cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.574sv
title: Data from: Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook Salmon (Oncorhynchus tshawytscha) in the California Current Large Marine Ecosystem

description: Chinook Salmon is an economically and ecologically important species, and
 populations from the west coast of North America are a major component of
 fisheries in the North Pacific Ocean. The anadromous life history strategy
 of this species generates populations (or stocks) that typically are
 differentiated from neighboring populations. In many cases, it is
 desirable to discern the stock of origin of an individual fish or the
 stock composition of a mixed sample to monitor the stock-specific effects
 of anthropogenic impacts and alter management strategies accordingly.
 Genetic stock identification (GSI) provides such discrimination, and we
 describe here a novel GSI baseline composed of genotypes from more than
 8000 individual fish from 69 distinct populations at 96 single nucleotide
 polymorphism (SNP) loci. The populations included in this baseline
 represent the likely sources for more than 99% of the salmon encountered
 in ocean fisheries of California and Oregon. This new genetic baseline
 permits GSI with the use of rapid and cost-effective SNP genotyping, and
 power analyses indicate that it provides very accurate identification of
 important stocks of Chinook Salmon. In an ocean fishery sample, GSI
 assignments of more than 1000 fish, with our baseline, were highly
 concordant (98.95%) at the reporting unit level with information from the
 physical tags recovered from the same fish. This SNP baseline represents
 an important advance in the technologies available to managers and
 researchers of this species.
description: Chinook salmon SNP
 baseline 2014Included here are
 baseline genotypes at 95 SNPs (species diagnostic marker has been
 excluded) for 7984 Chinook salmon from 68 distinct populations, ranging
 from California to Alaska. Genotypes are also included for a single sample
 (n=47) of California coho salmon. Data were collected on a Fluidigm EP1
 platform using 96.96 Dynamic Arrays. The archive contains three files: 1)
 2010_Baseline_SNPset.txt is the genotype data in gsi_sim format (very
 similar to GENEPOP) with a header indicating the number of samples and
 loci, a list of assay names, population blocks denoted with
 "POP", and tab-delimited genotypes with one allele per column;
 2) ReportingUnits_SNPset_2010.txt indicates which populations are included
 in each reporting unit; 3) SNP_names.txt is simply a list of assay names.
 In order to these data with the software gsi_sim, all three files should
 be present in the Baseline directory.Clemento_etal_2014_Chinook_SNP_baseline.zip
DOI: 10.5061/dryad.819b0
title: Data from: Parental and hybrid Daphnia from the D. longispina complex: long-term dynamics in genetic structure and significance of overwintering modes

description: In recent decades, hybridization has become a focus of attention because
 of its role in evolutionary processes. However, little is known about
 changes in genetic structure within and between parental species and
 hybrids over time. Here, we studied processes of genetic change in
 parental species and hybrids from the Daphnia longispina complex
 (Crustacea, Cladocera) over a period of six years across ten habitats.
 These cyclical parthenogens respond to fluctuating environments by
 switching from asexual to sexual reproduction. Importantly, sexually
 produced diapausing eggs, which resist extreme conditions such as low
 temperatures and serve as dispersal stages, are produced to a lower extent
 by hybrids. Long-term microsatellite data revealed clear differences
 between hybrids and parental species. In hybrids, clonal diversity values
 were lower, whereas heterozygosity and linkage disequilibrium values were
 higher compared to parental species. Clonal diversity of hybrids responded
 to the strength of the winter, with cold winters resulting in few
 genotypes in the following spring. In time windows when only asexual
 hybrid females survive, priority effects will favour the establishment of
 the hybrid offspring before hatchlings from parental diapause eggs can
 enter the community. The constant high levels of heterozygosity maintained
 by clonal reproduction in hybrids might lead to their successful
 establishment over time, when they are able to escape competition from
 both parental species. Although we found evidence that hybrids diversity
 depends on fluctuating environments, a direct link between hybrid
 abundance and the strength of winter was missing. Because of reduced
 adaptability in clonally reproducing hybrids, multiple factors must
 contribute to promoting their long-term success in fluctuating
 environments.
description: microsatellite
 dataGenepop file of the
 whole microsatellite data used for species assignment with DFCA and
 NewHybrid.dryadNewHybridmicrosatellite data without individuals with missing loci (expect SwiD2)Genepop file for microsatellite data used for all analyses. Individuals with missing loci were deleted for this file.dryadnomissing
DOI: 10.5061/dryad.4j07v
title: Data from: Extensive heterosis in growth of yeast hybrids is explained by a combination of genetic models

description: Heterosis, also known as hybrid vigor, is the superior performance of a
 heterozygous hybrid relative to its homozygous parents. Despite the
 scientific curiosity of this phenotypic phenomenon and its significance
 for food production in agriculture, its genetic basis is insufficiently
 understood. Studying heterosis in yeast can potentially yield insights
 into its genetic basis, can allow one to test the different hypotheses
 that have been proposed to explain the phenomenon and allows better
 understanding of how to take advantage of this phenomenon to enhance food
 production. We therefore crossed 16 parental yeast strains to form 120
 yeast hybrids, and measured their growth rates under five environmental
 conditions. A considerable amount of dominant genetic variation was found
 in growth performance, and heterosis was measured in 35% of the
 hybrid–condition combinations. Despite previous reports of correlations
 between heterosis and measures of sequence divergence between parents, we
 detected no such relationship. We used several analyses to examine which
 genetic model might explain heterosis. We found that dominance
 complementation of recessive alleles, overdominant interactions within
 loci and epistatic interactions among loci each contribute to heterosis.
 We concluded that in yeast heterosis is a complex phenotype created by the
 combined contribution of different genetic interactions.
description: Table S3. Strain growth
 phenotypes under five conditions.This table contains the
 doubling time value of all strains under five conditions. For each strain,
 replicate measurements are included.Table
 S3.xlsxTable S4. Growth
 phenotype of the 7 x 37 BC1 population.This file contains the
 mean doubling time of parents, hybrid and each BC1 strain under two
 temperatures.Table
 S4.xlsxTable S5. Growth
 phenotype of the 38 x 37 BC1 population.This file contains the
 mean doubling time of parents, hybrid and BC1 strains under two
 temperatures.Table
 S5.xlsx
DOI: 10.5061/dryad.c8335
title: Data from: Evolution of the ARF gene family in land plants: old domains, new tricks

description: Auxin Response Factors (ARF) are key players in plant development. They
 mediate the cellular response to the plant hormone auxin by activating or
 repressing the expression of downstream developmental genes. The pivotal
 activation function of ARF proteins is enabled by their four-domain
 architecture, which includes both DNA-binding and protein dimerization
 motifs. To determine the evolutionary origin of this characteristic
 architecture, we built a comprehensive dataset of 224 ARF-related protein
 sequences that represents all major living divisions of land plants,
 except hornworts. We found that ARFs are split into three subfamilies that
 could be traced back to the origin of the land plants. We also show that
 repeated events of extensive gene duplication contributed to the expansion
 of those three original subfamilies. Further examination of our dataset
 uncovered a broad diversity in the structure of ARF transcripts and
 allowed us to identify an additional conserved motif in ARF proteins. We
 found that additional structural diversity in ARF proteins is mainly
 generated by two mechanisms: genomic truncation and alternative splicing.
 We propose that the loss of domains from the canonical, four-domain ARF
 structure has promoted functional shifts within the ARF family by
 disrupting either dimerization or DNA binding capabilities. For instance,
 the loss of dimerization domains in some ARFs from moss and spikemoss
 genomes leads to proteins which are reminiscent of Aux/IAA proteins,
 possibly providing a clue on the evolution of these modulators of ARF
 function. We also assessed the functional impact of alternative splicing
 in the case of ARF4, for which we have identified a novel isoform in
 Arabidopsis thaliana. Genetic analysis showed that these two transcripts
 exhibit markedly different developmental roles in A. thaliana. Gene
 duplications, domain rearrangement and post-transcriptional regulation
 have thus enabled a subtle control of auxin signaling through ARF proteins
 that may have contributed to the critical importance of these regulators
 in plant development and evolution.
description: figS1figS1_PhyloBayesfigs1_RAxMLfigS1_RAxMLfigS2figS2_RAxMLfigS3_domainARFfigS3_domainARF_RAxMLfigS3_domainB3figS3_domainB3_RAxMLfigS3_domains34figS3_domains34_RAxMLfigS4figS4_RAxML
DOI: 10.5061/dryad.70c34
title: Data from: Comparative analysis of principal components can be misleading

description: Most existing methods for modeling trait evolution are univariate,
 although researchers are often interested in investigating evolutionary
 patterns and processes across multiple traits. Principal components
 analysis (PCA) is commonly used to reduce the dimensionality of
 multivariate data so that univariate trait models can be fit to individual
 principal components. The problem with using standard PCA on
 phylogenetically structured data has been previously pointed out yet it
 continues to be widely used in the literature. Here we demonstrate
 precisely how using standard PCA can mislead inferences: The first few
 principal components of traits evolved under constant-rate multivariate
 Brownian motion will appear to have evolved via an “early burst” process.
 A phylogenetic PCA (pPCA) has been proprosed to alleviate these issues.
 However, when the true model of trait evolution deviates from the model
 assumed in the calculation of the pPCA axes, we find that the use of pPCA
 suffers from similar artifacts as standard PCA. We show that data sets
 with high effective dimensionality are particularly likely to lead to
 erroneous inferences. Ultimately, all of the problems we report stem from
 the same underlying issue—by considering only the first few principal
 components as univariate traits, we are effectively examining a biased
 sample of a multivariate pattern. These results highlight the need for
 truly multivariate phylogenetic comparative methods. As these methods are
 still being developed, we discuss potential alternative strategies for
 using and interpreting models fit to univariate axes of multivariate data.
description: Online
 AppendicesAppendix showing the
 mathematical equivalency between Ornstein-Uhlenbeck and accelerating
 change models, as well as supplementary figures.suppmat-phylopca.pdf
DOI: 10.5061/dryad.v4t80
title: Data from: Persistent directional selection on body size and a resolution to the paradox of stasis

description: Directional selection on size is common but often fails to result in
 micro-evolution in the wild. Similarly, macro-evolutionary rates in size
 are low relative to the observed strength of selection in nature. We show
 that many estimates of selection on size have been measured on juveniles,
 not adults. Further, parents influence juvenile size by adjusting
 investment per offspring. In light of these observations, we help resolve
 this paradox by suggesting that the observed upward selection on size is
 balanced by selection against investment per offspring, resulting in
 little or no net selection gradient. We find that trade-offs between
 fecundity and juvenile size are common, consistent with the notion of
 selection against investment per offspring. We also find that median
 directional selection on size is positive for juveniles but no net
 directional selection exists for adult size. This is expected because
 parent-offspring conflict exists over size, and juvenile size is more
 strongly affected by investment per offspring than adult size. These
 findings provide qualitative support for the hypothesis that upward
 selection on size is balanced by selection against investment per
 offspring, where parent-offspring conflict over size is embodied in the
 opposing signs of the two selection gradients.
description: JS
 DatabaseEstimates of selection
 on juvenile size traits, compiled by Njal Rollinson and Locke Rowe in
 September 2013. These data are are described as the "J-S
 Database" in the main text. Both the data included in our formal
 selection analyses as well as data omitted from formal analyses are
 included in this dataset.JS_Database_Dryad.csvGenetic & Phenotypic CorrelationsGenetic (rA) and phenotypic (rP) correlations between size and number of offspring collected from the literature.Genetic_Phenotypic_Correlations_Dryad.csvKD-DatabaseThese data represent the K-D Database, as defined in the main text. These selection estimates are not new; they were extracted from previously-compiled databases on phenotypic selection. They are presented here in Dryad only to facilitate replication of results presented in the main text, and to allow the reader to determine which studies estimated selection on juvenile size traits, and which studies estimated selection on adult size traits. For original data, consult: [Kingsolver, J., and S. Diamond. 2011. Data from: Phenotypic selection in natural populations: what limits directional selection? Dryad Digit. Repos. doi10.5061/dryad.7996.] and [Siepielski, A. M., K. M. Gotanda, M. B. Morrissey, S. E. Diamond, J. D. DiBattista, and S. M. Carlson. 2013. The spatial patterns of directional phenotypic selection. Ecol. Lett. 16:1382–92.]
DOI: 10.5061/dryad.5n7p9
title: Data from: In-kennel behavior predicts length of stay in shelter dogs

description: Previous empirical evaluations of training programs aimed at improving dog
 adoption rates assume that dogs exhibiting certain behaviors are more
 adoptable. However, no systematic data are available to indicate that the
 spontaneous behavior of shelter dogs has an effect on adopter preference.
 The aim of the present study was to determine whether any behaviors that
 dogs exhibit spontaneously in the presence of potential adopters were
 associated with the dogs' length of stay in the shelter. A sample of
 289 dogs was videotaped for 1 min daily throughout their stay at a county
 shelter. To account for differences in adopter behavior, experimenters
 varied from solitary passive observers to pairs of interactive observers.
 Dogs behaved more attentively to active observers. To account for adopter
 preference for morphology, dogs were divided into “morphologically
 preferred” and “non-preferred” groups. Morphologically preferred dogs were
 small, long coated, ratters, herders, and lap dogs. No theoretically
 significant differences in behavior were observed between the two
 different dog morphologies. When accounting for morphological preference,
 three behaviors were found to have a significant effect on length of stay
 in all dogs: leaning or rubbing on the enclosure wall (increased median
 length of stay by 30 days), facing away from the front of the enclosure
 (increased by 15 days), and standing (increased by 7 days). When
 combinations of behaviors were assessed, back and forth motion was found
 to predict a longer stay (increased by 24 days). No consistent behavioral
 changes were observed due to time spent at the shelter. These findings
 will allow shelters to focus behavioral modification efforts only on
 behaviors likely to influence adopters' choices.
description: Protopopova et al. Raw
 DataThis is the raw data for
 all dogs across all days. Please contact the main author if any
 clarifications are required.Protopopova et al.
 InKennelBxPredictsStay.xlsxProtopopova et al. All
 CodesAll codes (STATA) used
 to analyze data. Please contact the first author for any
 clarifications.Protopopova et
 al.Codes.zip
DOI: 10.5061/dryad.r620q
title: Data from: Genetic perturbation of key central metabolic genes extends life span in Drosophila and affects response to dietary restriction

description: There is a connection between nutrient inputs, energy-sensing pathways,
 lifespan variation and aging. Despite the role of metabolic enzymes in
 energy homeostasis and their metabolites as nutrient signals, little is
 known about how their gene expression impacts lifespan. In this report, we
 use P-element mutagenesis in Drosophila to study the effect on lifespan of
 reductions in expression of seven central metabolic enzymes, and contrast
 the effects on normal diet and dietary restriction. The major observation
 is that for five of seven genes, the reduction of gene expression extends
 lifespan on one or both diets. Two genes are involved in redox balance,
 and we observe that lower activity genotypes significantly extend
 lifespan. The hexokinases also show extension of lifespan with reduced
 gene activity. Since both affect the ATP/ADP ratio, this connects with the
 role of AMP-activated protein kinase as an energy sensor in regulating
 lifespan and mediating caloric restriction. These genes possess
 significant expression variation in natural populations, and our
 experimental genotypes span this level of natural activity variation. Our
 studies link the readout of energy state with the perturbation of the
 genes of central metabolism and demonstrate their effect on lifespan.
description: Gdh Life Span Raw
 DataGPDH Life Span Raw
 DataHexA Life Span Raw
 DataHexC Life Span Raw
 DataIdh Life Span Raw
 DataMDH2 Life Span Raw
 DataMen Life Span Raw
 Data
DOI: 10.5061/dryad.p3v3n
title: Data from: Muscle-tendon unit length changes differ between young and adult sprinters in first stance phase of sprint running

description: The aim of this study was to compare young and adult sprinters on several
 biomechanical parameters that were previously highlighted as
 performance-related and to determine the behaviour of several
 muscle-tendon units (MTU) in the first stance phase following a block
 start in sprint running. The ground reaction force (GRF) and kinematic
 data were collected from 16 adult and 21 young well-trained sprinters. No
 difference between the groups was found in some of the
 previously-highlighted performance-related parameters (ankle joint
 stiffness, the range of dorsiflexion and plantar flexor moment).
 Interestingly, the young sprinters showed a greater maximal and mean ratio
 of horizontal to total GRF, which was mainly attributed to a greater
 horizontal GRF relative to body mass and resulted in a greater change in
 horizontal centre of mass (COM) velocity during the stance phase in the
 young compared to the adult sprinters.. Results from the MTU length
 analyses showed that adult sprinters had more MTU shortening and higher
 maximal MTU shortening velocities in all plantar flexors and the rectus
 femoris. Although previously-highlighted performance-related parameters
 could not explain the greater 100 m sprinting times in the adult
 sprinters, differences were found in the behaviour of the MTU of the
 plantar flexors and rectus femoris during the first stance phase. The
 pattern of length changes in these MTUs provide ideal conditions for the
 use of elastic energy storage and release for power enhancement.
description: MatlabData_RSOSMatlab file containing all data to be published
DOI: 10.5061/dryad.2434f
title: Data from: Chromosome numbers, Sudanese wild forms, and classification of the watermelon genus Citrullus, with 50 names allocated to seven biological species

description: Watermelons are among the most important vegetable crops worldwide, but
 targeted breeding is hindered by problems with Citrullus taxonomy. Here we
 clarify nomenclature and species relationships in Citrullus, its
 chromosome numbers, and the likely geographic region of watermelon
 domestication. We correct an erroneous chromosome count in recent
 literature, provide a count for an understudied species, and data on
 chromosome numbers for the entire genus. We also use a nuclear/plastid
 locus phylogeny to summarize data on Citrullus sexual systems, loss of
 tendrils, life history, and geographic ranges. Key insights from new
 sequences are that (i) material of C. vulgaris var. “colocynthoides”,
 collected by Schweinfurth in Egypt in 1882 represents the colocynth, C.
 colocynthis, and (ii) the citron or bitter watermelon, C. amarus, is
 indeed a separate species, not a subspecies of the dessert watermelon.
 Schweinfurth’s varietal name, a nomen nudum, has been widely used for
 seeds as old as 5400 BP, and it now needs to be investigated whether these
 seeds are colocynths, watermelon or a hybrid. To help improve Citrullus
 taxonomy and nomenclature, we allocate some 50 scientific names to seven
 biological species, tabulate chromosome counts, and provide notes on
 misidentified germplasms traceable by accession numbers. More
 wild-collected herbarium-verified material from northeast Africa is
 urgently needed, especially given the discovery of Russian breeders that
 populations of wild “cordophanus” from Sudan are closer to the cultivated
 watermelon than are any other wild populations so far known.
description: Citrullus_matrix_for_Taxon_paper_20Nov2017DNA alignment, 47 taxa, NCHAR=9224
DOI: 10.5061/dryad.8651
title: Data from: Establishment and maintenance of adaptive genetic divergence under migration, selection, and drift

description: There is a long tradition in population genetics of exploring the
 maintenance of variation under migration-selection balance using
 deterministic models that assume infinite population size. With finite
 population size, stochastic dynamics can greatly reduce the potential for
 the maintenance of polymorphism, but this has yet to be explored in
 detail. Here, classical two-patch models are extended to predict: i) the
 probability of a locally beneficial mutation rising in frequency in the
 patch where it is favored, and ii) the critical threshold migration rate
 above which the maintenance of polymorphism is much less likely.
 Individual-based simulations show that these approximations provide
 accurate predictions across a wide range of parameter space.
description: yeaman_otto_whitlock_2011_source_code_documentation