cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nb301
title: Data from: What caused over a century of decline in general intelligence? Testing predictions from the genetic selection and neurotoxin hypotheses

description: Several converging lines of evidence indicate that general intelligence
 (g) has declined in Western populations. The causes of these declines are
 debated. Here, two hypotheses are tested: (1) selection acting against
 genetic variants that promote g causes the decline and (2) the presence of
 neurotoxic pollution in the environment causes the decline. A linear mixed
 model was devised to test (1) and (2), in which the secular decline in a
 “heritable g” (g.h) chronometric factor (comprised of convergent
 indicators of simple reaction time, working memory, utilization
 frequencies of high difficulty and also social-intelligence-indicating
 vocabulary items and per capita macro-innovation rates) was predicted
 using a neurotoxin chronometric factor (comprised of convergent secular
 trends among measures of lead, mercury and dioxin + furan pollution, in
 addition to alcohol consumption) and a polygenic score chronometric factor
 (comprised of polygenic score means for genetic variants predictive of g,
 sourced from US and Icelandic age-stratified cohorts). Bivariate
 correlations revealed that (other than time) only the polygenic score
 factor was significantly associated with declining g.h (r = .393, p
 &lt; .05 vs. .033, ns for the neurotoxin factor). Using a hierarchical
 linear mixed model approach incorporating 25 year lags between the
 predictors and g.h, time period, operationalized categorically as fifths
 of a century, accounted for the majority of the variance in the decline in
 g.h (partial η^2 = .584, p &lt; .05). Net of time period and
 neurotoxins, changing levels of polygenic scores also significantly
 predicted variance in the decline in g.h (partial η^2 = .253, p &lt;
 .05); however, changing levels of neurotoxins did not significantly
 predict variance in g.h net of time (partial η^2 = .027 ns). Within-period
 analysis indicates that the independent significant positive effect of the
 polygenic score factor on g.h was restricted to the third fifth of a
 century period (β = .202, p &lt; .05).
description: Public release dataset
 for Woodley of Menie et al. (2017) EPS
 doi.10.1007:s40806-017-0131-7File contains data on
 g.h, polygenic scores (Iceland and US), Neurotoxins (lead, mercury,
 dioxin+Furan and alcohol [US and UK]), along with latent chronometric
 polygenic score and neurotoxin factor values and data
 sources.
DOI: 10.5061/dryad.jg081
title: Data from: When hawks give rise to doves: the evolution and transition of enforcement strategies

description: The question of how altruism can evolve despite its local disadvantage to
 selfishness has produced a wealth of theoretical and empirical research
 capturing the attention of scientists across disciplines for decades. One
 feature that has remained consistent through this outpouring of knowledge
 has been that researchers have looked to the altruists themselves for
 mechanisms by which altruism can curtail selfishness. An alternative
 perspective may be that just as altruists want to limit selfishness in the
 population, so may the selfish individuals themselves. These alternative
 perspectives have been most evident in the fairly recent development of
 enforcement strategies. Punishment can effectively limit selfishness in
 the population, but it is not free. Thus when punishment evolves amongst
 altruists, the double costs of exploitation from cheaters and punishment
 make the evolution of punishment problematic. Here we show that punishment
 can more readily invade selfish populations when associated with
 selfishness, whereas altruistic punishers cannot. Thereafter, the
 establishment of altruism due to enforcement by selfish punishers provides
 the ideal invasion conditions for altruistic punishment, effectively
 creating a transition of punishment from selfishness to altruistic. Thus,
 from chaotic beginnings, a little hypocrisy may go a long way in the
 evolution and maintenance of altruism.
description: SPmodel_both
 typesThis is the computer
 simulation model used for data collection. The model is for the program
 netlogo, which is free to download at:
 http://ccl.northwestern.edu/netlogo/
DOI: 10.5061/dryad.t5c10
title: Data from: Individuals with higher metabolic rates have lower levels of reactive oxygen species hydrogen peroxide in vivo

description: There is increasing interest in the effect of energy metabolism on
 oxidative stress, but much ambiguity over the relationship between the
 rate of oxygen consumption and the generation of reactive oxygen species
 (ROS). Production of ROS (such as hydrogen peroxide, H2O2) in the
 mitochondria is primarily inferred indirectly from measurements in vitro,
 which may not reflect actual ROS production in living animals. Here, we
 measured in vivo H2O2 content using the recently developed MitoB probe
 that becomes concentrated in the mitochondria of living organisms, where
 it is converted by H2O2 into an alternative form termed MitoP; the ratio
 of MitoP/MitoB indicates the level of mitochondrial H2O2 in vivo. Using
 the brown trout Salmo trutta, we tested whether this measurement of in
 vivo H2O2 content over a 24 h-period was related to interindividual
 variation in standard metabolic rate (SMR). We showed that the H2O2
 content varied up to 26-fold among fish of the same age and under
 identical environmental conditions and nutritional states. Interindividual
 variation in H2O2 content was unrelated to mitochondrial density but was
 significantly associated with SMR: fish with a higher mass-independent SMR
 had a lower level of H2O2. The mechanism underlying this observed
 relationship between SMR and in vivo H2O2 content requires further
 investigation, but may implicate mitochondrial uncoupling which can
 simultaneously increase SMR but reduce ROS production. To our knowledge,
 this is the first study in living organisms to show that individuals with
 higher oxygen consumption rates can actually have lower levels of H2O2.
description: Salin et al 2015 Biol
 let - SMR and ROS in vivo
DOI: 10.5061/dryad.gc2260qm
title: Data from: Multi-scale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin

description: The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)
 system is a recently discovered type of adaptive immune defense in
 bacteria and archaea that functions via directed incorporation of viral
 and plasmid DNA into host genomes. Here, we introduce a multi-scale model
 of dynamic coevolution between hosts and viruses in an ecological context
 that incorporates CRISPR immunity principles. We analyze the model to test
 whether and how CRISPR immunity induces host and viral diversification and
 the maintenance of many coexisting strains. We show that hosts and viruses
 coevolve to form highly diverse communities. We observe the punctuated
 replacement of extant strains, so that populations have very low
 similarity compared over the long term. However in the short term, we
 observe evolutionary dynamics consistent with both incomplete selective
 sweeps of novel strains and the recurrence of previously rare strains.
 Coalitions of multiple dominant host strains are predicted to arise
 because host strains can have nearly identical immune phenotypes mediated
 by CRISPR defense albeit with different genotypes. We close by discussing
 how our explicit eco-evolutionary model of CRISPR immunity can help guide
 efforts to understand the drivers of diversity seen in microbial
 communities where CRISPR systems are active.
description: Multi-Scale Model of
 CRISPR-Induced Coevolutionary DynamicsThis code presents a
 flexible framework for considering the co-evolutionary dynamics of hosts
 and viruses which interact via a CRISPR immune mechanism. The code is
 written in Matlab. Instructions on how to utilize the code including an
 example file are found in the README file.CRISPRCoevol_Code_Childs_etal_Evolution2012.zip
DOI: 10.5061/dryad.f35n7
title: Data from: Nutritional geometry of paternal effects on embryo mortality

description: Well-established causal links exist between maternal nutritional deficits
 and embryo health and viability. By contrast, environmental effects
 operating through the father that could influence embryo mortality have
 seldom been examined. Yet, ejaculates can require non-trivial resource
 allocation, and seminal plasma components are increasingly recognized to
 exert wide-ranging effects on females and offspring, so paternal dietary
 effects on the embryo should be expected. We test for effects of varying
 levels of protein (P), carbohydrate (C) and caloric load in adult male
 diet on embryo mortality in Drosophila melanogaster. We demonstrate that
 macronutrient balance and caloric restriction exert significant effects,
 and that nutritional effects are more impactful when a prior mating has
 occurred. Once-mated males produced embryos with marginally elevated
 mortality under high-caloric densities and a 1 : 8 P : C ratio. In
 contrast, embryos produced by twice-mated males were significantly more
 likely to die under male caloric restriction, an outcome that may have
 resulted from shifts in ejaculate quality and/or epigenetic paternal
 effects. Body nutrient reserves were strongly and predictably altered by
 diet, and body condition, in turn, was negatively related to embryo
 mortality. Thus, sire nutritional history and resultant shifts in
 metabolic state predict embryo viability and post-fertilization fitness
 outcomes.
description: A_females_sugars_combinedEmbryo mortality data for "A" femalesB_females_sugars_combinedEmbryo mortality data for "B" femalesDeath_rate_and_nutrient_reservesAverage embryo mortality and nutrient reserves data
DOI: 10.5061/dryad.c18hh
title: Data from: MC1R variants affect the expression of melanocortin and melanogenic genes and the association between melanocortin genes and coloration

description: The melanocortin-1 receptor (MC1R) gene influences coloration by altering
 the expression of genes acting downstream in the melanin synthesis. MC1R
 belongs to the melanocortin system, a genetic network coding for the
 ligands that regulate MC1R and other melanocortin receptors controlling
 different physiological and behavioural traits. The impact of MC1R
 variants on these regulatory melanocortin genes was never considered, even
 though MC1R mutations could alter the influence of these genes on
 coloration (e.g. by decreasing MC1R response to melanocortin ligands).
 Using barn owl growing feathers, we investigated the differences between
 MC1R genotypes in the (co)expression of six melanocortin and nine
 melanogenic-related genes and in the association between melanocortin gene
 expression and phenotype (feather pheomelanin content). Compared to the
 MC1R rufous allele, responsible for reddish coloration, the white allele
 was not only associated with an expected lower expression of
 melanogenic-related genes (TYR, TYRP1, OCA2, SLC45A2, KIT, DCT) but also
 with a lower MC1R expression and a higher expression of ASIP, the MC1R
 antagonist. More importantly, the expression of PCSK2, responsible for the
 maturation of the MC1R agonist, α-melanocyte-stimulating hormone, was
 positively related to pheomelanin content in MC1R white homozygotes but
 not in individuals carrying the MC1R rufous allele. These findings
 indicate that MC1R mutations not only alter the expression of
 melanogenic-related genes but also the association between coloration and
 the expression of melanocortin genes upstream of MC1R. This suggests that
 MC1R mutations can modulate the regulation of coloration by the
 pleiotropic melanocortin genes, potentially decoupling the often-observed
 associations between coloration and other phenotypes.
description: Data San-Jose et al.
 2017Data.txt
DOI: 10.15468/dl.d5xqpv
title: Occurrence Download

description: A dataset containing 3775194 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Plantae, Undaria pinnatifida, Lindavia intermedia)",
 "Country is New Zealand",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 0",
 "DecimalLongitude is greater than or equal to -180",
 "DecimalLatitude is greater than or equal to -90",
 {
 "not" : {
 "or" : [
 "Issue is Zero coordinate",
 "Issue is Coordinate out of range",
 "Issue is Country coordinate mismatch"
 ]
 }
 }
 ]
}

 The dataset includes 3775194 records from 310 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001148-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cp39t21
title: Data from: The mismatch in distributions of vertebrates and the plants that they disperse

description: Little is known about how mutualistic interactions affect the distribution
 of species richness on broad geographic scales. Because mutualism
 positively affects the fitness of all species involved in the interaction,
 one hypothesis is that the richness of species involved should be
 positively correlated across their range, especially for obligate
 relationships. Alternatively, if mutualisms are facilitative (e.g.,
 involving multiple mutualistic partners), the distribution of mutualists
 should not necessarily be related, and patterns in species distributions
 might be more strongly correlated with environmental factors. In this
 study, we compared the distributions of plants and vertebrate animals
 involved in seed-dispersal mutualisms across the United States and Canada.
 We compiled geographic distributions of plants dispersed by frugivores and
 scatter-hoarding animals, and compared their distribution of richness to
 the distribution in disperser richness. We found that the distribution of
 animal dispersers shows a negative relationship to the distribution of the
 plants that they disperse, and this is true whether the plants dispersed
 by frugivores or scatter-hoarders are considered separately or combined.
 In fact, the mismatch in species richness between plants and the animals
 that disperse their seeds is dramatic, with plants species richness
 greatest in the in the eastern United States and the animal species
 richness greatest in the southwest United States. Environmental factors
 were corelated with the difference in the distribution of plants and their
 animal mutualists and likely are more important in the distribution of
 both plants and animals. This study is the first to describe the
 broad-scale distribution of seed-dispersing vertebrates and compare the
 distributions to the plants they disperse. With these data, we can now
 identify locations that warrant further study either to understand better
 seed-dispersal mutualisms or the factors that influence the distribution
 of the plants and animals involved in these mutualisms.
description: Ditteletal_EcographySee ReadMe
DOI: 10.5061/dryad.38q5pc1
title: Data from: Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates

description: Signaling filopodia, termed cytonemes, are dynamic actin-based membrane
 structures that regulate the exchange of signaling molecules and their
 receptors within tissues. However, how cytoneme formation is regulated
 remains unclear. Here, we show that Wnt/PCP autocrine signaling controls
 the emergence of cytonemes, and that cytonemes subsequently control
 paracrine Wnt/β-catenin signal activation. Upon binding of the Wnt family
 member Wnt8a, the receptor tyrosine kinase Ror2 gets activated. Ror2/PCP
 signaling leads to induction of cytonemes, which mediate transport of
 Wnt8a to neighboring cells. In the Wnt receiving cells, Wnt8a on cytonemes
 triggers Wnt/β-catenin-dependent gene transcription and proliferation. We
 show that cytoneme-based Wnt transport operates in diverse processes,
 including zebrafish development, the murine intestinal crypt, and human
 cancer organoids, demonstrating that Wnt transport by cytonemes and its
 control via the Ror2 pathway is highly conserved in vertebrates.
description: Data from Mattes
 2018Kinase Screen and
 automated image-analysis identifies the receptor tyrosine kinase Ror2 as a
 potential cytoneme regulator upstream of Cdc42. Wnt8a-GFP and a membrane
 bound mCherry was co-transfected with kinase library genes in Pac2 cells
 in a 96-well plate. Images were acquired automatically and analyzed for
 filopodia length and numbers by a filopodia detection software. Automated
 Image analysis software detects and counts filopodia of single cells using
 the memCherry signal and quantifies their length by automatically tracing
 the tips back to the cell body. Table shows transfected kinase genes and
 their relative filopodia number/cell and length.Screening Results Mattes
 2018.xlsx
DOI: 10.5061/dryad.m3q59
title: Data from: Genetic kinship analyses reveal that Gray's beaked whales strand in unrelated groups

description: Some marine mammals are so rarely seen that their life history and social
 structure remain a mystery. Around New Zealand, Gray’s beaked whales
 (Mesoplodon grayi) are almost never seen alive, yet they are a commonly
 stranded species. Gray’s are unique among the beaked whales in that they
 frequently strand in groups, providing an opportunity to investigate their
 social organization. We examined group composition and genetic kinship in
 113 Gray’s beaked whales with samples collected over a 20-year period.
 Fifty-six individuals stranded in 19 groups (2 or more individuals), and
 57 whales stranded individually. Mitochondrial control region haplotypes
 and microsatellite genotypes (16 loci) were obtained for 103 whales. We
 estimated pairwise relatedness between all pairs of individuals and
 average relatedness within, and between, groups. We identified 6
 mother–calf pairs and 2 half-siblings, including 2 whales in different
 strandings 17 years and 1500 km apart. Surprisingly, none of the adults
 stranding together were related suggesting that groups are not formed
 through the retention of kin. These data suggest that both sexes may
 disperse from their mothers, and groups consisting of unrelated subadults
 are common. We also found no instances of paternity within the groups. Our
 results provide the first insights into dispersal, social organization,
 and the mating system in this rarely sighted species. Why whales strand is
 still unknown but, in Gray’s beaked whales, the dead can tell us much
 about the living.
description: Gray's_Allsamples16LociThis file includes all genotypes for all samples used in the analyses along with individual codes used by the University of Auckland and the New Zealand Cetacean Tissue Archive. We also include mitochondrial haplotype codes (for further information see Thompson et al. (2016) Heredity) and dates of strandings.
DOI: 10.15468/dl.mztyye
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-52.54887 -60.17895,-21.61844 -60.17895,-21.61844 -48.75617,-52.54887 -48.75617,-52.54887 -60.17895))",
 "HasGeospatialIssue is false",
 "TaxonKey is Pseudochaenichthys georgianus",
 "Year 2021-2021"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001198-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6kt34
title: Data from: Comparison of pollen gene flow among four European beech (Fagus sylvatica L.) populations characterized by different management regimes

description: The study of dispersal capability of a species can provide essential
 information for the management and conservation of its genetic
 variability. Comparison of gene flow rates among populations characterized
 by different management and evolutionary histories allows one to decipher
 the role of factors such as isolation and tree density on gene movements.
 We used two paternity analysis approaches and different strategies to
 handle possible presence of genotyping errors to obtain robust estimates
 of pollen flow in four beech (Fagus sylvatica L.) populations from Austria
 and France. In each country one of the two plots is located in an
 unmanaged forest, the other plots are managed with a shelterwood system
 and inside a colonization area (in Austria and France, respectively). The
 two paternity analysis approaches provided almost identical estimates of
 gene flow. We found high pollen immigration (~75% of pollen from outside),
 with the exception of the plot from a highly isolated forest remnant
 (~50%). In the unmanaged plots the average within-population pollen
 dispersal distances (from 80 to 184 m) were higher than previously
 estimated for beech. From the comparison between the Austrian managed and
 unmanaged plots, that are only 500 m apart, we found no evidence that
 either gene flow or reproductive success distributions were significantly
 altered by forest management. Shelterwood seems to have an effect on the
 distribution of within-population pollen dispersal distances. In the
 managed plot, pollen dispersal distances were shorter, possibly because
 adult tree density is threefold (163 vs. 57 trees/ha) with respect to the
 unmanaged one.
description: Genotypes and phenotypes
 of adults and seeds from four Fagus sylvatica stands characterised by
 different management regimesThe archive contains
 microsatellite genotypes, geographical locations and phenotypic
 characteristics of adults and seeds of four beech stands characterised by
 different management regimes. Details are reported in the readme.txt
 file.Dryad_data_Piotti_Heredity.rar
DOI: 10.5061/dryad.7g8q2
title: Data from: Resource- and pollinator-mediated selection on floral traits

description: Female reproductive success is predicted to be simultaneously limited by
 the availability of pollen and resources. Selection on floral traits
 results from both factors, but their relative importance and interaction
 is poorly understood. We increased nutrient and pollen availability of the
 orchid Dactylorhiza lapponica in a factorial experiment to quantify
 resource- and pollinator-mediated selection on floral traits.
 Hand-pollination increased female fitness (number of fruits × mean fruit
 mass) by 74% in both nutrient treatments, whereas nutrient addition did
 not significantly affect female fitness. There was selection for more
 flowers and longer spurs, and selection on spur length was significantly
 pollinator-mediated and of similar strength across nutrient treatments
 (Δβpoll = 0·54 and Δβpoll_NPK = 0·59). There was no statistically
 significant resource-mediated selection. Nutrient addition increased
 flower size the following year, but did not affect flower or fruit
 production, or selection on any trait. The results demonstrate that D.
 lapponica does not increase flower production in response to nutrient
 addition, that the increase in female fitness in response to
 hand-pollination is not resource limited, and suggest that natural
 resource variation does not influence selection on floral traits. The
 study illustrates that crossed manipulations of pollen and resources can
 clarify their relative importance for selection on floral traits.
description: Phenotypic selection
 dataExcel file containing
 standardized trait values and relative fitness for all individuals in the
 four treatments in the factorial experiment conducted in
 2014D_lapponica_Dryad_FE.xlsx