cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8nc8480
title: Data from: Fires in protected areas reveal unforeseen costs of Colombian peace

description: Armed conflict, and its end, can have powerful effects on natural
 resources, but the influence of war and peace on highly biodiverse
 tropical forests remains disputed. We found a sixfold increase in fires in
 protected areas across biodiversity hotspots following guerrilla
 demobilization in Colombia, and a 52% increase in the probability of
 per-pixel deforestation within parks for 2018. Peace requires urgent
 shifts to include real-time forest monitoring, expand programmes to pay
 for ecosystem services at the frontier, integrate demobilized armed groups
 as staff of protected areas, and establish a domestic market for frontier
 deforestation permits.
description: R code for Fires in
 Protected Areas Reveal Unforeseen Costs of Colombian
 Peacefires.RR script to compare models to forest losscompare2LandSat.RR code for Fires in Protected Areas Reveal Unforeseen Costs of Colombian Peaceparks.RR Code to plot Figure in Fires in Protected Areas Reveal Unforeseen Costs of Colombian Peaceplot_figure.RData setFire densities per year inside, within 5-km buffer zone from the protected area limit and outsidetime.csvMODIS Active Fire Detections for January and February 2017MODIS Collection 6 NRT Hotspot / Active Fire Detections MCD14DL for January and February 2017 for Colombia with information on the distance to the nearest protected area and location within FARC 2013 territory for each detected hotspotfires_year_2017.zipMODIS Active Fire Detections for January and February 2018MODIS Collection 6 NRT Hotspot / Active Fire Detections MCD14DL for January and February 2018 for Colombia with information on the distance to the nearest protected area and location within FARC 2013 territory for each detected hotspotfires_year_2018.zip
DOI: 10.5061/dryad.fn4cj0d
title: Data from: Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska

description: Understanding the genetic mechanisms that facilitate adaptive radiation is
 an important component of evolutionary biology. Here, we genotyped 82
 neutral SNPs, seven SNPs in islands of divergence identified in a previous
 study (island SNPs), and a region of the major histocompatibility complex
 (MHC) in 32 populations of sockeye salmon to investigate whether conserved
 genes and genomic regions are involved in adaptive radiation. Populations
 representing three ecotypes were sampled from seven drainages with
 differing habitats and colonization histories spanning a range of 2,000
 km. We found strong signatures of parallel selection across drainages at
 the island SNPs and MHC, suggesting that the same loci undergo divergent
 selection during adaptive radiation. However, patterns of differentiation
 at most island SNPs and the MHC were not associated with ecotypes,
 suggesting that these loci are responding differently to a mosaic of
 selective pressures. Our study provides some of the first evidence that
 conserved genomic islands may be involved in adaptive divergence of salmon
 populations. Additionally, our data provide further support for the
 hypothesis that sockeye salmon inhabiting rivers unconnected to lakes
 harbor similar genetic diversity across large distances, are likely the
 ancestral form of the species, and have repeatedly recolonized lake
 systems as they have become available after glacial recession. Finally,
 our results highlight the value and importance of validating outlier loci
 by screening additional populations and regions, a practice that will
 hopefully become more common in the future.
description: SNP
 genotypesGenotypes from 7 island
 SNPs and 89 previously developed SNPs including some found to be outliers
 that were removed from further analyses. Information on which SNPs were
 retained to form the neutral dataset is found in Table S5. Information on
 population abbreviations found in dryad file "population
 info."full_snp_genotypes_no_filters.txtMHC genotypesMHC genotypes. Numbers correspond to haplotype numbers in Table S3. Population information can be found in the "population information" filemhc_genotypes.txtPopulation InformationPopulation information with abbreviations used in genotype files.pop_info_with_abbreviations.xlsx
DOI: 10.5061/dryad.87hm1
title: Data from: Market forces influence helping behaviour in cooperatively breeding paper wasps

description: Biological market theory is potentially useful for understanding helping
 behaviour in animal societies. It predicts that competition for trading
 partners will affect the value of commodities exchanged. It has gained
 empirical support in cooperative breeders, where subordinates help
 dominant breeders in exchange for group membership, but so far without
 considering one crucial aspect: outside options. We find support for the
 existence of a biological market in paper wasps, Polistes dominula. We
 first show that females have a choice of cooperative partners. Second, by
 manipulating entire subpopulations in the field, we increased the supply
 of outside options for subordinates, freeing up suitable nesting spots and
 providing additional nesting partners. We predicted that by intensifying
 competition for help, our manipulation would force dominants to accept a
 lower price for group membership. As expected, subordinates reduced their
 foraging effort following our treatments. We conclude that to accurately
 predict the amount of help provided, social units cannot be viewed in
 isolation as has traditionally been done: the surrounding market must also
 be considered.
description: Partner Choice
 ExperimentData from the Partner
 Choice experimentMarket Manipulation main
 dataMain data (information
 about individual wasps and nests before and after treatment) from the
 Market Manipulation experimentMarket Manipulation
 relatedness dataGenetic relatedness data
 (at the individual level and at nest level) from the Market Manipulation
 experimentMarket Manipulation
 video dataVideo data (food
 returns, foraging time and aggression) before and after treatment in the
 Market Manipulation experiment
DOI: 10.5061/dryad.6pv38
title: Data from: A tilt after-effect for images of buildings: evidence of selectivity for the orientation of everyday scenes

description: The tilt after-effect (TAE) is thought to be a manifestation of gain
 control in mechanisms selective for spatial orientation in visual stimuli.
 It has been demonstrated with luminance-defined stripes, contrast-defined
 stripes, orientation-defined stripes and even with natural images. Of
 course, all images can be decomposed into a sum of stripes, so it should
 not be surprising to find a TAE when adapting and test images contain
 stripes that differ by 15° or so. We show this latter condition is not
 necessary for the TAE with natural images: adaptation to slightly tilted
 and vertically filtered houses produced a ‘repulsive’ bias in the
 perceived orientation of horizontally filtered houses. These results
 suggest gain control in mechanisms selective for spatial orientation in
 natural images.
description: Ismail et
 al(2016)-PROSRaw Data files have been
 organized by unique initials of each observer who participated in the
 study (eg., 'AM'). Some observers participated in more than one
 test condition. Each Excel file corresponds to one unique observer. Each
 work-sheet within an Excel file corresponds to data from one test
 condition (eg., 'same house'). Within each work-sheet data for
 all 3 test blocks (baseline, CW adaptor and CCW adaptor) are given. For a
 given test block: Column 1: trial number Column 2: tilt of the
 'pedestal' test stimulus (in degrees) Column 3: tilt of the
 'comparison' test stimulus (in degrees) Column 4: spatial
 position of the 'pedestal' test (1 - left of fixation, 2 - right
 of fixation) Column 5: observer's response (97 - if the test stimulus
 to the left of fixation was chosen as appearing more upright or 98 - if
 the test stimulus to the right of fixation was chosen as appearing more
 upright) Note: For tilts of the 'pedestal' and
 'comparison' test stimuli, positive tilts represent CCW
 rotations in the fronto-parallel plane and negative tilts represent CW
 rotations in the fronto-parallel plane.
DOI: 10.5061/dryad.k42dg
title: Data from: Postglacial climate changes and rise of three ecotypes of harbor porpoises, Phocoena phocoena, in western Palearctic waters

description: Despite no obvious barriers to gene flow in the marine realm,
 environmental variation and ecological specializations can lead to genetic
 differentiation in highly mobile predators. Here, we investigated the
 genetic structure of the harbor porpoise over the entire species
 distribution range in western Palearctic waters. Combined analyses of ten
 microsatellite loci and a 5,085 bases-pairs portion of the mitochondrial
 genome revealed the existence of three ecotypes, equally divergent at the
 mitochondrial genome, distributed in the Black Sea, the European
 continental shelf waters, and a previously overlooked ecotype in the
 upwelling zones of Iberia and Mauritania. Historical demographic
 inferences using Approximate Bayesian Computation (ABC) suggest that these
 ecotypes diverged during the Last Glacial Maximum (~23–19 kilo-years ago,
 kyrBP). ABC supports the hypothesis that the Black Sea and upwelling
 ecotypes share a more recent common ancestor (~14 kyrBP) than either does
 with the European continental shelf ecotype (~28 kyrBP), suggesting they
 likely descended from the extinct populations that once inhabited the
 Mediterranean during the glacial and post-glacial period. We showed that
 the two Atlantic ecotypes established a narrow admixture zone in the Bay
 of Biscay during the last millennium, with highly asymmetric gene flow.
 This study highlights the impacts that climate change may have on the
 distribution and speciation process in pelagic predators and shows that
 allopatric divergence can occur in these highly mobile species and be a
 source of genetic diversity.
description: FontaineMCetal_GPOP_SEQconc_DIYABCfinal_bDIY-ABC input file: Genepop format modified to include also sequences (See DIYABC V2 user manual). Data Fontaine et al. Mol. Ecol. 2014 = BMC Biol. 2007 + Mauritanian samples. 5 populations: 1. NAT (516); 2. NBB (124); 3. IB (31); 4 Mauritanie (15); 5. BS (78)). Loci: 10 microsattelites + 5085 bps MtDNA seq.(concatenated seq. ATP6_8_COI_CB_ND5).ATP6_8_COI_CB_ND5dDALLhaploMitochondrial haplotype data file in NEXUS format.
DOI: 10.5061/dryad.cf033
title: Data from: Maternal, social and abiotic environment effects on growth vary across life stages in a cooperative mammal

description: 1. Resource availability plays a key role in driving variation in somatic
 growth and body condition, and the factors determining access to resources
 vary considerably across life stages. Parents and carers may exert
 important influences in early life, when individuals are nutritionally
 dependent, with abiotic environmental effects having stronger influences
 later in development as individuals forage independently. 2. Most studies
 have measured specific factors influencing growth across development, or
 have compared relative influences of different factors within specific
 life stages. Such studies may not capture whether early-life factors
 continue have delayed effects at later stages, or if social factors change
 when individuals become nutritionally independent and adults become
 competitors for, rather than providers of, food. 3. Here, we examined
 variation in the influence of the abiotic, social and maternal environment
 on growth across life stages in a wild population of cooperatively
 breeding meerkats. Cooperatively breeding vertebrates are ideal for
 investigating environmental influences on growth. In addition to
 experiencing highly variable abiotic conditions, cooperative breeders are
 typified by heterogeneity both among breeders, with mothers varying in age
 and social status, and in the number of carers present. 4. Recent rainfall
 had a consistently marked effect on growth across life stages, yet other
 seasonal terms only influenced growth during stages when individuals were
 growing fastest. Group size and maternal dominance status had positive
 effects on growth during the period of nutritional dependence on carers,
 yet did not influence mass at emergence (at one month) or growth at
 independent stages (&gt;4 months). Pups born to older mothers were
 lighter at one month of age, and subsequently grew faster as subadults.
 Males grew faster than females during the juvenile and subadult stage
 only. 5. Our findings demonstrate the complex ways in which the external
 environment influences development in a cooperative mammal. Individuals
 are most sensitive to social and maternal factors during the period of
 nutritional dependence on carers, whereas direct environmental effects are
 relatively more important later in development. Understanding the way in
 which environmental sensitivity varies across life stages is likely to be
 an important consideration in predicting trait responses to environmental
 change.
description: Mass and growth
 measurements for wild meerkats across five lifestagesEnglishetal_DryadData.csv
DOI: 10.5061/dryad.n5d5t
title: Data from: How lizards survived blizzards: phylogeography of the Liolaemus lineomaculatus group (Liolaemidae) reveals multiple breaks and refugia in southern Patagonia, and their concordance with other co-distributed taxa

description: Patagonia was shaped by a complex geological history, including the
 Miocene uplift of the Andes, followed by volcanism, marine introgressions,
 and extreme climatic oscillations during Pleistocene
 glaciation–deglaciation cycles. The distributional patterns and
 phylogenetic relationships of southern patagonian animals and plants were
 affected in different ways, and those imprints are reflected in the seven
 phylogeographic breaks and eight refugia that have been previously
 proposed. In this study we estimated time-calibrated
 phylogenetic/phylogeographic patterns in lizards of the Liolaemus
 lineomaculatus group, and related them to historical
 Miocene-to-Pleistocene events of Patagonia and the previously proposed
 phylogeographic patterns. Individuals from 51 localities were sequenced
 for the mitochondrial marker (cyt-b) and a sub-sample of individuals from
 each mitochondrial lineage was sequenced for one nuclear (LDA12D) and one
 slow evolving mitochondrial gene (12S). Our analyses revealed strong
 phylogeographic structure among lineages and, in most cases, no signal of
 population changes through time. The lineomaculatus group is composed of
 three strongly supported clades (lineomaculatus, hatcheri and
 kolengh+silvanae), and divergence estimates suggested their origins
 associated with the oldest known Patagonian glaciation (7-5 Ma);
 subsequent diversification within the lineomaculatus clade coincided with
 the large Pliocene glaciations (~3.5 Ma). The lineomaculatus clade
 includes nine strongly structured genetically and geographically lineages
 and five of them are interpreted candidate species. Our findings suggest
 that some Liolaemus lineages have persisted in situ in multiple refugia
 through several glaciation-deglaciation cycles in southern Patagonia
 without demographic fluctuations. We also provide qualitative evidence of
 some shared phylogeographic breaks and refugia among plants, rodents, and
 lizards.
description: 1- All
 cytb2- cytb
 haplotypesAlignment of all
 cytochrome b haplotypes used in the study.3- cytb for
 calibrationCytochrome b alignment
 used for calibration.4- 12S for
 calibration5- LDA12D for
 calibrationAlignment of LDA12D for
 calibration.6- 12S tree
 MB12s
 gene tree recovered using Mr Bayes program.7- arbolito LDA12D
 MBLDA12D gene tree
 recovered using Mr Bayes program
DOI: 10.5061/dryad.52b22
title: Data from: Shifts in outcrossing rates and changes to floral traits are associated with the evolution of herbicide resistance in the common morning glory

description: Human-mediated selection can strongly influence the evolutionary response
 of natural organisms within ecological timescales. But what traits allow
 for, or even facilitate, adaptation to the strong selection humans impose
 on natural systems? Using a combination of laboratory and greenhouse
 studies of 32 natural populations of the common agricultural weed, Ipomoea
 purpurea, we show that herbicide-resistant populations self-fertilise more
 than susceptible populations. We likewise show that anther–stigma
 distance, a floral trait associated with self-fertilisation in this
 species, exhibits a nonlinear relationship with resistance such that the
 most and least resistant populations exhibit lower anther–stigma
 separation compared to populations with moderate levels of resistance.
 Overall, our results extend the general finding that plant mating can be
 impacted by human-mediated agents of selection to that of the extreme
 selection of the agricultural system. This work highlights the influence
 of human-mediated selection on rapid responses of natural populations that
 can lead to unexpected long-term evolutionary consequences.
description: Spatial and Temporal
 Floral PhenotypesThis data file contains
 floral phenotypic data for populations sampled in 2012 and 2003. The
 spatial analysis uses only data from 2012. The 'temporal' label
 (1) indicates if populations were paired between 2003 and
 2012.SpatiallandTemporalFloral.csvLatitudeLatitudes for each population.Lat.csvResistance levels for each populationResistance is defined as the proportion of the population remaining alive post-herbicide application. More information can be found in Kuester et al (2015) Evolutionary Applications.ResLevelQuan.csvMating System Genotypes 2012Genotypes used to estimate mating system from the 2012 sampling of populations.MatingSystemGenotypes2012.csvR CodeR Code in markdown format.KuesterELE-2016.Rmd
DOI: 10.5061/dryad.482q2rh
title: Data from: Magnetoliposomes containing magnesium ferrite nanoparticles as nanocarriers for the model drug curcumin

description: Magnesium ferrite nanoparticles, with diameters around 25 nm, were
 synthesized by coprecipitation method. The magnetic properties indicate a
 superparamagnetic behavior, with a maximum magnetization of 16.2 emu/g, a
 coercive field of 22.1 Oe and a blocking temperature of 183.2 K. These
 MgFe2O4 nanoparticles were used to produce aqueous and solid
 magnetoliposomes, with sizes below 130 nm. The potential drug curcumin was
 successfully incorporated in these nanosystems, with high encapsulation
 efficiencies (above 89%). Interaction by fusion between both types of drug
 loaded magnetoliposomes (with or without PEGylation) and models of
 biological membranes was demonstrated, using FRET or fluorescence
 quenching assays. These results point to future applications of
 magnetoliposomes containing MgFe2O4 nanoparticles in cancer therapy,
 allowing combined magnetic hyperthermia and chemotherapy.
description: Data supporting Table
 1_SQUID measurementsExperimental results of
 SQUID measurements supporting data in Table 1 - Magnetic properties of
 magnesium ferrite nanoparticlesCurcumin emission using
 polarized light_Table 2Fluorescence spectra
 obtained using polarized light for curcumin fluorescence steady-state
 anisotropy determination. Data supporting Table 2 - Anisotropy of curcumin
 in the several nanosystems.Data_Supporting_Table3_EE%Experimental measurements of curcumin fluorescence emission spectra for determination of encapsulation efficiencies. Data supporting Table 3
DOI: 10.5061/dryad.jt18m
title: Data from: Hiding in plain sight: Koshicola spirodelophila gen. et sp. nov. (Chaetopeltidales, Chlorophyceae), a novel green alga associated with the aquatic angiosperm Spirodela polyrhiza

description: Premise of the study: Discovery and morphological characterization of a
 novel epiphytic aquatic green alga increases our understanding of
 Chaetopeltidales, a poorly known order in Chlorophyceae. Chloroplast
 genomic data from this taxon reveals an unusual architecture previously
 unknown in green algae. Methods: Using light and electron microscopy, we
 characterized the morphology and ultrastructure of a novel taxon of green
 algae. Bayesian phylogenetic analyses of nuclear and plastid genes were
 used to test the hypothesized membership of this taxon in order
 Chaetopeltidales. With next-generation sequence data, we assembled the
 plastid genome of this novel taxon and compared its gene content and
 architecture to that of related species to further investigate plastid
 genome traits. Key results: The morphology and ultrastructure of this alga
 are consistent with placement in Chaetopeltidales (Chlorophyceae), but a
 distinct trait combination supports recognition of this alga as a new
 genus and species—Koshicola spirodelophila gen. et sp. nov. Its placement
 in the phylogeny as a descendant of a deep division in the
 Chaetopeltidales is supported by analysis of molecular data sets. The
 chloroplast genome is among the largest reported in green algae and the
 genes are distributed on three large (rather than a single) chromosome, in
 contrast to other studied green algae. Conclusions: The discovery of
 Koshicola spirodelophila gen. et sp. nov. highlights the importance of
 investigating even commonplace habitats to explore new microalgal
 diversity. This work expands our understanding of the morphological and
 chloroplast genomic features of green algae, and in particular those of
 the poorly studied Chaetopeltidales.
description: DNA sequence alignments
 and Python scripts for performing analysesNucleotide alignments of
 individual chloroplast genes. Python scripts for removal of masked sites.
 Deploy scripts for producing concatenated data set from individual
 genes.Watanabe.et.al.Koshicola.DATA.zip
DOI: 10.5061/dryad.150v8g3
title: Data from: Crossmodal congruency effect scores decrease with repeat test exposure

description: The incorporation of feedback into a person’s body schema is well
 established. The crossmodal congruency effect (CCE) task is used to
 objectively quantify incorporation without being susceptible to
 experimenter biases. This visual-tactile interference task is used to
 calculate the CCE score as a difference in response time for incongruent
 and congruent trials. Here we show that this metric is susceptible to a
 learning effect that causes attenuation of the CCE score due to repeated
 task exposure sessions. We demonstrate that this learning effect is
 persistent, even after a 6 month hiatus in testing. Two mitigation
 strategies are proposed: 1. Only use CCE scores that are taken after
 learning has stabilized, or 2. Use a modified CCE protocol that decreases
 the task exposure time. We show that the modified and shortened CCE
 protocol, which may be required to meet time or logistical constraints in
 laboratory or clinical settings, reduced the impact of the learning effect
 on CCE results. Importantly, the CCE scores from the modified protocol
 were not significantly more variable than results obtained with the
 original protocol. This study highlights the importance of considering
 exposure time to the CCE task when designing experiments and suggests two
 mitigation strategies to improve the utility of this psychophysical
 assessment.
description: CCE data with repeat
 exposuresData from three
 experiments: 1. 12 subjects with five consecutive days of CCE testing. 2.
 8 subjects with five consecutive days of CCE testing plus a 6th test that
 occurred 6 months later. 3. 18 subjects with two consecutive days of CCE
 testing, half with 8 block protocol and the other half with a 4 block
 protocol. Summary and raw data are included.Gill2018Dataset.zip