cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f7dm5v5j
title: Data from: Strong divergence in trait means but not in plasticity across hatchery and wild populations of sea-run brown trout Salmo trutta

description: There is ample evidence that organisms adapt to their native environment
 when gene flow is restricted. However, evolution of plastic responses
 across discrete environments is less well examined. We studied divergence
 in means and plasticity across wild and hatchery populations of sea-run
 brown trout (Salmo trutta) in a common garden experiment with two rearing
 environments (hatchery and a nearly natural experimental stream). Since
 natural and hatchery environments differ, this arrangement provides an
 experiment in contemporary adaptation across the two environments. A
 QST-FST approach was used to investigate local adaptation in survival and
 growth over the first summer. We found evidence for divergent selection in
 survival in one year and in body length in both years and rearing
 environments. In general, the hatchery populations had higher survival and
 larger body size in both environments. QST in body size did not differ
 between the rearing environments and constitutive divergence in the means
 was in all cases stronger than divergence in the plastic responses. These
 results suggest that in this system constitutive changes in mean trait
 values are more important for local adaptation than increased plasticity.
 In addition, ex-situ rearing conditions induce changes in trait means that
 are adaptive in the hatchery, but potentially harmful in the wild,
 suggesting that hatchery rearing is likely to be a sub-optimal management
 strategy for trout populations facing selection in the stream environment.
description: longdataYEAR1Data for the first year's experiment. Under Rearing_environment, exp is the experimental stream and lab the hatchery.longdataYEAR2Data for the second year's experiment. Under Rearing_environment, exp is the experimental stream and lab the hatchery.MicrosatelitesMicrosatellite data used in the manuscript. See the manuscript for details of the loci.
DOI: 10.5061/dryad.44pm4pq6
title: Data from: Short-term genetic changes: evaluating effective population size estimates in a comprehensively described brown trout (Salmo trutta) population

description: The effective population size (Ne) is notoriously difficult to accurately
 estimate in wild populations as it is influenced by a number of parameters
 that are difficult to delineate in natural systems. The different methods
 that are used to estimate Ne are impacted variously by different processes
 at the population level, such as the life-history characteristics of the
 organism, gene flow, population substructure, as well as by the frequency
 patterns of genetic markers used and the sampling design. Here, we compare
 Ne estimates obtained by different genetic methods and from demographic
 data, and elucidate how the estimates are impacted by various factors in
 an exhaustively sampled and comprehensively described natural brown trout
 (Salmo trutta) system. In general, the methods yielded rather congruent
 estimates, and we ascribe that to the adequate genotyping and exhaustive
 sampling. Effects of violating the assumptions of the different methods
 were nevertheless apparent. In accordance with theoretical studies, skewed
 allele frequencies would underestimate temporal allele frequency changes
 and thereby upwardly bias Ne if not accounted for. Overlapping generations
 and iteroparity would also upwardly bias Ne when applied to temporal
 samples taken over short time spans. Gene flow from a genetically not very
 dissimilar source population decreases temporal allele frequency changes
 and thereby acts to increase estimates of Ne. Our study reiterates the
 importance of adequate sampling, quantification of life-history parameters
 and gene flow, and incorporating these data into the Ne estimation.
description: ALLIncludes all genotypes
 obtained from the focal Bellbekken river as well as the adjacent Julussa
 river, SE Norway. In the file are included a column with the individual ID
 (trout), the season (fall/autumn), the year (2002-2006), the river
 (Bellbekken/Julussa), the age and correspondligly the year an individual
 is born, the station (2-25) for the Bellbekken fish, as well as all 15
 microsatellite loci the individuals were genotyped for. Julussa fish were
 not aged. The file also includes the recaptures from
 Bellbekken.
DOI: 10.5061/dryad.7th9747p
title: Data from: Demographic fate of Arabidopsis thaliana cohorts of autumn- and spring-germinated plants along an altitudinal gradient

description: SUMMARY: 1) Understanding how plants respond and adapt to varying
 environmental conditions has attracted the attention of plant ecologists
 for decades. To study this process, altitudinal gradients are used because
 of their inherent variation in environmental conditions. In the current
 scenario of global warming, altitudinal gradients may also represent a
 valuable resource to deepen our understanding about plant adaptive
 responses to predicted changes in environmental conditions. 2) Nowadays,
 the study of adaptive variation demands equal contributions from ecology
 and genetics. We need to assess the effects of selective pressures on
 phenotypic variation but also the genetic and molecular basis of
 phenotypic traits. The annual plant Arabidopsis thaliana represents a
 useful model system for investigating adaptive variation. Here, I
 characterized patterns of life cycle variation in natural A. thaliana
 populations along an altitudinal gradient to unravel how the species copes
 with different environmental conditions. 3) I periodically monitored
 thousands of plants from eight populations in NE Spain over five years
 (2007–2011) to estimate survival and fecundity schedules for autumn- and
 spring-germinated plants. Data were used to estimate net reproductive rate
 for each life cycle type. Data were regressed against altitude to detect
 altitudinal climatic clines for life cycle variation. 4) Survival of
 spring-germinated A. thaliana plants was significantly higher than that of
 winter-germinated plants. Plants from both cohorts exhibited similar
 fecundity values. The net reproductive rate of spring-germinated plants
 was four-fold higher than that of autumn-germinated plants. The proportion
 of spring-germinated plants increased significantly with altitude. 5)
 Synthesis. Arabidopsis thaliana can behave as a winter or spring annual
 plant. Nevertheless, the spring annual life cycle is clearly relevant to
 maintain A. thaliana populations, particularly at high-elevation
 locations. It is suggested that germination timing represents one of the
 most relevant traits to focus our efforts to understand adaptive variation
 in A. thaliana. The results illustrate the potential of annual plants to
 adjust their life cycles to varying environmental conditions encountered
 along a climatic gradient, which could mitigate the effects of global
 warming on annual plant populations.
description: Dryad_cohort_data_23mar12Survival and fecundity data of autumn- and spring-germinated individuals from eight populations of Arabidopsis thaliana during five years (2007-2011).
DOI: 10.5061/dryad.6r42r366
title: Data from: Assessment of the food habits of the Moroccan dorcas gazelle in M’Sabih Talaa, West central Morocco, using the trnL approach

description: Food habits of the Moroccan dorcas gazelle, Gazella dorcas massaesyla,
 previously investigated in the 1980s using microhistological fecal
 analysis, in the M’Sabih Talaa reserve west central Morocco, were
 re-evaluated over three seasons (spring, summer and autumn 2009) using the
 trnL approach to determine the diet composition and its seasonal variation
 from fecal samples. Taxonomic identification was carried out using the
 identification originating from the database built from EMBL and the list
 of plant species within the reserve. The total taxonomic richness in the
 reserve was 130 instead of 171 species in the 1980s. The diet composition
 revealed to be much more diversified (71 plant taxa belonging to 57 genus
 and 29 families) than it was 22 years ago (29 identified taxa). Thirty
 four taxa were newly identified in the diet while 13 reported in 1986-87
 were not found. Moroccan dorcas gazelle showed a high preference to Acacia
 gummifera, Anagallis arvensis, Glebionis coronaria, Cladanthus arabicus,
 Diplotaxis tenuisiliqua, Erodium salzmannii, Limonium thouini, Lotus
 arenarius and Zizyphus lotus. Seasonal variations occurred in both number
 (40-41 taxa in spring-summer and 49 taxa in autumn vs. respectively 23-22
 and 26 in 1986-1987) and taxonomic type of eaten plant taxa. This dietary
 diversification could be attributed either to the difference in methods of
 analysis, trnL approach having a higher taxonomic resolution, or a
 potential change in nutritional quality of plants over time.
description: Baamrane_gh_sequence_dataBaamrane_gh_filtered_dataBaamrane_ITSAst_sequence_dataBaamrane_ITSAst_filtered_dataBaamrane_ITSPoa_sequence_dataBaamrane_ITAPoa_filtered_data
DOI: 10.5061/dryad.2m3h2m5p
title: Data from: Development and evaluation of 200 novel SNP assays for population genetic studies of westslope cutthroat trout and genetic identification of related taxa

description: DNA sequence data were collected and screened for single nucleotide
 polymorphisms (SNPs) in westslope cutthroat trout (Oncorhynchus clarki
 lewisi) and also for substitutions that could be used to genetically
 discriminate rainbow trout (O. mykiss) and cutthroat trout, as well as
 several cutthroat trout subspecies. In total, 260 expressed sequence
 tag-derived loci were sequenced and allelic discrimination genotyping
 assays developed from 217 of the variable sites. Another 50 putative SNPs
 in westslope cutthroat trout were identified by
 restriction-site-associated DNA sequencing, and seven of these were
 developed into assays. Twelve O. mykiss SNP assays that were variable
 within westslope cutthroat trout and 12 previously published SNP assays
 were also included in downstream testing. A total of 241 assays were
 tested on six westslope cutthroat trout populations (N = 32 per
 population), as well as collections of four other cutthroat trout
 subspecies and a population of rainbow trout. All assays were evaluated
 for reliability and deviation from Hardy–Weinberg and linkage equilibria.
 Poorly performing and duplicate assays were removed from the data set, and
 the remaining 200 assays were used in tests of population differentiation.
 The remaining markers easily distinguished the various subspecies tested,
 as evidenced by mean GST of 0.74. A smaller subset of the markers (N = 86;
 average GST = 0.40) was useful for distinguishing the six populations of
 westslope cutthroat trout. This study increases by an order of magnitude
 the number of genetic markers available for the study of westslope
 cutthroat trout and closely related taxa and includes many markers in
 genes (developed from ESTs).
description: Genotypes and related
 dataThis file contains
 genotypes for all 12 collections tested in the ms as well as related data
 such as GenePop files and raw data used to generate
 figures.Ocl_analysis_All-Loci.xlsx
DOI: 10.5061/dryad.5k3t47p0
title: Data from: The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes

description: Wood is a major pool of organic carbon that is highly resistant to decay,
 owing largely to the presence of lignin. The only organisms capable of
 substantial lignin decay are white rot fungi in the Agaricomycetes, which
 also contains non–lignin-degrading brown rot and ectomycorrhizal species.
 Comparative analyses of 31 fungal genomes (12 generated for this study)
 suggest that lignin-degrading peroxidases expanded in the lineage leading
 to the ancestor of the Agaricomycetes, which is reconstructed as a white
 rot species, and then contracted in parallel lineages leading to brown rot
 and mycorrhizal species. Molecular clock analyses suggest that the origin
 of lignin degradation might have coincided with the sharp decrease in the
 rate of organic carbon burial around the end of the Carboniferous period.
description: Supplementary Electronic
 Files
DOI: 10.5061/dryad.ff586c8k
title: Data from: Endosymbiotic calcifying bacteria: a new cue for the origin of calcification in Metazoa?

description: Sponges show the highest diversity of associated bacteria among marine
 invertebrates. Immunological evidence traces the origin of the sponge
 bacterial symbioses to the Precambrian era. Hence, sponges appear to be
 ideally suited for studying the evolutionary origins of
 prokaryote-metazoan associations. Sponges produce either calcareous or
 siliceous skeletons, which only coexist in a relict group of demosponges,
 the sclerosponges. We report here, for the first time, intensive
 calcification in non-sclerosponge siliceous demosponges. Calcification is
 mediated by endosymbiotic bacteria (calcibacteria) located in
 archeocyte-like sponge cells. These calcibacteria are deprived from
 bacterial walls and divide within sponge cells until they became
 surrounded by a calcitic sheet, being subsequently extruded to the sponge
 subectosomal (subepithelial) zone. Thousands of bacteria-produced calcitic
 spherules cover the surface of the host sponges, forming a cortex-like
 structure that mimics a rudimentary peripheral skeleton. Calcibacteria are
 vertically transferred to the sponge larvae during embryogenesis. Calcium
 detoxification may have generated this symbiotic association, with some
 additional benefits for the sponges, such as skeletal formation and
 deterrence from predation. This unique symbiosis holds implications for
 sponge biology and may advance discussions on the role of bacteria in
 early biocalcification processes in metazoans.
description: Fig2Simbiotic calcifying
 bacteria in sponges, showed by optical microscopy and In situ
 hibridation.
DOI: 10.5061/dryad.rd45qj52
title: Data from: Genetic polymorphism in dopamine receptor D4 is associated with early body condition in a large population of greater flamingos, Phoenicopterus roseus

description: Body condition is an important determinant of fitness in many natural
 populations. However, as for many fitness traits, the underlying genes
 that regulate body condition remain elusive. The dopamine receptor D4 gene
 (DRD4) is a promising candidate as dopamine is known to play an important
 role in the regulation of food intake and the metabolism of both glucose
 and lipids in vertebrates. In this study we take advantage of a large
 dataset of greater flamingos, Phoenicopterus roseus, to test whether DRD4
 polymorphism predicts early body condition (EBC) while controlling for
 whole genome effects of inbreeding and outbreeding using microsatellite
 multi-locus heterozygosity (MLH). We typed 670 of these individuals for
 exon 3 of the homologue of the human DRD4 gene and 10 microsatellite
 markers. When controlling for effects of yearly environmental variations
 and differences between sexes, we found strong evidence of an association
 between exon 3 DRD4 polymorphisms and EBC, with 2.2-2.3% of the variation
 being explained by DRD4 polymorphism, whereas there was only weak evidence
 that MLH predicts EBC. Because EBC is most likely a polygenic trait, this
 is a considerable amount of variation explained by a single gene. This is
 to our knowledge the first study to show an association between exon 3
 DRD4 polymorphism and body condition in nonhuman animals. We anticipate
 that the DRD4 gene as well as other genes coding for neurotransmitters and
 their receptors may play an important role in explaining variation in
 traits that affect fitness.
description: DRD4 polymorphism and
 EBC in greater flamingosOriginal data set from
 which analyses were carried outMolecularEcology.xls
DOI: 10.5061/dryad.qv6hr4mq
title: Data from: Mate choice and the genetic basis for color variation in a polymorphic dart frog: inferences from a wild pedigree

description: Understanding how reproductive barriers evolve during speciation remains
 an important question in evolution. Divergence in mating preferences may
 be a common first step in this process. The striking colour pattern
 diversity of strawberry dart frog (Dendrobates pumilio) populations has
 likely been shaped by sexual selection. Previous laboratory studies have
 shown that females attend to male coloration and prefer to court with
 males of their own colour, suggesting that divergent morphs may be
 reproductively isolated. To test this hypothesis, we used molecular data
 to estimate pedigree relationships from a polymorphic population. Whereas
 in the laboratory both red and yellow females preferred to court with
 males of their own phenotype, our pedigree shows a pattern of assortative
 mating only for red females. In the wild, yellow females appear to be less
 choosy about their mates, perhaps because they incur higher costs
 associated with searching than females of the more common red phenotype.
 We also used our pedigree to investigate the genetic basis for
 colour-pattern variation. The phenotype frequencies we observed were
 consistent with those expected if dorsal background coloration is
 controlled by a single locus, with complete dominance of red over yellow.
 Our results not only help clarify the role of sexual selection in reducing
 gene flow, but also shed light on the mechanisms underlying colour-pattern
 variation among sympatric colour morphs. The difference we observed
 between mating preferences measured under laboratory conditions and the
 pattern of mate choice observed in the wild highlight the importance of
 field studies for understanding behavioural reproductive isolation.
description: Richards-Zawacki et al.
 - COLOR ANALYSISAnalysis of dorsal and
 ventral coloration of the poison frog Dendrobates pumilio from a
 polymorphic (red and yellow) population on Bastimentos Island, Panama.
 Comparisons are made between color classifications made "by eye"
 and those made using analysis of RGB color scores derived from
 standardized photographs using Principle Components Analysis and a
 two-step clustering algorithm in SPSS.Richards-Zawacki et al.
 - FROG MSAT GENOTYPESMicrosatellite
 genotypes, sex, age class, and dorsal color phenotype information for all
 frogs in the study. Missing genotypes are denoted as 000. Input files for
 GenePop 4.1, ARLEQUIN 3.0, CERVUS 3.0, COLONY 2.0 and MASTERBAYES 2.47
 were derived from the data in this Excel file.
DOI: 10.48656/106t-rf75
title: Language Quantification Dataset
DOI: 10.48656/xgfg-fb27
title: Language Quantification Dataset
DOI: 10.5061/dryad.t3pr6
title: Data from: Variation in the transcriptional response of threatened coral larvae to elevated temperatures

description: Coral populations have declined worldwide largely due to increased sea
 surface temperatures. Recovery of coral populations depends in part upon
 larval recruitment. Many corals reproduce during the warmest time of year
 when further increases in temperature can lead to low fertilization rates
 of eggs and high larval mortality. Microarray experiments were designed to
 capture and assess variability in the thermal stress responses of Acropora
 palmata larvae from Puerto Rico. Transcription profiles showed a striking
 acceleration of normal developmental gene expression patterns with
 increased temperature. The transcriptional response to heat suggested
 rapid depletion of larval energy stores via peroxisomal lipid oxidation
 and included key enzymes that indicated the activation of the glyoxylate
 cycle. High temperature also resulted in expression differences in key
 developmental signalling genes including the conserved WNT pathway that is
 critical for pattern formation and tissue differentiation in developing
 embryos. Expression of these and other important developmental and thermal
 stress genes such as ferritin, heat shock proteins, cytoskeletal
 components, cell adhesion and autophagy proteins also varied among larvae
 derived from different parent colonies. Disruption of normal developmental
 and metabolic processes will have negative impacts on larval survival and
 dispersal as temperatures rise. However, it appears that variation in
 larval response to high temperature remains despite the dramatic
 population declines. Further research is needed to determine whether this
 variation is heritable or attributable to maternal effects.
description: SuppTableS3_FinalExpression behavior for all probes expressed over background in response to time, temperature, batch, and interactions among the factors. LFC indicates log fold change between treatments. Expression pattern denotes probes that were avove the threshold for significance (LFC&gt;1.5 and Q.value&lt;0.05), and indicates which treatement had higher expression levels.
DOI: 10.5061/dryad.kq5q3
title: Data from: Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces

description: DNA-based techniques have proven useful for defining trophic links in a
 variety of ecosystems and recently developed sequencing technologies
 provide new opportunities for dietary studies. We investigated the diet of
 Australian fur seals (Arctocephalus pusillus doriferus) by pyrosequencing
 prey DNA from faeces collected at three breeding colonies across the
 seals’ range. DNA from 270 faecal samples was amplified with four
 polymerase chain reaction primer sets and a blocking primer was used to
 limit amplification of fur seal DNA. Pooled amplicons from each colony
 were sequenced using the Roche GS-FLX platform, generating &gt; 20 000
 sequences. Software was developed to sort and group similar sequences. A
 total of 54 bony fish, 4 cartilaginous fish and 4 cephalopods were
 identified based on the most taxonomically informative amplicons sequenced
 (mitochondrial 16S). The prevalence of sequences from redbait
 (Emmelichthys nitidus) and jack mackerel (Trachurus declivis) confirm the
 importance of these species in the seals’ diet. A third fish species, blue
 mackerel (Scomber australasicus), may be a more important prey species
 than previously recognised. There were major differences in the
 proportions of prey DNA recovered in faeces from different colonies,
 probably reflecting differences in prey availability. Parallel hard-part
 analysis identified largely the same main prey species as did the
 DNA-based technique, but with lower species diversity and no remains from
 cartilaginous prey. The pyrosequencing approach presented significantly
 expands the capabilities of DNA-based methods of dietary analysis and is
 suitable for large-scale diet investigations on a broad range of animals.
description: 1.SealRocks.454ReadsSequence data (n=8674 reads) from amplicons recovered from Australian fur seal scats collected at Seal Rocks. In fasta format.2.LadyJuliaPercy.454ReadsSequence data (n=9793 reads) from amplicons recovered from Australian fur seal scats collected at Lady Julia Percy. In fasta format.3.Skerries.454ReadsSequence data (n=11648 reads) from amplicons recovered from Australian fur seal scats collected at The Skerries. In fasta format.Seq Quality (zipped) FolderSequence for the corresponding 454 datasetsReference Sequences 16S shortReference Sequences 16S long