cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v7r0b
title: Data from: Cline coupling and uncoupling in a stickleback hybrid zone

description: Strong ecological selection on a genetic locus can maintain allele
 frequency differences between populations in different environments, even
 in the face of hybridization. When alleles at divergent loci come into
 tight linkage disequilibrium, selection acts on them as a unit and can
 significantly reduce gene flow. For populations interbreeding across a
 hybrid zone, linkage disequilibria between loci can force clines to share
 the same slopes and centers. However, strong ecological selection on a
 locus can also pull its cline away from the others, reducing linkage
 disequilibrium and weakening the barrier to gene flow. We looked for this
 ‘cline uncoupling’ effect in a hybrid zone between stream resident and
 anadromous sticklebacks at two genes known to be under divergent natural
 selection (Eda and ATP1a1) and five morphological traits that repeatedly
 evolve in freshwater stickleback. These clines were all steep and located
 together at the top of the estuary, such that we found no evidence for
 cline uncoupling. However, we did not observe the stepped shape normally
 associated with steep concordant clines. It thus remains possible that
 these clines cluster together because their individual selection regimes
 are identical, but this would be very surprising given their diverse roles
 in osmoregulation, body armor and swimming performance.
description: SNP
 dataThe raw SNP data for the
 15 genetic lociBonsall_Morph_Gen_dataA csv file containing the morphological and SNP data for all individualsCFit Input fileAn example CFit7 input file for the CFit analysesVines et al Evolution R codeThe R code for the parts of the analysis that were carried out in R, and the code for making the figures.Vines et al Bonsall Creek AnalysisAn Excel spreadsheet containing preliminary analysis for the genetic dataVines et al Bonsall Creek ReadmeA readme for the Vines et al Bonsall Creek data files
DOI: 10.5061/dryad.d6q7q72g
title: Data from: Gentle Africanized bees on an oceanic island

description: Oceanic islands have reduced resources and natural enemies and potentially
 affect life history traits of arriving organisms. Among the most
 spectacular invasions in the Western hemisphere is that of the Africanized
 honey bee. We hypothesized that in the oceanic island Puerto Rico
 Africanized bees will exhibit differences from the mainland population
 such as for defensiveness and other linked traits. We evaluated the extent
 of Africanization through three typical Africanized traits: wing size,
 defensive behavior, and resistance to Varroa destructor mites. All sampled
 colonies were Africanized by maternal descent, with over 65% presence of
 European alleles at the S-3 nuclear locus. In two assays evaluating
 defense, Puerto Rican bees showed low defensiveness similar to European
 bees. In morphology and resistance to mites Africanized bees from Puerto
 Rico are similar to other Africanized bees. In behavioral assays on
 mechanisms of resistance to Varroa, we directly observed that Puerto Rican
 Africanized bees groomed-off and bit the mites as been observed in other
 studies. In no other location Africanized bees have reduced defensiveness
 while retaining typical traits such as wing size and mite resistance. This
 mosaic of traits that has resulted during the invasion of an oceanic
 island has implications for behavior, evolution, and agriculture.
description: Apis vs Native 20 yr
 interval mar 2010DRONE
 DATAWING MORPHOLOGY DATA
 HIGH VARAHB Sample Sizes by
 ArticleDEF DATA for PUB
 ANALYSISHYGENE FROZEN BROOD
 ASSAYVARROA DATA JULY
 4Varroa groom
 intensity
DOI: 10.5061/dryad.hj2j3
title: Data from: New sporopollenin-based β-cyclodextrin functionalized magnetic hybrid adsorbent for magnetic solid-phase extraction of nonsteroidal anti-inflammatory drugs from water samples.

description: A magnetic solid-phase extraction (MSPE) procedure on the newly
 synthesized magnetic β-cyclodextrin functionalized with toluene
 diisocyanate (TDI) as a linker and was further modified with bio-polymeric
 spores of sporopollenin (MSp-TDI-βCD) was developed for the extraction of
 nonsteroidal anti-inflammatory drugs (NSAIDs) namely indoprofen (INP),
 ketoprofen (KTP), ibuprofen (IBP) and fenoprofen (FNP) from water samples
 prior to their HPLC-DAD determination. The newly synthesised MSp-TDI-βCD
 was comprehensibly characterized using FT-IR, XRD, SEM-EDX, BET and VSM
 analyses. The separation of selected NSAIDs on MSp-TDI-βCD from aqueous
 solution was simply achieved by applying an external magnetic field via a
 permanent magnet. The MSPE parameters affecting extraction performance
 i.e., sorbent dosage, sample volume, extraction and desorption time, type
 of organic eluent and volume and solution pH were investigated and
 optimized. The proposed method showed linear range between 0.5 - 500
 ng/mL, low limit of detection at S/N = 3 (0.16 - 0.37 ng/mL) and limit of
 quantification at S/N = 10 (0.53 - 1.22 ng/mL). The interday (n = 15) and
 intraday (n = 5) precision for the proposed methods given by relative
 standard deviation (RSD%) in the range of 2.5 - 4.0 and 2.1 - 5.5
 respectively. The extraction recoveries of NSAIDs from environmental
 samples (tap, drinking and river water) ranged from 92.5 - 123.6%, with
 satisfactory precision (RSD% less than 12.4%).
description: Sharifah Mohamad -
 Dataset
DOI: 10.5061/dryad.6t161c3
title: Data from: Species coexistence through simultaneous fluctuation-dependent mechanisms

description: Understanding the origins and maintenance of biodiversity remains one of
 biology's grand challenges. From theory and observational evidence we
 know that variability in environmental conditions through time is likely
 critical to the coexistence of competing species. Nevertheless, strong
 experimental tests of fluctuation-driven coexistence are rare, and have
 typically focused on just one of two potential mechanisms, the temporal
 storage effect, to the neglect of the theoretically equally plausible
 mechanism known as relatively nonlinearity of competition. We combined
 experiments and simulations in a system of nectar yeasts to quantify the
 relative contribution of the two mechanisms to coexistence. Resource
 competition models parameterized from single-species assays predicted the
 outcomes of mixed-culture competition experiments with 83% accuracy. Model
 simulations revealed that both mechanisms have measurable effects on
 coexistence, and relative nonlinearity can be equal or greater in
 magnitude to the temporal storage effect. In addition, we show that their
 effect on coexistence can be both antagonistic and complementary. These
 results falsify the common assumption that relative nonlinearity is of
 negligible importance, and in doing so reveal the importance of testing
 coexistence mechanisms in combination.
description: dryad-monoculture-growth-expsMonoculture data from 48hr growth experiments used to estimate Monod growth parameters for simulationsdryad-mixed-culture-expsMixed and monoculture experimental data from 24 day competition experiments
DOI: 10.5061/dryad.577q1
title: Data from: Global biogeography of mating system variation in seed plants

description: Latitudinal gradients in biotic interactions have been suggested as causes
 of global patterns of biodiversity and phenotypic variation. Plant
 biologists have long speculated that outcrossing mating systems are more
 common at low than high latitudes owing to a greater predictability of
 plant–pollinator interactions in the tropics; however, these ideas have
 not previously been tested. Here, we present the first global
 biogeographic analysis of plant mating systems based on 624 published
 studies from 492 taxa. We found a weak decline in outcrossing rate towards
 higher latitudes and among some biomes, but no biogeographic patterns in
 the frequency of self-incompatibility. Incorporating life history and
 growth form into biogeographic analyses reduced or eliminated the
 importance of latitude and biome in predicting outcrossing or
 self-incompatibility. Our results suggest that biogeographic patterns in
 mating system are more likely a reflection of the frequency of life forms
 across latitudes rather than the strength of plant–pollinator
 interactions.
description: Database with
 biogeographic and mating system informationThe datafile contains
 all of the data on biogeography and outcrossing rates. The column heading
 definitions are as follows: year: Year in which the study was published
 reference: Reference containing estimates of outcrossing rate family:
 Plant family name of the species studied genus: Genus-level name of the
 species studied species: species-level name of the species studied m.d.g:
 Broad taxonomic category; m = monocot, d = dicot, g = gymnosperm latitude:
 Degree of latitude (range from 0 – 90) for the population in which
 outcrossing rate was measured. If multiple populations were studied for a
 given species this value is the average of the population-level latitudes.
 Latitudes are expressed as decimal degrees and the absolute value from the
 equator. hemisphere: N = northern hemisphere; S = southern hemisphere
 biome: Biome categories ordered by net ecosystem productivity: 1 =
 Desert/arid scrub; 2 = Temperate grasslands; 3 = Shrubland/chaparral; 4 =
 Taiga; 5 = Tropical savannah; 6 = Temperate deciduous forest and
 rainforest; 7 = Tropical seasonal forest; 8 = Tropical rainforest growth:
 Growth form categories: 1 = Herbaceous; 2 = Vine; 3 = Schrub; 4 = Tree; 5
 = Varies life.history: Life history categories: 1 = Annual; 2 = Biennial;
 3 = Semelparous perennial; 4 = Iteroparous perennial; 5 = Varies si: 0 =
 Self-incompatible; 1 = Self-compatible mean.tm: Outcrossing rate. If
 multiple populations were studied for a given species this value is the
 average of the population-level outcrossing rates. References: A list of
 references used to gather biological data on species.Database_BioGeo_mating.csv
DOI: 10.5061/dryad.78p90
title: Data from: Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

description: Whole genome sequencing is helping generate robust phylogenetic hypotheses
 for a range of taxonomic groups that were previously recalcitrant to
 classical molecular phylogenetic approaches. As a case study, we performed
 a shallow shotgun sequencing of eight species in the tropical tree family
 Chrysobalanaceae to retrieve large fragments of high-copy number DNA
 regions and test the potential of these regions for phylogeny
 reconstruction. We were able to assemble the nuclear ribosomal cluster
 (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the
 mitochondrial genome (mtDNA) with approximately 1000x, 450x and 120x
 sequencing depth respectively. The phylogenetic tree obtained with ptDNA
 resolved five of the seven internal nodes. In contrast, the tree obtained
 with mtDNA and nrDNA data were largely unresolved. This study demonstrates
 that genome skimming is a cost-effective approach and shows potential in
 plant molecular systematics within Chrysobalanaceae and other understudied
 groups.
description: script_chloroUNIX script used for plastid reconstruction. The following tools must be installed: VELVET, PLAST, COPE, OBITOOLSscript_plastid.txtalignmentsPlastid DNA, mitochondrial DNA and nuclear ribosomic regions alignments, including the complete sequences or the non-intronic transcribed sequences only. Alignments were performed using MAFFT and cleaned using Gblocks. Files are in fasta format.treesTrees obtained with plastid DNA, mitochondrial DNA and nuclear ribosomic regions alignments, including the complete sequences or the non-intronic transcribed sequences only, using RAxML and MrBayes. Files are in NEXUS format.chrysobalanaceae_phylogenomic_trees(1).rar
DOI: 10.5061/dryad.6qf10
title: Data from: Latitudinal and altitudinal patterns of plant community diversity on mountain summits across the tropical Andes

description: The high tropical Andes host one of the richest alpine floras of the
 world, with exceptionally high levels of endemism and turnover rates. Yet,
 little is known about the patterns and processes that structure
 altitudinal and latitudinal variation in plant community diversity. Herein
 we present the first continental-scale comparative study of plant
 community diversity on summits of the tropical Andes. Data were obtained
 from 792 permanent vegetation plots (1m2) within 50 summits, distributed
 along a 4200 km transect; summit elevations ranged between 3220 and 5498
 m.a.s.l. We analyzed the plant community data to assess: (1) differences
 in species abundance patterns in summits across the region, (2) the role
 of geographic distance in explaining floristic similarity, and (3) the
 importance of altitudinal and latitudinal environmental gradients in
 explaining plant community composition and richness. On the basis of
 species abundance patterns, our summit communities were separated into two
 major groups: Puna and Páramo. Floristic similarity declined with
 increasing geographic distance between study-sites, the correlation being
 stronger in the more insular Páramo than in the Puna (corresponding to
 higher species turnover rates within the Páramo). Ordination analysis
 (CCA) showed that precipitation, maximum temperature and rock cover were
 the strongest predictors of community similarity across all summits.
 Generalized Linear Model (GLM) quasi-Poisson regression indicated that
 across all summits species richness increased with maximum air temperature
 and above-ground necromass and decreased on summits where scree was the
 dominant substrate. Our results point to different environmental variables
 as key factors for explaining vertical and latitudinal species turnover
 and species richness patterns on high Andean summits, offering a powerful
 tool to detect contrasting latitudinal and altitudinal effects of climate
 change across the tropical Andes.
description: Cuesta_etal_Gloria_Baseline-data_12.11.2016Vegetation baseline data from 13 GLORIA-Andes long-term monitoring sites. The file contains: (1) a matrix of the average cover of each vascular plant species, averaged over the sixteen 1x1 m quadrats in each of the 50 summits, (2) environmental matrix that containes fine and broad-scale habitat variables for each summit, (3) A species richness matrix that contains the total number of species found in the sixteen quadrats established in each summit, and (4) a species richness matrix at the site scale
DOI: 10.5061/dryad.t8p51
title: Data from: Chimpanzee fathers bias their behaviour towards their offspring

description: Promiscuous mating was traditionally thought to curtail paternal
 investment owing to the potential costs of providing care to unrelated
 infants. However, mounting evidence suggests that males in some
 promiscuous species can recognize offspring. In primates, evidence for
 paternal care exists in promiscuous Cercopithecines, but less is known
 about these patterns in other taxa. Here, we examine two hypotheses for
 paternal associations with lactating mothers in eastern chimpanzees (Pan
 troglodytes schweinfurthii): paternal effort, whereby males associate and
 interact more with their own infants, and mating effort, whereby males
 invest in mothers and offspring for mating privileges. We found that
 fathers associated more with their offspring than they did with non-kin
 infants, particularly early in life when infanticide risk is highest.
 Additionally, fathers and their infant offspring interacted more than
 expected. Notably, association between fathers and mother–infant pairs did
 not predict the probability of siring the mother's next offspring.
 Our results support the paternal effort, but not the mating effort
 hypothesis in this species. Chimpanzees are one of the most salient models
 for the last common ancestor between Pan and Homo, thus our results
 suggest that a capacity for paternal care, possibly independent of
 long-term mother–father bonds, existed early in hominin evolution.
description: Male - MI pair
 Associations for Within Period AnalysisWithinPeriodAnalysisTableForDryad.csvMale - MI pair Associations for Between Period AnalysisBetweenPeriodAnalysisTableForDryad.csvInfant - Adult Male Dyadic Interaction RatesInteractionsAnalysisTableForDryad.csv
DOI: 10.5061/dryad.bs515
title: Data from: Neonicotinoid insecticides can serve as inadvertent insect contraceptives

description: There is clear evidence for sublethal effects of neonicotinoid
 insecticides on non-target ecosystem service-providing insects. However,
 their possible impact on male insect reproduction is currently unknown,
 despite the key role of sex. Here, we show that two neonicotinoids (4.5
 ppb thiamethoxam and 1.5 ppb clothianidin) significantly reduce the
 reproductive capacity of male honeybees (drones), Apis mellifera. Drones
 were obtained from colonies exposed to the neonicotinoid insecticides or
 controls, and subsequently maintained in laboratory cages until they
 reached sexual maturity. While no significant effects were observed for
 male teneral (newly emerged adult) body mass and sperm quantity, the data
 clearly showed reduced drone lifespan, as well as reduced sperm viability
 (percentage living versus dead) and living sperm quantity by 39%. Our
 results demonstrate for the first time that neonicotinoid insecticides can
 negatively affect male insect reproductive capacity, and provide a
 possible mechanistic explanation for managed honeybee queen failure and
 wild insect pollinator decline. The widespread prophylactic use of
 neonicotinoids may have previously overlooked inadvertent contraceptive
 effects on non-target insects, thereby limiting conservation efforts.
description: Straub_et_al_Drone_Pesticide_Complete_DataComplete data used within the study 'Neonicotinoid insecticides serve as inadvertent insect contraceptives'
DOI: 10.5061/dryad.qk746
title: Data from: Dispersal and selection mediate hybridization between a native and invasive species

description: Hybridization between native and non-native species has serious biological
 consequences, but our understanding of how dispersal and selection
 interact to influence invasive hybridization is limited. Here, we document
 the spread of genetic introgression between a native (Oncorhynchus
 clarkii) and invasive (Oncorhynchus mykiss) trout, and identify the
 mechanisms influencing genetic admixture. In two populations inhabiting
 contrasting environments, non-native admixture increased rapidly from 1984
 to 2007 and was driven by surprisingly consistent processes. Individual
 admixture was related to two phenotypic traits associated with fitness:
 size at spawning and age of juvenile emigration. Fish with higher
 non-native admixture were larger and tended to emigrate at a younger
 age―relationships that are expected to confer fitness advantages to hybrid
 individuals. However, strong selection against non-native admixture was
 evident across streams and cohorts (mean selection coefficient against
 genotypes with non-native alleles (s) = 0.60; s.e. = 0.10). Nevertheless,
 hybridization was promoted in both streams by the continuous immigration
 of individuals with high levels of non-native admixture from other hybrid
 source populations. Thus, antagonistic relationships between dispersal and
 selection are mediating invasive hybridization between these fish,
 emphasizing that data on dispersal and natural selection are needed to
 fully understand the dynamics of introgression between native and
 non-native species.
description: Kovach_etal_WCTRBT_hybridizationThe excel file contains the genotypic data for all individual trout (Oncorhynchus) that were sampled from 2003 - 2007. Fish were genotyped at 8 species diagnostic microsatellite loci. Columns D-S are the raw allele lengths, while columns T - AI describe whether each allele at each locus is of westslope cutthroat trout ancestry (denoted by 0) or rainbow trout ancestry (denoted by 1). Other descriptive columns include individual ID, maturity (spawning adult or outmigrating juvenile), date captured (i.e., migration date), length (in mm), and age (for Langford juveniles only). Data for Langford and Cyclone are on two separate sheets.Kovach_etal_WCT:RBT_hybridization.xlsx
DOI: 10.5061/dryad.2r3f2
title: Data from: Deep genetic structure and ecological divergence in a widespread human commensal toad

description: The Asian common toad (Duttaphrynus melanostictus) is a human commensal
 species that occupies a wide variety of habitats across tropical Southeast
 Asia. We test the hypothesis that genetic variation in D. melanostictus is
 weakly associated with geography owing to natural and human-mediated
 dispersal facilitated by its commensal nature. Phylogenetic and population
 genetic analyses of mitochondrial and nuclear DNA sequence variation, and
 predictive species distribution modelling, unexpectedly recovered three
 distinct evolutionary lineages that differ genetically and ecologically,
 corresponding to the Asian mainland, coastal Myanmar and the Sundaic
 islands. The persistence of these three divergent lineages, despite ample
 opportunities for recent human-mediated and geological dispersal, suggests
 that D. melanostictus actually consists of multiple species, each having
 narrower geographical ranges and ecological niches, and higher
 conservation value, than is currently recognized. These findings also have
 implications for the invasion potential of this human commensal elsewhere,
 such as in its recently introduced ranges on the islands of Borneo,
 Sulawesi, Seram and Madagascar.
description: Dmelanostictus_WoganetalBioLettersnexus file of 3 concatenated genes
DOI: 10.5061/dryad.1dj62
title: Data from: No early warning signals for stochastic transitions: insights from large deviation theory

description: [No abstract entered]
description: Code to replicate the
 analysis and generate Figure 1A dynamic document for
 running the analysis and generating the data and graphs shown in Figure 1.
 After installing the packages indicated, this code can be run by
 copy-pasting the code blocks into any R terminal, or compiled at once by
 running `knit("Figure1.Rmd")` in the R terminal using the knitr
 package.Figure1.RmdData from: No early warning signals for stochastic transitions: insights from large deviation theoryA csv file containing the raw data shown in Figure 1. This data can also be re-generated using the code provided in the dynamic documentation file (Figure1.Rmd)Figure1.csv