we demonstrate that the frequency of extra-pair
 parentage differs across small social and spatial scales.
description: Parentage
 groupsSubordinates
DOI: 10.5061/dryad.s8330
title: Data from: Spontaneous mutation accumulation in multiple strains of the green alga, Chlamydomonas reinhardtii

description: Estimates of mutational parameters, such as the average fitness effect of
 a new mutation and the rate at which new genetic variation for fitness is
 created by mutation, are important for the understanding of many
 biological processes. However, the causes of interspecific variation in
 mutational parameters and the extent to which they vary within species
 remain largely unknown. We maintained multiple strains of the unicellular
 eukaryote Chlamydomonas reinhardtii, for approximately 1000 generations
 under relaxed selection by transferring a single cell every ∼10
 generations. Mean fitness of the lines tended to decline with generations
 of mutation accumulation whereas mutational variance increased. We did not
 find any evidence for differences among strains in any of the mutational
 parameters estimated. The overall change in mean fitness per cell division
 and rate of input of mutational variance per cell division were more
 similar to values observed in multicellular organisms than to those in
 other single-celled microbes. However, after taking into account
 differences in genome size among species, estimates from multicellular
 organisms and microbes, including our new estimates from C. reinhardtii,
 become substantially more similar. Thus, we suggest that variation in
 genome size is an important determinant of interspecific variation in
 mutational parameters.
description: fitness data assay block
 1Contains the fitness
 data for all MA lines as well as the number of generations of MA
 associated with each line1st fitness assay with fitness
 and generations.xlsx2nd fitness
 assaycontains fitness data
 for all lines from the second assay blockgeneration time
 dataContains the data on
 colony numbers used to calculate the generation times of lines growing on
 plates during the MA part of the experimentgenerations during
 MA.xlsx
DOI: 10.5061/dryad.91kk8
title: Data from: Managing Neotropical oil palm expansion to retain phylogenetic diversity

description: The expansion of tropical agriculture is a major driver of the extinction
 crisis. A key question is whether biodiversity losses can be minimized by
 restricting future expansion to low-productivity farmland and retaining
 forest fragments, especially in rapidly changing Neotropical landscapes.
 We investigated these methods in the context of avian phylogenetic
 diversity, which summarizes the evolutionary history preserved within
 communities. Evidence suggests that phylogenetic diversity plays an
 important role in maintaining key ecosystem functions. We collected data
 on avian communities in the Colombian Llanos, a region highlighted as
 being optimal for the expansion of oil palm, at the expense of existing
 habitats including forest remnants and improved cattle pastures. PD, a
 measure of phylogenetic richness, and MPD, a measure of the phylogenetic
 distance between individuals in a community in deep evolutionary time,
 were significantly higher in forest than in oil palm or pasture, but did
 not differ significantly between oil palm and pasture. MNTD, a measure of
 distance between individuals in a community at the intra-familial and
 intra-generic level, was significantly higher in oil palm and pasture than
 in forest. However, median evolutionary distinctiveness (ED) was highest
 in pasture, partly due to the abundance of distinct waterbirds, but did
 not differ between oil palm and forest. PD in oil palm and pasture
 increased with the extent of remnant forest cover. Synthesis and
 applications. The PD (a measure of phylogenetic richness) and MPD (a
 measure of the phylogenetic distance) of bird communities in this region
 can best be conserved by ensuring that new oil palm plantations replace
 pasturelands rather than forest. A secondary benefit of preserving forest
 would be the enhancement of PD in the surrounding agricultural landscape.
 This strategy will need to be coupled with measures to either reduce
 pasture demand or to intensify existing cattle production to ensure that
 forest is not replaced by pasture elsewhere.
description: Species
 dataOccurrences of 244 bird
 species (following the taxonomy by Jetz et al. 2012) at 106 sample points
 in Colombia. Each cell contains the highest abundance of birds recorded at
 each sample point.species.csvSite dataData associated with each sample point: transect, site, habitat (forest, oil palm, or pasture), and the proportion of forest in a 250 m radius surrounding each point (in oil palm and pasture).sitedata.csv
DOI: 10.5061/dryad.ss17b
title: Data from: Effects of prey quality and predator body size on prey DNA detection success in a centipede predator

description: Predator body size and prey quality are important factors driving prey
 choice and consumption rates. Both factors might affect prey detection
 success in PCR-based gut content analysis, potentially resulting in over-
 or underestimation of feeding rates. Experimental evidence, however, is
 scarce. We examined how body size and prey quality affect prey DNA
 detection success in centipede predators. Due to metabolic rates
 increasing with body size, we hypothesized that prey DNA detection
 intervals will be significantly shorter in large predators than in smaller
 ones. Moreover, we hypothesized that prey detection intervals of
 high-quality prey will be shorter than in low-quality prey due to faster
 assimilation. Small, medium and large individuals of Lithobius spp.,
 abundant generalist predators in forest litter layers, were fed with
 Collembola and allowed to digest their prey for up to 168 h post-feeding.
 Additionally, medium-sized lithobiids were fed with either Diptera or
 Lumbricidae prey. No significant differences in 50% prey DNA detection
 success time intervals for a 272 bp prey DNA fragment were found between
 the predator size groups, indicating that predator body size does not
 affect prey DNA detection success. Post-feeding detection intervals were
 significantly shorter in Lumbricidae and Diptera compared to Collembola
 prey, apparently supporting the second hypothesis. However, sensitivity of
 diagnostic PCR differed between prey types and quantitative PCR revealed
 that concentration of targeted DNA varied significantly between prey
 types. This suggests that both DNA concentration and assay sensitivity
 need to be considered when assessing prey quality effects on prey DNA
 detection success.
description: Raw data_Eitzinger et
 al_Effect of prey qualityTime series experiment
 with Lithobius spp. fed with either Collembola (Sinella curviseta),
 Lumbricidae (Lumbricus terrestris) or Diptera prey (Drosophila
 melanogaster). File includes data on succesful prey DNA detection,
 predator body mass before and after feeding and prey DNA quantity in
 predator guts. Missing data is indicated as NAraw data_Eitzinger et
 al_Effects of prey quality.csv
DOI: 10.5061/dryad.67140
title: Data from: Using trophic structure to reveal patterns of trait-based community assembly across niche dimensions

description: 1. Trait-based approaches for studying community assembly have improved
 understanding of mechanisms; however, the challenge of interpreting
 process from pattern is complicated by the possibility of multiple
 mechanisms operating simultaneously. Different traits may influence the
 assembly process in different ways. Analyzing patterns of functional
 diversity among co-occurring species for each trait individually may aid
 interpretation of complex assembly processes; yet, few studies have tested
 whether patterns vary depending on trait function. 2. We used tropical
 fish assemblages from the Xingu River, Brazil to test whether traits
 associated with resource acquisition play a stronger role in niche
 segregation relative to other traits. First, a null modeling approach was
 used to determine how trait distributions within local assemblages
 deviated from expectations under random assembly. Then, correlations
 between functional traits and stable isotope ratios (δ13C, δ15N) were used
 as a measure of a trait’s association with trophic structure. Finally, we
 used mixed effects models to test whether traits having higher
 correlations with trophic structure also had greater deviation from null
 expectations. In addition, we explored how well stable isotopes explain
 multivariate functional trait variation and compared our correlation-based
 approach for organizing traits with previous categorical approaches. 3. A
 significant relationship was found between a trait’s deviation from null
 expectations and its correlation with isotopic patterns. Traits strongly
 associated with trophic structure had greater dispersion from the
 assemblage mean and were more evenly spaced than weakly associated traits.
 Traits strongly associated with trophic structure also were more clustered
 because trophic diversification tended to occur around some basic feeding
 strategies, such as benthic grazing or capturing food items from the water
 column. Based on redundancy analysis, isotopic ratios explained a low
 (11.6%) but significant portion of trait variation. 4. In this study
 system, traits strongly associated with trophic ecology were more
 influential in niche differentiation among coexisting species compared to
 weakly associated traits. These results suggest that certain traits may
 respond to assembly mechanisms in predictable ways despite the complex,
 multidimensional nature of the assembly process. Methods designed to
 identify differential trait response will be critical to developing a
 general theory of trait-based community assembly.
description: ReadMeDescription of data
 filescommunity_dryPresence-absence data for dry-season fish assemblagescommunity_wetPresence-absence data for wet-season fish assemblagesisotopesIsotope ratios for fishes from dry and wet seasonstraitsFunctional trait measurements for fishes
DOI: 10.5061/dryad.5n2s7
title: Data from: Determinants of genetic structure in a nonequilibrium metapopulation of the plant Silene latifolia

description: Population genetic differentiation will be influenced by the demographic
 history of populations, opportunities for migration among neighboring
 demes and founder effects associated with repeated extinction and
 recolonization. In natural populations, these factors are expected to
 interact with each other and their magnitudes will vary depending on the
 spatial distribution and age structure of local demes. Although each of
 these effects has been individually identified as important in structuring
 genetic variance, their relative magnitude is seldom estimated in nature.
 We conducted a population genetic analysis in a metapopulation of the
 angiosperm, Silene latifolia, from which we had more than 20 years of data
 on the spatial distribution, demographic history, and extinction and
 colonization of demes. We used hierarchical Bayesian methods to
 disentangle which features of the populations contributed to among
 population variation in allele frequencies, including the magnitude and
 direction of their effects. We show that population age, long-term size
 and degree of connectivity all combine to affect the distribution of
 genetic variance; small, recently-founded, isolated populations
 contributed most to increase FST in the metapopulation. However, the
 effects of population size and population age are best understood as being
 modulated through the effects of connectivity to other extant populations,
 i.e. FST diminishes as populations age, but at a rate that depends how
 isolated the population is. These spatial and temporal correlates of
 population structure give insight into how migration, founder effect and
 within-deme genetic drift have combined to enhance and restrict genetic
 divergence in a natural metapopulation.
description: Raw_GenotypesRaw microsatellite fragment lengths in CONVERT format.alleles.txtGESTE allelic input file.factors.txtGESTE factors input file.Demographic_data.txtLong term population size of individual Silene latifolia populations.
DOI: 10.5061/dryad.732d5
title: Data from: Color-biased dispersal inferred by fine-scale genetic spatial autocorrelation in a color polymorphic salamander

description: Behavioral traits can be influenced by predation rates of color morphs,
 potentially leading to reduced boldness or increased escape behaviors in
 one color morph. The red-backed salamander, Plethodon cinereus, is a small
 terrestrial salamander whose color morphs have different diets and select
 different microhabitats, but little is known about potential differences
 in dispersal behaviors. We used fine-scale genetic spatial autocorrelation
 to examine 122 P. cinereus in a color-polymorphic population at ten
 microsatellite loci in order to generate estimates of spatial genetic
 structure for each color morph. Differences in spatial genetic structure
 have been used extensively to infer within-population sex-biased dispersal
 but have never been used to test for dispersal differences between other
 groups within populations such as color morphs. We found evidence for
 color-biased dispersal, but not sex-biased dispersal. Striped salamanders
 had significant positive genetic structure in the shortest distance
 classes indicating philopatry. In contrast, unstriped salamanders showed a
 lack of spatial genetic structure at shorter distances and higher than
 expected genetic similarity at further distances, as expected if they are
 dispersing from their natal site. These results show that genetic methods
 typically used for sex-biased dispersal can be used to investigate
 differences in dispersal between morphs that vary discretely in
 polymorphic populations, such as color morphs.
description: Genetic and spatial data
 for Grant and Liebgold 2017This file has the
 microsatellite scores and the x,y spatial locations of the salamanders
 (Plethodon cinereus) used in the analyses of Grant and Liebgold
 2017.