cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.80m5b
title: Data from: ABC inference of multi-population divergence with admixture from unphased population genomic data

description: Rapidly developing sequencing technologies and declining costs have made
 it possible to collect genome-scale data from population-level samples in
 non-model systems. Inferential tools for historical demography given these
 datasets are, at present, underdeveloped. In particular, approximate
 Bayesian computation (ABC) has yet to be widely embraced by researchers
 generating these data. Here, we demonstrate the promise of ABC for
 analysis of the large datasets that are now attainable from non-model taxa
 through current genomic sequencing technologies. We develop and test an
 ABC framework for model selection and parameter estimation given histories
 of three-population divergence with admixture. We then explore different
 sampling regimes to illustrate how sampling more loci, longer loci, or
 more individuals affects the quality of model selection and parameter
 estimation in this ABC framework. Our results show that inferences
 improved substantially with increases in the number and/or length of
 sequenced loci, while less benefit was gained by sampling large numbers of
 individuals. Optimal sampling strategies given our inferential models
 included at least 2000 loci, each approximately 2kb in length, sampled
 from five diploid individuals per population, although specific strategies
 are model- and question-dependent. We tested our ABC approach through
 simulation-based cross-validations and illustrate its application using
 previously analyzed data from the oak gall wasp, Biorhiza pallida.
description: Analysis scripts from
 simulation studyThe contents of this
 zipped file include i) the cross-validation scripts for assessing the
 model selection performance (modCV scripts), and ii) the PODS analysis
 scripts for assessing parameter estimation (POD
 scripts).analysis-scripts.zipSimulation scripts for reference table generationThis zipped archive file contains the 14 R scripts used to simulate data for the simulation study portion of our manuscript. Each script corresponds to one sampling scheme, but all share the same structure and code. The first few lines of the script (ll. 15-17) set the length of loci in the dataset ('size' scripts vary this by scaling theta), the number of individuals sampled ('ind' scripts vary this), and the number of loci sampled ('block' scripts vary this).simulation-scripts.zipScripts for empirical application to B. pallida dataThe R scripts in this file were used to simulate data for the Biorhiza pallida analysis.Bpal-scripts.zipLines used to simulate models in msABCThis text file gives the basic msABC (Pavlidis et al. 2010) lines used to simulate data under the 7 models considered in our study, using parameter/variable names instead of values in the command line code.ms-lines.txt
DOI: 10.5061/dryad.8698
title: Data from: Experimental evidence for genetic heritability of maternal hormone transfer to offspring

description: In many animal species, embryos are exposed to maternal hormones that
 affect their development. Maternal hormone transfer varies with
 environmental conditions of the mother and is often interpreted as being
 shaped by natural selection to adjust the offspring to prevailing
 environmental conditions. Such hormone transfer requires genetic
 variability which has not yet been experimentally demonstrated. Our study
 reports direct evidence for additive genetic variance of maternal
 androgens through a bi-directional selection on yolk testosterone (T)
 levels in Japanese quail. Lines selected for high (HET) and low (LET) egg
 T concentration differed in yolk levels of this androgen resulting in high
 realised heritability (h2 = 0.42). Correlated responses to selection on
 other gonadal hormones indicate that selection specifically targeted
 biological active androgens. Eggs of HET quail contained higher
 androstenedione and lower estradiol concentrations than those of LET
 quail, with no line differences in yolk progesterone. Plasma T
 concentrations of adult females were not affected by selection, seriously
 challenging the hypothesis that transfer of maternal hormones to offspring
 is constrained by hormone levels in a mother's circulation. Our
 results suggest that transfer of maternal T represents an indirect genetic
 effect with important consequences for the evolution of traits in
 offspring.
description: F0_generationEgg characteristics in randomly-bred line of japanese quailF1_generationEgg characteristics in F1 generation of high and low egg testosterone linesF2_generationEgg characteristics in F2 generation of high and low egg testosterone linesF3_generationEgg characteristics in F3 generation of high and low egg testosterone linesPlasma_TestosteronePlasma testosterone levels in females of F2 generation of low and high egg testosterone lines
DOI: 10.5061/dryad.6c4k28q
title: Data from: Quantification and decomposition of environment-selection relationships

description: In nature, selection varies across time in most environments, but we lack
 an understanding of how specific ecological changes drive this variation.
 Ecological factors can alter phenotypic selection coefficients through
 changes in trait distributions or individual mean fitness, even when the
 trait-absolute fitness relationship remains constant. We apply and extend
 a regression-based approach in a population of Soay sheep (Ovis aries) and
 suggest metrics of environment-selection relationships that can be
 compared across studies. We then introduce a novel method which constructs
 an environmentally-structured fitness function. This allows calculation of
 full (as in existing approaches) and partial (acting separately through
 the absolute fitness function slope, mean fitness, and phenotype
 distribution) sensitivities of selection to an ecological variable. Both
 approaches show positive overall effects of density on viability selection
 of lamb mass. However, the second approach demonstrates that this
 relationship is largely driven by effects of density on mean fitness,
 rather than on the trait-fitness relationship slope. If such mechanisms of
 environmental dependence of selection are common, this could have
 important implications regarding the frequency of fluctuating selection,
 and how previous selection inferences relate to longer-term evolutionary
 dynamics.
description: survivaldata.csv
DOI: 10.5061/dryad.m7d12
title: Data from: The influence of herbivores on primary producers can vary spatially and interact with disturbance

description: Identifying the major drivers of ecosystem change remains a central area
 of ecological research. Although top–down drivers of change have received
 particular focus, we still have little understanding of how consistently
 these factors control an ecosystem's shift in both directions,
 between different ecosystem states. Using a crossed experiment in a
 shallow embayment in southeastern Australia, we investigated the roles of
 disturbance (kelp removal) and sea urchin herbivory (via increased
 density) to determine their contributions to shifts away from a
 kelp-dominated community. In a second experiment, done in urchin barren
 areas at two sites, we tested whether reductions in ambient sea urchin
 densities allowed an algal shift in the reverse direction. In both
 experiments, we observed that high densities of sea urchins could
 negatively influence kelp and macroalgal abundance. However, in the kelp
 bed, a moderate or severe disturbance resulted in a comparable algal
 response, irrespective of urchin density. The influence of sea urchins
 also varied dramatically between the two urchin barren sites. Here,
 reducing urchin densities resulted in algal recovery at one site, but at
 the other site, substantial colonisation of barren areas by canopy-forming
 brown algae and Ulvales occurred across all (low, medium, and high) urchin
 density treatments. Our findings illustrate multiple pathways of urchin
 barren creation and algal recovery, and reveal that shifts both to and
 from an urchin barren state can occur irrespective of herbivore pressure.
 These alternate pathways can operate over short spatial distances or with
 different regimes of disturbance.
description: Carnell and Keough Oikos
 2016 The influence of herbivores on primary producers can vary spatially
 and interact with disturbance
DOI: 10.5061/dryad.1455
title: Data from: Exploring the mechanisms underlying a heterozygosity-fitness correlation for canine size in the Antarctic fur seal Arctocephalus gazella

description: Although heterozygosity-fitness correlations (HFCs) are widely reported in
 the literature, most studies use too few markers to allow the proximate
 mechanisms to be convincingly resolved. Two competing hypotheses have been
 proposed: the general effects hypothesis, in which marker heterozygosity
 correlates with genome-wide heterozygosity and hence the inbreeding
 coefficient f, and the local effects hypothesis, in which one or more of
 the markers by chance exhibit associative overdominance. To explore the
 relative contributions of general and local effects in a free-ranging
 marine mammal population, we revisited a strong HFC found using nine
 microsatellite loci for canine tooth size in 84 male Antarctic fur seals
 Arctocephalus gazella (Hoffman et al. 2010). Increasing the number of
 markers to 76, we find that heterozygosity is uncorrelated across markers,
 indicating that inbred individuals are rare or absent. Similarly, while
 the HFC based on overall heterozygosity is lost, stochastic simulations
 indicate that when an HFC is due to inbreeding depression, increasing
 marker number effectively invariably strengthens the HFC. Together these
 observations argue strongly that the original HFC was not due to
 inbreeding depression. In contrast, a subset of markers show individually
 significant effects, and these are non-randomly distributed across the
 marker panel, being preferentially associated with markers cloned from
 other species. Using BLAST searches, we were able to locate 94% of loci to
 unique locations in the dog genome, but the local genes are functionally
 diverse, and the majority cannot be linked directly to growth. Our results
 suggest that inbreeding depression contributes little if at all to the
 relationship between heterozygosity and tooth size, but that instead the
 primary mechanism involves associative overdominance. These findings
 contribute to a growing body of evidence suggesting that general effects
 are likely to be uncommon in natural populations
description: Fur seal
 genotypesMultilocus genotypes of
 84 dead male Antarctic fur sealssupplementary
 datafile.xls
DOI: 10.5061/dryad.40vv8
title: Data from: Landscape-scale variation in an anthropogenic factor shapes immune gene variation within a wild population

description: Understanding the spatial scale at which selection acts upon adaptive
 genetic variation in natural populations is fundamental to our
 understanding of evolutionary ecology, and has important ramifications for
 conservation. The environmental factors to which individuals of a
 population are exposed can vary at fine spatial scales, potentially
 generating localized patterns of adaptation. Here, we compared patterns of
 neutral and major histocompatibility complex (MHC) variation within an
 island population of Berthelot's pipit (Anthus berthelotii) to assess
 whether landscape-level differences in pathogen-mediated selection
 generate fine-scale spatial structuring in these immune genes.
 Specifically, we tested for spatial associations between the distribution
 of avian malaria, and the factors previously shown to influence that
 distribution, and MHC variation within resident individuals. Although we
 found no overall genetic structure across the population for either
 neutral or MHC loci, we did find localized associations between
 environmental factors and MHC variation. One MHC class I allele (ANBE48)
 was directly associated with malaria infection risk, while the presence of
 the ANBE48 and ANBE38 alleles within individuals correlated (positively
 and negatively, respectively) with distance to the nearest poultry farm,
 an anthropogenic factor previously shown to be an important determinant of
 disease distribution in the study population. Our findings highlight the
 importance of considering small spatial scales when studying the patterns
 and processes involved in evolution at adaptive loci.
description: Microsatellite
 genotypesMicrosats.xlsxMHC genotypes by zoneThis file contains the MHC genotypes for 310 Berthelot's pipits divided by zone. There are four zones. The first part of the table shows the frquency of each MHC allele in each of the four geographical zones.
DOI: 10.5061/dryad.5v3b8gh
title: Data from: Sorghum and groundnut sole and intercrop nutrient response in semi-arid West Africa

description: Sorghum (Sorghum bicolor L. Moench)–groundnut (Arachis hypogaea L.)
 intercropping is important in the Sahel and Sudan Savanna. Nineteen trials
 were conducted during 2014 and 2015 in Mali and Niger for determination
 of: response functions for sorghum sole crop (SSC) and intercrop to N, P,
 and K; effects of the P×N interaction and of a nutrient package for
 diagnosis of other deficiencies; and a procedure for estimation of
 intercrop functions from SSC response functions. Six Niger on-station
 trials included treatments for determination of intercrop effects on
 sorghum yield and response. Mean grain and fodder yield increases for SSC
 were, respectively, 18.8 and 17.6% with 10 kg ha–1 P, 30.7 and 18.8% with
 30 kg ha–1 N, and 0 and 6.8% with 10 kg ha–1 K applied. The diagnostic
 treatment increased grain yield for only 1 of 19 site-years (SYs). Sorghum
 grain yield was 30% less with intercropping compared with SSC for 2 of 6
 SY but 11% less overall. Overall, sorghum fodder yield was 23% more with
 intercropping. Sorghum response to P was 86% greater for SSC compared with
 intercrop. With intercropping, groundnut pod yield exceeded sorghum grain
 yield. The value of intercrop production was higher than for SSC. Fodder
 added 23 and 30% to the value of SSC and intercrop harvests, respectively.
 Equations were developed for determining optimal nutrient rates and
 intercrop response functions from SSC functions. Fertilizer applied to the
 intercrop compared with SSC has much more profit potential for this part
 of West Africa.
description: W Africa Sorghum data
 setResearch was conducted
 in Burkina Faso, Mali and Niger for determination of response functions
 for fertilizer nutrients. Trials had similar basic treatment structures
 for determination of response functions for N, P, and K, and a diagnostic
 treatment for resposne to Mg, S, Zn and B. Most treatments in Niger were
 intercroped with groundnut and had 2.5 Mg ha-1 yr-1 manure applied but had
 additional treatments for determination of the effect of manure and/or
 intercropping on yield and response. Treatments in Mali were sole crop
 sorghum, all with no manure applied. In Burkina Faso, all treatments were
 with sorghum sole crop with or without 5 Mg ha-1 manure applied in 2014
 and evaluating the residual effect of manure in 2015.
DOI: 10.5061/dryad.j1v7g05
title: Data from: Relationship between wear formation and large-particle motion in a pipe bend

description: Fine and large particles flowing through a bend in a pipe move differently
 and therefore erode the pipe differently. The present paper simulates
 solid–liquid two-phase flow containing large particles in a bend and
 analyzes the relationship between the wear formation and particle motion.
 Wear experiments are carried out using 3-mm glass bead particles at a mass
 concentration of 1%–15%. At the same time, the flow field and the motion
 of the granular system are obtained in computational fluid
 dynamics–discrete element method simulation. The wear formation mechanism
 is revealed by comparing experiments with numerical simulations. The wear
 rate of the wall surface increases with the mass concentration, while the
 marginal growth rate decreases as the mass concentration increases. As the
 mass concentration increases to a certain value, the degree of wear
 reaches a maximum and remains unchanged subsequently because of the
 formation of a particle barrier along the bend wall. The particles near
 the wall region will bouncing forward because of the periodic disturbance
 flow around particles. The impacting of mass bouncing particles makes the
 formation of the erosion ripple on the test sheet.
description: Relationship between
 Wear Formation and Large-particle Motion in a Pipe BendThis data file contains
 all the chart data sources in the《Relationship between Wear Formation and
 Large-particle Motion in a Pipe Bend》
DOI: 10.5061/dryad.qm83p
title: Data from: The influence of social preferences and reputational concerns on intergroup prosocial behavior in gains and losses contexts

description: To what extent do people help ingroup members based on a social preference
 to improve ingroup members’ outcomes, versus strategic concerns about
 preserving their reputation within their group? And do these motives
 manifest differently when a prosocial behaviour occurs in the context of
 helping another gain a positive outcome (study 1), versus helping another
 to avoid losing a positive outcome (study 2)? In both contexts, we find
 that participants are more prosocial towards ingroup (versus outgroup
 members) and more prosocial when decisions are public (versus private) but
 find no interaction between group membership and either anonymity of the
 decision or expected economic value of helping. Therefore, consistent with
 a preference-based account of ingroup favouritism, people appear to prefer
 to help ingroup members more than outgroup members, regardless of whether
 helping can improve their reputation within their group. Moreover, this
 preference to help ingroup members appears to take the form of an
 intuitive social heuristic to help ingroup members, regardless of the
 economic incentives or possibility of reputation management. Theoretical
 and practical implications for the study of intergroup prosocial behaviour
 are discussed.
description: Open Science Everett
 Faber Crockett RSOS 23.11.15
DOI: 10.5061/dryad.24k0s
title: Data from: Multiple-strain infections of borrelia afzelii: a role for within-host interactions in the maintenance of antigenic diversity?

description: Genetically diverse infections are common but little is known about what
 effects coinfecting strains have on each other in natural host-parasite
 systems. To explore the nature and consequences of interactions in the
 wild, we studied the tick-transmitted bacterium Borrelia afzelii in one of
 its main reservoir hosts, the bank vole Myodes glareolus. We measured
 overall infection intensity with quantitative polymerase chain reaction
 (PCR) and resolved the composition of multiple infections using
 strain-specific PCR assays targeting the ospC gene (which encodes an
 immunodominant surface protein). We found seven different strains, as
 defined by ospC genotype. There was little evidence for interactions
 affecting infection intensities, but strains were highly aggregated (i.e.,
 there were more multiple infections than expected from random
 co-occurrence). Moreover, there was a positive correlation between the
 difference at the amino acid level between two OspC types and their degree
 of association. Overall, the observed patterns suggest that facilitation
 is more important than competition in this system and that more diverse
 infections have an advantage in establishing and/or maintaining infection.
 We propose that this advantage is one of the factors that favors antigenic
 diversity.
description: Andersson2013_AmNatAndersson2013.xlsx
DOI: 10.5061/dryad.5cb17
title: Data from: Reverse genetics in the tidepool: knockdown of target gene expression via RNA interference in the copepod Tigriopus californicus

description: Reverse genetic tools are essential for characterizing phenotypes of novel
 genes and testing functional hypotheses generated from next-generation
 sequencing studies. RNA interference (RNAi) has been a widely used
 technique for describing or quantifying physiological, developmental or
 behavioural roles of target genes by suppressing their expression. The
 marine intertidal copepod Tigriopus californicus has become an emerging
 model for evolutionary and physiological studies, but this species is not
 amenable to most genetic manipulation approaches. As crustaceans are
 susceptible to RNAi-mediated gene knock-down, we developed a simple method
 for delivery of gene-specific double-stranded RNA that results in
 significant suppression of target gene transcription levels. The protocol
 was examined on five genes of interest, and for each, at least 50%
 knock-down in expression was achieved. While knock-down levels did not
 reach 100% in any trial, a well-controlled experiment with one heat-shock
 gene showed unambiguously that such partial gene suppression may cause
 dramatic changes in phenotype. Copepods with suppressed expression of
 heat-shock protein beta 1 (hspb1) exhibited dramatically decreased
 tolerance to high temperatures, validating the importance of this gene
 during thermal stress, as proposed by a previous study. The application of
 this RNAi protocol in T. californicus will be invaluable for examining the
 role of genes putatively involved in reproductive isolation, mitochondrial
 function and local adaptation.
description: Ct values from
 qPCRThe file contains raw Ct
 values from qPCR for all genes assayed in the study. Data are organized by
 the three main experiments performed in the study, and can be used to
 reconstruct all gene expression analyses and figures in the
 paper.Ct_values.xlsxSurvivorship after heat stress during hspb1 suppressionThis file contains the proportion of copepods surviving each day for 5 days post heat stress.survivorship_after_heat-stress.xlsx
DOI: 10.5061/dryad.611310kt
title: Data from: The foraging ecology of the Mountain long-eared bat Plecotus macrobullaris revealed with DNA mini-barcodes

description: Molecular analysis of diet overcomes the considerable limitations of
 traditional techniques for identifying prey remains in bat faeces. We
 collected faeces from individual Mountain long-eared bats Plecotus
 macrobullaris trapped using mist nets during the summers of 2009 and 2010
 in the Pyrenees. We analysed their diet using DNA mini-barcodes to
 identify prey species. In addition, we inferred some basic features of the
 bat’s foraging ecology that had not yet been addressed. P. macrobullaris
 fed almost exclusively on moths (97.8%). As prey we detected one dipteran
 genus (Tipulidae) and 29 moth taxa: 28 were identified at species level
 (23 Noctuidae, 1 Crambidae, 1 Geometridae, 1 Pyralidae, 1 Sphingidae, 1
 Tortricidae), and one at genus level (Rhyacia sp., Noctuidae). Known
 ecological information about the prey species allowed us to determine that
 bats had foraged at elevations between 1,500 and 2,500 m amsl (above mean
 sea level), mostly in subalpine meadows, followed by other open habitats
 such as orophilous grasslands and alpine meadows. No forest prey species
 were identified in the diet. As 96.4% of identified prey species were
 tympanate moths and no evidence of gleaning behaviour was revealed, we
 suggest P. macrobullaris probably forages by aerial hawking using faint
 echolocation pulses to avoid detection by hearing moths. As we could
 identify 87.8% of the analysed sequences (64.1% of the MOTUs, Molecular
 Operational Taxonomic Units) at species level, we conclude that DNA
 mini-barcodes are a very useful tool to analyse the diet of
 moth-specialist bats.
description: Analysed DNA
 sequencesAll the sequences
 analysed in the study in FASTA format. The name includes the MOTU number,
 the sequence identification number and the species or genus level
 identification.motu_dryad.txt