cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m06t1
title: Data from: Evolution: are the monkeys’ typewriters rigged?

description: Evolution is presumed to proceed by random mutations, which increase an
 individual’s fitness. Increased fitness produces a higher survival rate
 for those individuals within populations and drives the variants to
 fixation over large timescales to produce new species. We recently
 identified positively selected sites in mitochondrial complex I in
 numerous, diverse taxa. In one taxon, a simple sequence repeat (SSR)
 encompassed the positively selected sites. We hypothesized a model in
 which: (i) slip-strand mis-pairing during replication due to the SSR
 increases the mutation rate at these sites, and (ii) a functional
 constraint at the protein level maintains the SSR and therefore a higher
 mutation rate at this site over large time scales to drive evolution. We
 tested this model by identifying SSRs in a mitochondrial-encoded protein
 in species from our previous work and determined that nearly all of the
 positively selected sites encompass an SSR. Furthermore, we show that our
 proposed model accounts for most of the mutations at neutral sites but it
 is probably the predominant mechanism at positively selected sites. This
 suggests that evolution does not proceed by simple random processes but is
 guided by physical properties of the DNA itself and functional constraint
 of the proteins encoded by the DNA.
description: Supplementary File
 1SSRs
 identified in each of the positively selected sites in the 14 taxa from
 our previous study.AnguillaFull ND5 sequence alignment for Freshwater eels.Angulla.xlsxArgentinoideiFull ND5 sequence alignment for Smels and Barreleyes.BalaenopteridaeFull ND5 sequence alignment for Baleen whales.CaprinaeFull ND5 sequence alignment for Antelope-goats.DelphinidaeFull ND5 sequence alignment for Whales and Dolphins.GrusFull ND5 sequence alignment for Cranes.HominidaeFull ND5 sequence alignment for Hominids.HypsiglenaFull ND5 sequence alignment for Night Snakes.OryziasFull ND5 sequence alignment for Rice Fish.Olatipes.xlsxOncorhynchusFull ND5 sequence alignment for Pacific Salmon.OtariidaeFull ND5 sequence alignment for Eared seals.PhocidaeFull ND5 sequence alignment for True seals.TakifuguFull ND5 sequence alignment for Puffer Fish.UrsidaeFull ND5 sequence alignment for Bears.
DOI: 10.5061/dryad.pk045
title: Data from: Temperature stress mediates decanalization and dominance of gene expression in Drosophila melanogaster

description: The regulatory architecture of gene expression remains an area of active
 research. Here, we studied how the interplay of genetic and environmental
 variation affects gene expression by exposing Drosophila melanogaster
 strains to four different developmental temperatures. At 18°C we observed
 almost complete canalization with only very few allelic effects on gene
 expression. In contrast, at the two temperature extremes, 13°C and 29°C a
 large number of allelic differences in gene expression were detected due
 to both cis- and trans-regulatory effects. Allelic differences in gene
 expression were mainly dominant, but for up to 62% of the genes the
 dominance swapped between 13 and 29°C. Our results are consistent with
 stabilizing selection causing buffering of allelic expression variation in
 non-stressful environments. We propose that decanalization of gene
 expression in stressful environments is not only central to adaptation,
 but may also contribute to genetic disorders in human populations.
description: tables and
 scriptsThis contains all tables
 we generated from RNAseq libraries as read counts as well as statistic
 results. It also contains the r scripts used in this
 studydrosophila-regulatory.zipdownsampling_tablesIt contains read counts tables as results of down-sampling as well as the expression of last 500bp at 3'end genes
DOI: 10.5061/dryad.ps515
title: Data from: Does inbreeding affect gene expression in birds?

description: Inbreeding increases homozygosity, exposes genome-wide recessive
 deleterious alleles and often reduces fitness. The physiological and
 reproductive consequences of inbreeding may be manifested already during
 gene regulation, but the degree to which inbreeding influences gene
 expression is unknown in most organisms, including in birds. To evaluate
 the pattern of inbreeding-affected gene expression over the genome and in
 relation to sex, we performed a transcriptome-wide gene expression (10 695
 genes) study of brain tissue of 10-day-old inbred and outbred, male and
 female zebra finches. We found significantly lower gene expression in
 females compared with males at Z-linked genes, confirming that dosage
 compensation is incomplete in female birds. However, inbreeding did not
 affect gene expression at autosomal or sex-linked genes, neither in males
 nor in females. Analyses of single genes again found a clear sex-biased
 expression at Z-linked genes, whereas only a single gene was significantly
 affected by inbreeding. The weak effect of inbreeding on gene expression
 in zebra finches contrasts to the situation, for example, in Drosophila
 where inbreeding has been found to influence gene expression more
 generally and at stress-related genes in particular.
description: Gene expression data of
 inbred and outbred zebra finchesMicroarray expression
 signal intensity (log2 signal intensity) at 10695 genes in male and
 female, inbred and outbred (control), zebra finches (in total 40
 individuals). RNA was extracted from full telencephalon of 10 days old
 birds. Gene location is given as autosomal or
 sex-linked.Hansson et al
 Data.xlsx
DOI: 10.5061/dryad.8c9s1
title: Data from: Genetic depletion at adaptive but not neutral loci in an endangered bird species

description: Many endangered species suffer from the loss of genetic diversity, but
 some populations may be able to thrive even if genetically depleted. To
 investigate the underlying genetic processes of population bottlenecks, we
 apply an innovative approach for assessing genetic diversity in the last
 known population of the endangered Pale-headed Brushfinch (Atlapetes
 pallidiceps) in Ecuador. First, we measure genetic diversity at eleven
 neutral microsatellite loci and adaptive SNP variation in five Toll-like
 receptor (TLR) immune system genes. Bottleneck tests confirm genetic drift
 as the main force shaping genetic diversity in this species and indicate a
 99 % reduction in population size dating back several hundred years.
 Second, we compare contemporary microsatellite diversity with historic
 museum samples of A. pallidiceps, finding no change in genetic diversity.
 Third, we compare genetic diversity in the Pale-headed Brushfinch with two
 co-occurring-related brushfinch species (Atlapetes latinuchus, Buarremon
 torquatus), finding a reduction of up to 91% diversity in the immune
 system genes but not in microsatellites. High TLR diversity is linked to
 decreased survival probabilities in A. pallidiceps. Low TLR diversity is
 thus probably an adaptation to the specific selection regime within its
 currently very restricted distribution (approximately 200 ha), but could
 severely restrict the adaptive potential of the species in the long run.
 Our study illustrates the importance of investigating both neutral and
 adaptive markers to assess the effect of population bottlenecks and for
 recommending specific management plans in endangered species.
description: MSAT MASTERFILE
 genotypes Apallidiceps Alatinuchus Btorquatusincludes all genotypes
 of all three species including museum samples across all 11
 microsatellitesT1A_Toll like receptor
 sequences_allspeciescontains all TLR 1A
 sequences for all individuals across all three species as analysed in our
 study.T1B_Toll like receptor
 sequences_allspeciescontains all TLR 1B
 sequences for all individuals across all three species as analysed in our
 study.T4_Toll like receptor
 sequences_allspeciescontains all TLR 4
 sequences for all individuals across all three species as analysed in our
 study.T5_Toll like receptor
 sequences_allspeciescontains all TLR 5
 sequences for all individuals across all three species as analysed in our
 study.T21_Toll like receptor
 sequences_allspeciescontains all TLR 21
 sequences for all individuals across all three species as analysed in our
 study.MSvar evaluation
 RcodeThe R code we used to
 assess the output from MSvar simulationshpars_output_input_MSVar
 evaluation Rthe output (hpars file)
 which one receives after each MSvar simulation. This is the file you need
 as input for the assessment in R the code for which is equally uploaded
 here.
DOI: 10.5061/dryad.4bm76
title: Data from: Listening to the environment: hearing differences from an epigenetic effect in solitarious and gregarious locusts

description: Locusts display a striking form of phenotypic plasticity, developing into
 either a lone-living solitarious phase or a swarming gregarious phase
 depending on population density. The two phases differ extensively in
 appearance, behaviour and physiology. We found that solitarious and
 gregarious locusts have clear differences in their hearing, both in their
 tympanal and neuronal responses. We identified significant differences in
 the shape of the tympana that may be responsible for the variations in
 hearing between locust phases. We measured the nanometre mechanical
 responses of the ear's tympanal membrane to sound, finding that
 solitarious animals exhibit greater displacement. Finally, neural
 experiments signified that solitarious locusts have a relatively stronger
 response to high frequencies. The enhanced response to high-frequency
 sounds in the nocturnally flying solitarious locusts suggests greater
 investment in detecting the ultrasonic echolocation calls of bats, to
 which they are more vulnerable than diurnally active gregarious locusts.
 This study highlights the importance of epigenetic effects set forth
 during development and begins to identify how animals are equipped to
 match their immediate environmental needs.
description: ProcB
 dataComressInside this folder is
 all of the data used for the paper. The excel file has the tympanal
 membrane measurements. The Neuro folder is first subdivided into
 'latency' and 'RMS' folders. Each folder is subdivided
 into 'gregarious' and 'solitarious' folders which each
 contain folders for every animal--with all of the raw data. The Laser data
 is subdivided into 'gregarious' and 'solitarious'
 folders. Inside each folder is all of the data with each animal having 8
 files (a scan and a file per point measured).
DOI: 10.7927/nqqw-6r39
title: IPCC AR6 Synthesis Report SPM.4 (c) and LR Figure 3.3 (c) (linear graph): Global mean sea level rise relative to 1900

description: Global mean sea level change in centimetres, relative to 1900. The historical changes (black) are observed by tide gauges before 1992 and altimeters afterwards. The future changes to 2100 (coloured lines and shading) are assessed consistently with observational constraints based on emulation of CMIP, ice-sheet, and glacier models, and likely ranges are shown for SSP1-2.6 and SSP3-7.0. The dashed curve indicates the potential impact of these deeply uncertain processes. It shows the 83rd percentile of SSP5-8.5 projections that include low-likelihood, high-impact ice-sheet processes that cannot be ruled out; because of low confidence in projections of these processes, this curve does not constitute part of a likely range. Changes relative to 1900 are calculated by adding 0.158 m (observed global mean sea level rise from 1900 to 1995–2014) to simulated and observed changes relative to 1995–2014.
DOI: 10.5061/dryad.h7m7t
title: Data from: Selective pressures on MHC class II genes in the guppy (Poecilia reticulata) as inferred by hierarchical analysis of population structure.

description: Genes of the major histocompatibility complex, which are the most
 polymorphic of all vertebrate genes, are a pre-eminent system for the
 study of selective pressures that arise from host–pathogen interactions.
 Balancing selection capable of maintaining high polymorphism should lead
 to the homogenization of MHC allele frequencies among populations, but
 there is some evidence to suggest that diversifying selection also
 operates on the MHC. However, the pattern of population structure observed
 at MHC loci is likely to depend on the spatial and/or temporal scale
 examined. Here, we investigated selection acting on MHC genes at different
 geographic scales using Venezuelan guppy populations inhabiting four
 regions. We found a significant correlation between MHC and microsatellite
 allelic richness across populations, which suggests the role of genetic
 drift in shaping MHC diversity. However, compared to microsatellites, more
 MHC variation was explained by differences between populations within
 larger geographic regions and less by the differences between the regions.
 Furthermore, among proximate populations, variation in MHC allele
 frequencies was significantly higher compared to microsatellites,
 indicating that selection acting on MHC may increase population structure
 at small spatial scales. However, in populations that have significantly
 diverged at neutral markers, the population-genetic signature of
 diversifying selection may be eradicated in the long term by that of
 balancing selection, which acts to preserve rare alleles and thus maintain
 a common pool of MHC alleles.
description: Microsatellite_genotypes_Genepop_formatMicrosatellite genotypes in Genepop formatMHC_genotypes_Genepop_formatMHC genotypes in Genepop format. Microsatellite alleles were encoded as dominant biallelic loci.
DOI: 10.5061/dryad.1hn66
title: Data from: ABCG transporters are required for suberin and pollen wall extracellular barriers in Arabidopsis

description: Effective regulation of water balance in plants requires localized
 extracellular barriers that control water and solute movement. We describe
 a clade of five Arabidopsis thaliana ABCG half-transporters that are
 required for synthesis of an effective suberin barrier in roots and seed
 coats (ABCG2, ABCG6, and ABCG20) and for synthesis of an intact pollen
 wall (ABCG1 and ABCG16). Seed coats of abcg2 abcg6 abcg20 triple mutant
 plants had increased permeability to tetrazolium red and decreased suberin
 content. The root system of triple mutant plants was more permeable to
 water and salts in a zone complementary to that affected by the Casparian
 strip. Suberin of mutant roots and seed coats had distorted lamellar
 structure and reduced proportions of aliphatic components. Root wax from
 the mutant was deficient in alkylhydroxycinnamate esters. These mutant
 plants also had few lateral roots and precocious secondary growth in
 primary roots. abcg1 abcg16 double mutants defective in the other two
 members of the clade had pollen with defects in the nexine layer of the
 tapetum-derived exine pollen wall and in the pollen-derived intine layer.
 Mutant pollen collapsed at the time of anther desiccation. These mutants
 reveal transport requirements for barrier synthesis as well as
 physiological and developmental consequences of barrier deficiency.
description: Supplemental
 datapdf file of supplemental
 Figures S1-S17 and Tables S1-S3 from the publication.Supplementary material 8-14
 smaller.pdfSupp dataset 1 seq
 alignment for phylogenyText file of alignment
 of ABCG proteins studied in the work.Supp dataset
 S2Supplemental Dataset S2.
 Translatome data for suberin biosynthesis and ABCG genes in different root
 and shoot cell types.Supp dataset
 S3Supplemental Dataset S3.
 Expression of NaCl-inducible suberin biosynthesis and ABCG genes in
 selected root cell types.
DOI: 10.5061/dryad.j96r3
title: Data from: Evidence that microgynes of Myrmica rubra ants are social parasites that attack old host colonies

description: Ant microgynes are miniaturized queen forms found together with normal
 queens (macrogynes) in species occurring across the ant phylogeny. Their
 role is not yet fully understood: in some cases, they seem to be
 nonparasitic alternative reproductive morphs, in others incipient social
 parasites, and thus potential models for studying the evolution of social
 parasitism. Whether they are regarded as parasitic or not has
 traditionally been based on genetic differentiation from syntopic
 macrogynes and/or the queen/worker ratio of their offspring rather than
 measuring fitness traits. We confirmed previously reported genetic
 differentiation between microgynes and macrogynes of Myrmica rubra in a
 population studied for the first time. Further, we measured virulence and
 infectivity of M. rubra microgynes in a controlled laboratory experiment.
 Nests headed only by macrogynes (controls), only by microgynes, and
 naturally and artificially mixed nests were kept under identical
 conditions. We found reduction in worker numbers of both naturally and
 artificially mixed macrogyne/microgyne nests compared with controls, and
 strong reduction but also surprising variation in fitness of nests headed
 only by microgynes. Microgyne nests produced workers, males and
 microgynes. Microgynes did not themselves reproduce in artificially mixed
 nests, but reproduced most in naturally mixed nests that had lost their
 macrogyne queen. This, together with higher mortality of field-collected
 macrogyne queens from naturally infested colonies and greater estimated
 relative age of macrogyne queens in naturally infected nests, suggests
 that they preferentially exploit older host colonies. We conclude that M.
 rubra microgynes are intraspecific social parasites specialized on
 exploiting old host colonies.
description: Data
 JEB-2014-00383.R1Excel file with 8 sheets
 containing all data used for this publication. Sheet 1: microsatellite
 allele calls underlying Figure 1. Sheet 2: survey of original nests (Fig.
 2). Sheet 3: all observational counts on laboratory nests, including nests
 that changed type (used for the comparison of pupae produced). Sheet 4:
 observational counts on laboratory nests encluding nests that changed type
 (used for the comparison of relative worker no.). Sheet 5: macrogyne queen
 longevity data, e.g. used in Fig. 3d. Sheet 6: longevity data of
 microgynes introduced into foreign colonies. Sheet 7: the comparison of
 macrogyne production in the field vs the lab (binary presence/absence
 data). Sheet 8: grey scale data of pictures taken from thorax' of
 macrogyne queens, used for estimation of relative age.
DOI: 10.5061/dryad.8f64f
title: Data from: Hallauer's Tusón: a decade of selection for tropical- to-temperate phenological adaptation in maize

description: Crop species exhibit an astounding capacity for environmental adaptation,
 but genetic bottlenecks resulting from intense selection for adaptation
 and productivity can lead to a genetically vulnerable crop. Improving the
 genetic resiliency of temperate maize depends upon the use of tropical
 germplasm, which harbors a rich source of natural allelic diversity. Here,
 the adaptation process was studied in a tropical maize population
 subjected to 10 recurrent generations of directional selection for early
 flowering in a single temperate environment in Iowa, USA. We evaluated the
 response to this selection across a geographical range spanning from
 43.05° (WI) to 18.00° (PR) latitude. The capacity for an all-tropical
 maize population to become adapted to a temperate environment was revealed
 in a marked fashion: on average, families from generation 10 flowered 20
 days earlier than families in generation 0, with a nine-day separation
 between the latest generation 10 family and the earliest generation 0
 family. Results suggest that adaptation was primarily due to selection on
 genetic main effects tailored to temperature-dependent plasticity in
 flowering time. Genotype-by-environment interactions represented a
 relatively small component of the phenotypic variation in flowering time,
 but were sufficient to produce a signature of localized adaptation that
 radiated latitudinally, in partial association with daylength and
 temperature, from the original location of selection. Furthermore, the
 original population exhibited a maladaptive syndrome including excessive
 ear and plant heights along with later flowering; this was reduced in
 frequency by selection for flowering time.
description: Raw and filtered trial
 dataData from
 multi-environment trial. Raw and filtered trial data. Includes brief
 description of content. See publication for additional
 details.teixeira_etal_rawdata.csv
DOI: 10.5061/dryad.rb5nc
title: Data from: Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia)

description: Next-generation genomic sequencing promises to quickly and cheaply resolve
 remaining contentious nodes in the Tree of Life, and facilitates
 species-tree estimation while taking into account stochastic genealogical
 discordance among loci. Recent methods for estimating species trees bypass
 full likelihood-based estimates of the multi-species coalescent, and
 approximate the true species-tree using simpler summary metrics. These
 methods converge on the true species-tree with sufficient genomic
 sampling, even in the anomaly zone. However, no studies have yet evaluated
 their efficacy on a large-scale phylogenomic dataset, and compared them to
 previous concatenation strategies. Here, we generate such a dataset for
 Caenophidian snakes, a group with &gt;2500 species that contains
 several rapid radiations that were poorly resolved with fewer loci. We
 generate sequence data for 333 single-copy nuclear loci with ∼100%
 coverage (∼0% missing data) for 31 major lineages. We estimate phylogenies
 using neighbor joining, maximum parsimony, maximum likelihood, and three
 summary species-tree approaches (NJst, STAR, and MP-EST). All methods
 yield similar resolution and support for most nodes. However, not all
 methods support monophyly of Caenophidia, with Acrochordidae placed as the
 sister taxon to Pythonidae in some analyses. Thus, phylogenomic
 species-tree estimation may occasionally disagree with well-supported
 relationships from concatenated analyses of small numbers of nuclear or
 mitochondrial genes, a consideration for future studies. In contrast for
 at least two diverse, rapid radiations (Lamprophiidae and Colubridae),
 phylogenomic data and species-tree inference do little to improve
 resolution and support. Thus, certain nodes may lack strong signal, and
 larger datasets and more sophisticated analyses may still fail to resolve
 them.
description: col33_EMREMR Treecol33_MLML Treecol33_MLML gene trees, in ordercol33_MPMP Treecol33_MPEstMPEST Treecol33_NJNJ Treecol33_NJstNJst Treecol33_STARSTAR TreeColubroidea33_Data33 taxa sequenced for 333 loci