cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h95t0
title: Data from: Environmental effects on the structure of the G-matrix

description: Genetic correlations between traits determine the multivariate response to
 selection in the short term, and thereby play a causal role in
 evolutionary change. While individual studies have documented
 environmentally induced changes in genetic correlations, the nature and
 extent of environmental effects on multivariate genetic architecture
 across species and environments remain largely uncharacterized. We
 reviewed the literature for estimates of the genetic variance-covariance
 (G) matrix in multiple environments, and compared differences in G between
 environments to the divergence in G between conspecific populations
 (measured in a common garden). We found that the predicted evolutionary
 trajectory differed as strongly between environments as it did between
 populations. Between-environment differences in the underlying structure
 of G (total genetic variance and the relative magnitude and orientation of
 genetic correlations) were equal to or greater than between-population
 differences. Neither environmental novelty nor the difference in mean
 phenotype predicted these differences in G. Our results suggest that
 environmental effects on multivariate genetic architecture may be
 comparable to the divergence that accumulates over dozens or hundreds of
 generations between populations. We outline avenues of future research to
 address the limitations of existing data and characterize the extent to
 which lability in genetic correlations shapes evolution in changing
 environments.
description: MatrixComparisonDatasetThe final data file used for the matrix comparison analyses described in the manuscript. This file includes relevant metadata for each matrix comparison, the reference that it came from, and all the matrix comparison statistics. A second tab in this Excel workbook ("Key to column names") describes what the values in each column represent.G-matricesAll G-matrices used in the analyses. There are two matrices for each comparison, with the naming convention STUDYNAME_E# for between-environment comparisons) or STUDYNAME_P# (for between-population comparisons)MatrixComparisonAnalysisThis R script was used to calculate matrix comparison metrics from G-matrices contained in .csv files, performs the analyses described in the manuscript, and creates the figures presented in the manuscript. It relies on metadata contained in the file "Metadata_forRscript.csv" and the list of comparisons in the file "matrixList_forRscript.csv".matrixList_forRscriptList of matrices to compare that is used in the "MatrixComparisonAnalysis.R" R script.Metadata_forRscriptMetadata file that is used in the "MatrixComparisonAnalysis.R" R script.
DOI: 10.5061/dryad.4bm3739j
title: Data from: Using seedling and pericarp tissues to determine maternal parentage of dispersed valley oak recruits

description: The spatial pattern of established seedlings yields valuable information
 about variation in fecundity, dispersal, and spatial structure of
 distributed recruits, but separating maternal and paternal contributions
 in monoecious species has been hampered by the “2 parent” problem. It is
 now possible to determine the maternal parentage of established recruits
 with genetic assay of maternally derived tissues of the seed or fruit, but
 the DNA of weathered maternal tissues often yields unreliable genotypes,
 reducing the practical range of such assay. We develop a mixed assay of
 seedling and seed (pericarp) tissues and illustrate it with distributed
 recruits of California valley oak (Quercus lobata Née). Detailed analysis
 indicates correct maternal assignment rates of canopy patch recruits of
 56% (seedling assay only) versus 94% (mixed assay). For open patch
 recruits, maternal assignment rates were less than 50% (seedling assay
 only) versus 91% (mixed assay). The strategy of choice is to use seedling
 genotypes to identify a small set of credible parental candidates and then
 deploy 3–4 well-chosen pericarp/endocarp loci to reduce that list to a
 single obvious maternal candidate. The increase in the number of recruits
 available for subsequent analysis is pronounced, increasing precision and
 statistical power for subsequent inference.
description: Smouse-et-al_JHered_mixed-assay-genotype-data_DATADRYADMicrosatellite genotypes and allele frequencies for datasets described in the paper. Included are genotypes for adult trees; pericarp- and leaf-derived genotypes for seedlings from open patches; and pericarp- and leaf-derived genotypes for seedlings from canopy patches. Genotype files are in GenAlEx format. Missing data are indicated with 0.
DOI: 10.5061/dryad.6q0q4
title: Data from: Consequences of multiple mating-system shifts for population and range-wide genetic structure in a coastal dune plant

description: Evolutionary transitions from outcrossing to selfing can strongly affect
 the genetic diversity and structure of species at multiple spatial scales.
 We investigated the genetic consequences of mating system shifts in the
 North American, Pacific coast dune endemic plant Camissoniopsis
 cheiranthifolia (Onagraceae) by assaying variation at 13 nuclear (n) and
 six chloroplast (cp) microsatellite (SSR) loci for 38 populations across
 the species range. As predicted from the expected reduction of effective
 population size (Ne) caused by selfing, small-flowered, predominantly
 selfing (SF) populations had much lower nSSR diversity (but not cpSSR)
 than large flowered, predominantly outcrossing (LF) populations. The
 reduction of nSSR diversity was greater than expected from the effects of
 selfing on Ne alone, but could not be accounted for by indirect effects of
 selfing on population density. Although selfing should reduce gene flow,
 SF populations were not more genetically differentiated than LF
 populations. We detected five clusters of nSSR genotypes and three groups
 of cpSSR haplotypes across the species range consisting of parapatric
 groups of populations that usually (but not always) differed in mating
 system, suggesting that selfing may often initiate ecogeographic
 isolation. However, lineage-wide genetic variation was not lower for
 selfing clusters, failing to support the hypothesis that selection for
 reproductive assurance spurred the evolution of selfing in this species.
 Within three populations where LF and SF plants coexist we detected
 genetic differentiation among diverged floral phenotypes suggesting that
 reproductive isolation (probably postzygotic) may help maintain the
 striking mating system differentiation observed across the range of this
 species
description: nSSRCamissoniopsis_cheiranthifolia987 nuclear microsatellite genotypes from 38 Camissoniopsis cheiranthifolia populationscpSSRCamissoniopsis_cheiranthifolia159 chloroplast microsatellite genotypesDensityCamissoniopsis_cheiranthifoliaPopulation density estimated in 2009 and 2010 from 38 C. cheiranthifolia populations.
DOI: 10.5061/dryad.62
title: Data from: Morphology, molecules, and the phylogenetics of cetaceans

description: Recent phylogenetic analyses of cetacean relationships based on DNA
 sequence data have challenged the traditional view that baleen whales
 (Mysticeti) and toothed whales (Odontoceti) are each monophyletic, arguing
 instead that baleen whales are the sister group of the odontocete family
 Physeteridae (sperm whales). We reexamined this issue in light of a
 morphological data set composed of 207 characters and molecular data sets
 of published 12S, 16S, and cytochrome b mitochondrial DNA sequences. We
 reach four primary conclusions: (1) Our morphological data set strongly
 supports the traditional view of odontocete monophyly; (2) the unrooted
 molecular and morphological trees are very similar, and most of the
 conflict results from alternative rooting positions; (3) the rooting
 position of the molecular tree is sensitive to choice of artiodactyl
 outgroup taxa and the treatment of two small but ambiguously aligned
 regions of the 12S and 16S sequences, whereas the morphological root is
 strongly supported; and (4) combined analyses of the morphological and
 molecular data provide a well-supported phylogenetic estimate consistent
 with that based on the morphological data alone (and the traditional view
 of toothed-whale monophyly) but with increased bootstrap support at nearly
 every node of the tree.
description: Messenger and McGuire
 data matrixmessenger.matrix.txt
DOI: 10.5061/dryad.68j14
title: Data from: A test of the eavesdropping avoidance hypothesis as an explanation for the structure of low amplitude aggressive signals in the song sparrow

description: Low amplitude signals function in private exchanges of information between
 signalers and nearby receivers. The eavesdropping avoidance hypothesis
 proposes that selection favors quiet threat signals in order to avoid the
 costs of eavesdroppers. If true, then selection should favor other
 acoustic traits in addition to low amplitude that lead to quiet signals
 transmitting less effectively through the environment compared to
 broadcast signals. The “warbled” soft songs of male song sparrows differ
 from “crystallized” soft songs and from broadcast songs in a number of
 acoustic traits, suggesting that these songs may transmit less
 effectively. We tested this prediction in a field experiment by playing
 broadcast songs, crystallized soft songs, and warbled soft songs through a
 loudspeaker at the same amplitude and recording the propagated songs at
 five distances, at two heights, and in two different habitat types.
 Counter to our prediction, we found no evidence that either form of soft
 song transmits differently than broadcast song when all were played
 loudly. If anything, soft songs transmitted more effectively when all
 songs were played quietly. Our results do not support one prediction made
 by the eavesdropping avoidance hypothesis, although the possibility
 remains that reduced amplitude alone is sufficient to reduce
 eavesdropping. The question of why warbled soft song differs in acoustic
 structure remains unresolved.
description: SOSP-Test of
 EAH-DataData from the song
 transmission analysis of song sparrow broadcast songs, crystallized soft
 songs, and warbled soft songs. All data were collected using SigPro
 3.25.
DOI: 10.5061/dryad.86750
title: Data from: Sexual selection protects against extinction

description: Reproduction through sex carries substantial costs, mainly because only
 half of sexual adults produce offspring. It has been theorized that these
 costs could be countered if sex allows sexual selection to clear the
 universal fitness constraint of mutation load. Under sexual selection,
 competition between (usually) males and mate choice by (usually) females
 create important intraspecific filters for reproductive success, so that
 only a subset of males gains paternity. If reproductive success under
 sexual selection is dependent on individual condition, which is contingent
 to mutation load, then sexually selected filtering through ‘genic capture’
 could offset the costs of sex because it provides genetic benefits to
 populations. Here we test this theory experimentally by comparing whether
 populations with histories of strong versus weak sexual selection purge
 mutation load and resist extinction differently. After evolving replicate
 populations of the flour beetle Tribolium castaneum for 6 to 7 years under
 conditions that differed solely in the strengths of sexual selection, we
 revealed mutation load using inbreeding. Lineages from populations that
 had previously experienced strong sexual selection were resilient to
 extinction and maintained fitness under inbreeding, with some families
 continuing to survive after 20 generations of sib × sib mating. By
 contrast, lineages derived from populations that experienced weak or
 non-existent sexual selection showed rapid fitness declines under
 inbreeding, and all were extinct after generation 10. Multiple mutations
 across the genome with individually small effects can be difficult to
 clear, yet sum to a significant fitness load; our findings reveal that
 sexual selection reduces this load, improving population viability in the
 face of genetic stress.
description: All Tribolium
 GenotypesThis file includes all
 the genotypes scored as part of this study in GenPop format. Sample names
 include either Fam (indicating that they are the first offspring from each
 family in the inbreeding assey) or Ind (indicating that these are
 additional individuals from the selection lines also included in the
 sample name).Allgenotypes.xlsxPer locus heterozygosityThe estimated heterozygosities for each locus for each population produced by GenPop.Het by locus.xlsxTribolium linear models R scriptThe R script used to fit linear models to the heterozygosities and plot the graph.Tribolium_linear_models_Nature.R
DOI: 10.5061/dryad.0qk7f
title: Data from: Identification of genetic defects in 33 probands with Stargardt disease by WES-based bioinformatics gene panel analysis

description: Stargardt disease (STGD) is the most common hereditary macular
 degeneration in juveniles, with loss of central vision occurring in the
 first or second decade of life. The aim of this study is to identify the
 genetic defects in 33 probands with Stargardt disease. Clinical data and
 genomic DNA were collected from 33 probands from unrelated families with
 STGD. Variants in coding genes were initially screened by whole exome
 sequencing. Candidate variants were selected from all known genes
 associated with hereditary retinal dystrophy and then confirmed by Sanger
 sequencing. Putative pathogenic variants were further validated in
 available family members and controls. Potential pathogenic mutations were
 identified in 19 of the 33 probands (57.6%). These mutations were all
 present in ABCA4, but not in the other four STGD-associated genes or in
 genes responsible for other retinal dystrophies. Of the 19 probands, ABCA4
 mutations were homozygous in one proband and compound heterozygous in 18
 probands, involving 28 variants (13 novel and 15 known). Analysis of
 normal controls and available family members in 12 of the 19 families
 further support the pathogenicity of these variants. Clinical
 manifestation of all probands met the diagnostic criteria of STGD. This
 study provides an overview of a genetic basis for STGD in Chinese
 patients. Mutations in ABCA4 are the most common cause of STGD in this
 cohort. Genetic defects in approximately 42.4% of STGD patients await
 identification in future studies.
description: All variants of five
 known STGD genes in 33 patients by WES
DOI: 10.5061/dryad.gf647cc0
title: Data from: Increased growth in sunflower correlates with reduced defenses and altered gene expression in response to biotic and abiotic stress

description: Cultivated plants have been selected by humans for increased yield in a
 relatively benign environment, where nutrient and water resources are
 often supplemented, and biotic enemy loads are kept artificially low.
 Agricultural weeds have adapted to this same benign environment as crops,
 and often have high growth and reproductive rates, even though they have
 not been specifically selected for yield. Considering the competing
 demands for resources in any plant, a key question is whether adaptation
 to agricultural environments has been accompanied by life-history
 trade-offs, in which resistance to (largely absent) stress has been lost
 in favor of growth and reproduction. The experiments reported here were
 designed to test for growth-defense trade-offs in agricultural weeds,
 crops, and native varieties of common sunflower (Helianthus annuus L.,
 Asteraceae) by comparing their performance in the presence or absence of
 abiotic (drought and crowding) or biotic (simulated herbivory, insect
 herbivory, and fungal) stress. We found that growth, as well viability of
 crops and weeds, were reduced by abiotic drought stress. The weakened
 defense in the agricultural genotypes was further evident as increased
 susceptibility to fungal infection and higher level of insect
 palatability. To uncover molecular mechanisms underlying these trade-offs
 we monitored gene expression kinetics in drought-stressed plants. By
 correlating phenotypic observations with molecular analyses, we report the
 identification of several genes, including a protein phosphatase 2C and
 the HD-Zip transcription factor Athb-8, whose expression is associated
 with the observed phenotypic variation in common sunflower.
description: DryadMEC_finalThe data file contains 4 spreadsheets. Sheet1: The first spreadsheet contains information on growth and morphological traits under 4 different treatments - control, drought, simulated herbivory and high density. The second sheet contains information about the botrytis experiment. Sheet 3 contains information about the insect herbivory experiment. Sheet 4 - expression data for each gene (named as in the text), for each genotype (column 1), based on fold expression changes relative to the control. See readme file for complete details.
DOI: 10.5061/dryad.kd1r2
title: Data from: Nest wax triggers worker reproduction in the bumblebee Bombus terrestris

description: Social insects are well known for their high level of cooperation. Workers
 of the primitively eusocial bumblebee Bombus terrestris are able to
 produce male offspring in the presence of a queen. Nonetheless, they only
 compete for reproduction, in the so-called competition phase, when the
 workforce is large enough to support the rearing of reproductives. So far,
 little is known about the proximate mechanisms underlying the shift
 between altruism and selfish behaviour in bumblebee workers. In this
 study, we have examined the influence of chemical cues from the nest wax
 on the onset of worker reproduction. Chemical analyses of wax extracts
 have revealed that the patterns and amounts of cuticular lipids change
 considerably during colony development. These changes in wax scent mirror
 worker abundance and the presence of fertile workers. In bioassays with
 queen-right worker groups, wax affects the dominance behaviour and ovarian
 development of workers. When exposed to wax from a colony in competition
 phase, workers start to compete for reproduction. We suggest that wax
 scent enables workers to time their reproduction by providing essential
 information concerning the social condition of the colony.
description: DataChemistry (gas
 chromatography results): relative amounts of cuticular compounds extracted
 from bumblebee nest wax and from cuticle surfaces of sterile and fertile
 workers and egg-laying queens; Results from group experiments: observed
 behaviour (neutral, aggressive, defensive) and ovarian development
 (percent)
DOI: 10.5061/dryad.4cp88
title: Data from: Heritabilities of directional asymmetry in the fore- and hindlimbs of rabbit fetuses

description: Directional asymmetry (DA), where at the population level symmetry differs
 from zero, has been reported in a wide range of traits and taxa, even for
 traits in which symmetry is expected to be the target of selection such as
 limbs or wings. In invertebrates, DA has been suggested to be
 non-adaptive. In vertebrates, there has been a wealth of research linking
 morphological asymmetry to behavioural lateralisation. On the other hand,
 the prenatal expression of DA and evidences for quantitative genetic
 variation for asymmetry may suggest it is not solely induced by
 differences in mechanic loading between sides. We estimate quantitative
 genetic variation of fetal limb asymmetry in a large dataset of rabbits.
 Our results showed a low but highly significant level of DA that is
 partially under genetic control for all traits, with forelimbs displaying
 higher levels of asymmetry. Genetic correlations were positive within
 limbs, but negative across bones of fore and hind limbs. Environmental
 correlations were positive for all, but smaller across fore and hind
 limbs. We discuss our results in light of the existence and maintenance of
 DA in locomotory traits.
description: rabbitmeasurementsRepeated left and right measurements of rabbit fetal limbs.
DOI: 10.5061/dryad.1m166
title: Data from: The direct effects of male-killer infection on fitness of ladybird hosts (Coleoptera: Coccinellidae)

description: Male-killing bacteria are common in insects, and are thought to persist in
 host populations primarily by indirect fitness benefits to infected
 females, while direct fitness effects are generally assumed to be neutral
 or deleterious. Here, we estimated the effect of male-killer infection on
 direct fitness (number of eggs laid, as a measure of fecundity, together
 with survival) and other life-history traits (development time and body
 size) in seven ladybird host/male-killer combinations. Effects of
 male-killers on fecundity ranged, as expected, from costly to neutral,
 however we found evidence of reduced development time and increased
 survival and body size, in infected strains. Greater body size in
 Spiroplasma-infected Harmonia axyridis corresponded to greater ovariole
 number, and therefore higher potential fecundity. To our knowledge, this
 is the first report of direct benefits of male-killer infection after
 explicitly controlling for indirect fitness effects. Neutral or
 deleterious fitness effects of male-killer infection should not therefore
 be automatically assumed.
description: Elnagdy et al
 dataExperimental data
 collected to test impact of various male-killing bacteria on the fitness
 of their ladybird hosts.
DOI: 10.5061/dryad.d1m02
title: Data from: Forest degradation and invasive species synergistically impact Mimusops andongensis (Sapotaceae) in Lama Forest Reserve, Benin

description: Harvesting of Non-Timber Forest Products (NTFPs) can threaten target
 species, especially those with limited distribution and density. Exploited
 species also face threats from habitat fragmentation, fire, and invasive
 species. We assessed the impact of human disturbances and invasive species
 on the population of a key multipurpose NTFP species, Mimusops
 andongensis, in Lama Forest reserve (Benin). The densities of adult trees
 and regenerative stems decreased with increasing degradation. Mimusops
 andongensis contributed less to total tree density with increasing human
 disturbance. There were significantly fewer M. andongensis recruits with
 increasing cover of invasive Chromolaena odorata. Smaller diameter
 individuals predominated in non-degraded and moderately degraded sites
 while in degraded sites, the structure showed a negative exponential trend
 with the density of small diameter individuals being less than two
 trees/ha. Larger individuals were also rare in degraded sites. The low
 density of both mature trees and seedlings in degraded sites may undermine
 the long-term viability of M. andongensis, despite existing protection
 against NTFP harvesting and other anthropogenic pressures. Management
 should emphasize facilitating recruitment subsidies and limiting the
 presence of C. odorata.
description: Data_Impact of Forest
 Degradation and Invasive species on Mimusops andongensis in Lama Forest
 Reserve in BeninData on trees
 occurrence, dbh and height, data on regeneration occurence, diameter and
 height, and data on Chromolaena odorata cover