cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8061
title: Data from: Do constructional constraints influence cyprinid (Cyprinidae: Leuciscinae) craniofacial coevolution?

description: Constraints on form may determine how organisms diversify. As a result of
 competition for the limited space within the body, investment in adjacent
 structures could represent an evolutionary compromise. For example,
 evolutionary trade-offs resulting from limited space in the head could
 have influenced how the sizes of the jaw muscle, as well as the eyes,
 evolved in North American cyprinid fishes. To test the evolutionary
 independence of the size of these structures, we measured the mass of the
 three major adductor mandibulae muscles and determined the eye volume in
 36 cyprinid species. Using a novel phylogeny, we tested the hypotheses
 that the sizes of these four structures were negatively correlated with
 each other during cyprinid evolution. We found that evolutionary change in
 the adductor mandibulae muscles was generally positively and/or not
 correlated, suggesting that competition for space among cyprinid jaw
 muscles has not influenced their evolution. However, there was a negative
 relationship between mass of adductor mandibulae 1 and eye volume,
 indicating that change in these physically adjacent structures is
 consistent with an evolutionary constructional constraint.
description: HulseyBJLS2011Table 2. Morphometrics of AM mass and Eye Size for the North American cyprinid fish examined. The standard length (SL) and Head length (HL) of fish are given. The mass of the AM1, AM2, and AM3 are given. The eye depth (ED), eye width (EW), and eye height (EH), as well as the calculated eye volume (EV) are also given. The species are placed in order of decreasing HL adjusted eye volumes.
DOI: 10.5061/dryad.0c116
title: Data from: Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells

description: Background: Pluripotent embryonic stem cells (ESCs) have the unique
 ability to differentiate into every cell type and to self-renew. These
 characteristics correlate with a distinct nuclear architecture, epigenetic
 signatures enriched for active chromatin marks and hyperdynamic binding of
 structural chromatin proteins. Recently, several chromatin-related
 proteins have been shown to regulate ESC pluripotency and/or
 differentiation, yet the role of the major heterochromatin proteins in
 pluripotency is unknown. Results: Here we identify Heterochromatin Protein
 1β (HP1β) as an essential protein for proper differentiation, and,
 unexpectedly, for the maintenance of pluripotency in ESCs. In pluripotent
 and differentiated cells HP1β is differentially localized and
 differentially associated with chromatin. Deletion of HP1β, but not HP1α,
 in ESCs provokes a loss of the morphological and proliferative
 characteristics of embryonic pluripotent cells, reduces expression of
 pluripotency factors and causes aberrant differentiation. However, in
 differentiated cells, loss of HP1β has the opposite effect, perturbing
 maintenance of the differentiation state and facilitating reprogramming to
 an induced pluripotent state. Microscopy, biochemical fractionation and
 chromatin immunoprecipitation reveal a diffuse nucleoplasmic distribution,
 weak association with chromatin and high expression levels for HP1β in
 ESCs. The minor fraction of HP1β that is chromatin-bound in ESCs is
 enriched within exons, unlike the situation in differentiated cells, where
 it binds heterochromatic satellite repeats and chromocenters. Conclusions:
 We demonstrate an unexpected duality in the role of HP1β: it is essential
 in ESCs for maintaining pluripotency, while it is required for proper
 differentiation in differentiated cells. Thus, HP1β function both depends
 on, and regulates, the pluripotent state.
description: HP1beta paper
 raw/original microscopy imagesAll raw images used in
 this study at 60X oil NA1.4 lens, were taken using a spinning disk
 confocal microscope (CSUX, Yokogawa, Japan) equipped with an iXon+
 DU-897-BV monochrome EMCCD camera (Andor, UK) mounted on an Olympus IX81
 fully automated microscope, or with an Olympus IX71 epifluorescent
 microscope equipped with a Dp71 camera (Olympus).HP1beta paper microscopy images
 for Dryad.zip
DOI: 10.5061/dryad.7gf83
title: Data from: Male investments in high quality sperm improve fertilization success, but may have negative impact on offspring fitness in whitefish

description: Many ejaculate traits show remarkable variation in relation to male social
 status. Males in disfavoured (subordinate) mating positions often invest
 heavily on sperm motility but may have less available resources on traits
 (e.g., secondary sexual ornaments) that improve the probability of gaining
 matings. Although higher investments in sperm motility can increase the
 relative fertilization success of subordinate males, it is unclear whether
 status-dependent differences in sperm traits could have any consequences
 for offspring fitness. We tested this possibility in whitefish (Coregonus
 lavaretus L.) by experimentally fertilizing the eggs of 24 females with
 the sperm of either highly-ornamented (large breeding tubercles, dominant)
 or less-ornamented (small tubercles, subordinate) males (split-clutch
 breeding design). In comparison to highly-ornamented individuals,
 less-ornamented males had higher sperm motility, which fertilized the eggs
 more efficiently, but produced embryos with impaired hatching success.
 Also offspring size and body condition were lower among less-ornamented
 males. Furthermore, sperm motility was positively associated with the
 fertilization success and offspring size, but only in highly-ornamented
 males. Together our results indicate that male investments on highly
 motile (fertile) sperm is not necessarily advantageous during later
 offspring ontogeny and that male status-dependent differences in sperm
 phenotype may have important effects on offspring fitness in different
 life-history stages.
description: Raw
 dataThis file contains raw
 data for our publication.Raw_data.xls
DOI: 10.5061/dryad.c400d
title: Data from: Genetic isolation between two recently diverged populations of a symbiotic fungus

description: Fungi are an omnipresent and highly diverse group of organisms, making up
 a significant part of eukaryotic diversity. Little is currently known
 about the drivers of fungal population differentiation and subsequent
 divergence of species, particularly in symbiotic, mycorrhizal fungi. Here,
 we investigate the population structure and environmental adaptation in
 Suillus brevipes (Peck) Kuntze, a wind-dispersed soil fungus that is
 symbiotic with pine trees. We assembled and annotated the reference genome
 for Su. brevipes and resequenced the whole genomes of 28 individuals from
 coastal and montane sites in California. We detected two clearly
 delineated coast and mountain populations with very low divergence.
 Genomic divergence was restricted to few regions, including a region of
 extreme divergence containing a gene encoding for a membrane Na+/H+
 exchanger known for enhancing salt tolerance in plants and yeast. Our
 results are consistent with a very recent split between the montane and
 coastal Su. brevipes populations, with few small genomic regions under
 positive selection and a pattern of dispersal and/or establishment
 limitation. Furthermore, we identify a putatively adaptive gene that
 motivates further functional analyses to link genotypes and phenotypes and
 shed light on the genetic basis of adaptive traits.
description: Suillus brevipes single
 nucleotide polymorphism listRaw SNP list from GATK
 on the Californian montane and coastal S. brevipes
 populations.Sb_GATK_SNP.vcfSuillus brevipes Neighbor Joining TreeS. brevipes SNP NJ tree (without singletons)Calculating Population HeterozygocityComputes observed and expected heterozygosity (under HW assumptions).Heterozygocity_population.py
DOI: 10.5061/dryad.b7bq47d
title: Data from: Understanding the evolutionary potential of epigenetic variation: a comparison of heritable phenotypic variation in epiRILs, RILs and natural ecotypes of Arabidopsis thaliana

description: Increasing evidence for epigenetic variation within and among natural
 plant populations has led to much speculation about its role in the
 evolution of plant phenotypes. However, we still have a very limited
 understanding of the evolutionary potential of epigenetic variation, in
 particular in comparison to DNA sequence-based variation. To address this
 question, we compared the magnitudes of heritable phenotypic variation in
 epigenetic recombinant inbred lines (epiRILs) of Arabidopsis thaliana–
 lines that mainly differ in DNA methylation but only very little in DNA
 sequence – with other types of A. thaliana lines that differ strongly also
 in DNA sequence. We grew subsets of two epiRIL populations with subsets of
 two genetic RIL populations, of natural ecotype collections, and of lines
 from a natural population, in a common environment and assessed their
 heritable variation in growth, phenology and fitness. Among-line
 phenotypic variation and broad-sense heritabilities tended to be largest
 in natural ecotypes, but for some traits the variation among epiRILs was
 comparable to that among RILs and natural ecotypes. Within-line phenotypic
 variation was generally similar in epiRILs, RILs and ecotypes. Provided
 that phenotypic variation in epiRILs is mainly caused by epigenetic
 differences, whereas in RILs and natural lines it is largely driven by
 sequence variation, our results indicate that epigenetic variation has the
 potential to create phenotypic variation that is stable and substantial,
 and thus of evolutionary significance.
description: Zhang et al Heredity
 data archiveThis file contains the
 names, descriptions, and phenotype data of each used lines or
 ecotypes.
DOI: 10.5061/dryad.f4t990h
title: Data from: Dead or alive? Sexual conflict and lethal copulatory interactions in long-jawed Tetragnatha spiders

description: Inter- and intra-sexual selection are important driving forces that lead
 to diversification of sexual characteristics. Tetragnatha spiders have
 elongated chelicerae and sexual dimorphism in chelicera length whose
 magnitude varies among species. Because they use their chelicerae during
 copulation and as weapons in male–male competition, this divergence
 reflects repeated inter- and intra-sexual selection. To infer the causes
 of chelicera length diversity, we examined the roles of the elongated
 chelicerae in copulatory behaviour of a Tetragnatha species and clarified
 the interspecific sexual dimorphism of chelicera length in 15 species. The
 longer chelicerae of female Tetragnatha allowed females to kill males,
 suggesting female rejection of mating using the elongated chelicerae.
 Comparisons based on independent contrasts showed that chelicera length
 was significantly positively correlated between the sexes across species,
 possibly reflecting sexually antagonistic coevolution of male and female
 chelicera lengths. However, some species showed male-biased sexual
 dimorphism, indicating that intra-sexual selection (male competition) may
 be more important than inter-sexual competition in some species. Our
 results demonstrate that both inter-sexual and intra-sexual selection led
 to inter-specific variation in sexual dimorphism of chelicera length in
 this group.
description: Mating experiment and
 Inter-species variation in Tetragnatha spidersThis excel file contains
 the mating experiment data (chelicera length, body weight and copulatory
 success) of Tetragnatha praedonia and the data on cheliceral length,
 carapace width, sexual dimorphism index (SDI) and relative chelicera data
 of 15 species of Tetragnatha spiders.Mating_Exp_and_Inter_sp_variation.xlsx
DOI: 10.25824/redu/0mool7
title: Dados de "Simulação numérica de escoamento bifásico vertical através de orificios finos"

description: Dados gerados para a dissetação de mestrado "Simulação Numérica de Escoamento Bifásico Vertical através de Orificios finos" defendida na FEM/Unicamp. As tabelas .xls demonstram os resultados obtidos de velocidade e de queda de pressão tanto para validação do modelo implementado quanto para os diferentes padrões de escoamento estudados durante o trabalho.
DOI: 10.5061/dryad.jn33140
title: Data from: Metabolic scope as a proximate constraint on individual behavioral variation: effects on 'personality', plasticity, and predictability

description: Behavioral ecologists have hypothesized that among-individual differences
 in resting metabolic rate (RMR) may predict consistent individual
 differences in mean values for costly behaviors, or for behaviors that
 affect energy intake rate. This hypothesis has empirical support and
 presently attracts considerable attention, but notably it does not provide
 predictions for individual differences in (a) behavioral plasticity or (b)
 unexplained variation (residual variation from mean individual behavior,
 here termed predictability). We outline how consideration of aerobic
 maximum metabolic rate (MMR) and particularly aerobic scope (= MMR - RMR)
 can be used to simultaneously make predictions about mean, among- and
 within-individual variation in behavior. We predict that while RMR should
 be proportional to an individuals’ mean level of sustained behavioral
 activity (one aspect of its personality), individuals with greater aerobic
 scope will also have greater scope to express behavioral plasticity and/or
 greater unpredictability in behavior (= greater residual variation). As a
 first step towards testing these predictions, we analyse existing activity
 data from selectively bred lines of mice that differ in both daily
 activity and aerobic scope. We find that replicate high-scope mice are
 more active on average, show greater among-individual variation in
 activity, greater among-individual variation in plasticity, and greater
 unpredictability. These data provide some tentative first support for our
 hypothesis, suggesting that further research on this topic would be
 valuable.
description: Data originally from
 EisenmannDaily running totals of
 mice w access to running wheels. Data originally collected by Garland lab
 for Eisenmann, J. C., E. E. Wickel, S. A. Kelly, K. M. Middleton, and T.
 Garland. 2009. Day-to-day variability in voluntary wheel running among
 genetically differentiated lines of mice that vary in activity level.
 European Journal of Applied Physiology 106:613-619.
 https://doi.org/10.1007/s00421-009-1056-zgarland mouse IIV
 data.xlsx
DOI: 10.5061/dryad.40sj6
title: Data from: A multivariate analysis of genetic variation in the advertisement call of the gray treefrog, Hyla versicolor

description: Genetic variation in sexual displays is crucial for an evolutionary
 response to sexual selection, but can be eroded by strong selection.
 Identifying the magnitude and sources of additive genetic variance
 underlying sexually-selected traits is thus an important issue in
 evolutionary biology. We conducted a quantitative genetics experiment with
 gray treefrogs (Hyla versicolor) to investigate genetic variances and
 covariances among features of the male advertisement call. Two
 energetically-expensive traits showed significant genetic variation: call
 duration, expressed as number of pulses per call, and call rate,
 represented by its inverse, call period. These two properties also showed
 significant genetic covariance, consistent with an energetic constraint to
 call production. Combining the genetic variance-covariance matrix with
 previous estimates of directional sexual selection imposed by female
 preferences predicts a limited increase in call duration but no change in
 call rate despite significant selection on both traits. In addition to
 constraints imposed by the genetic covariance structure, an evolutionary
 response to sexual selection may also be limited by high energetic costs
 of long-duration calls and by preferences that act most strongly against
 very short-duration calls. Meanwhile, the persistence of these preferences
 could be explained by costs of mating with males with especially
 unattractive calls.
description: Gray treefrog
 advertisement call propertiesAdvertisement call
 properties recorded from two generations of gray treefrogs (Hyla
 versicolor). Data are described in the accompanying ReadMe
 file.Hyla_versicolor_call_heritability.csv
DOI: 10.5061/dryad.72262
title: Data from: Immunogenetic novelty confers a selective advantage in host-pathogen coevolution

description: The major histocompatibility complex (MHC) is crucial to the adaptive
 immune response of vertebrates and is among the most polymorphic gene
 families known. Its high diversity is usually attributed to selection
 imposed by fast-evolving pathogens. Pathogens are thought to evolve to
 escape recognition by common immune alleles, and, hence, novel MHC
 alleles, introduced through mutation, recombination, or gene flow, are
 predicted to give hosts superior resistance. Although this theoretical
 prediction underpins host–pathogen “Red Queen” coevolution, it has not
 been demonstrated in the context of natural MHC diversity. Here, we
 experimentally tested whether novel MHC variants (both alleles and
 functional “supertypes”) increased resistance of guppies (Poecilia
 reticulata) to a common ectoparasite (Gyrodactylus turnbulli). We used
 exposure-controlled infection trials with wild-sourced parasites, and
 Gyrodactylus-naïve host fish that were F2 descendants of crossed wild
 populations. Hosts carrying MHC variants (alleles or supertypes) that were
 new to a given parasite population experienced a 35–37% reduction in
 infection intensity, but the number of MHC variants carried by an
 individual, analogous to heterozygosity in single-locus systems, was not a
 significant predictor. Our results provide direct evidence of novel MHC
 variant advantage, confirming a fundamental mechanism underpinning the
 exceptional polymorphism of this gene family and highlighting the role of
 immunogenetic novelty in host–pathogen coevolution.
description: Appendix_S04_2018-01-08Inputs data and analysis scripts for Appendix S4Appendix_S05a_2018-01-08Input data and analysis scripts for part of Appendix S5Appendix_S02_2018-01-08Input data and analysis scripts for Appendix S2Appendix_S06a_2018-01-08Input data and analysis scripts for part of Appendix S6Appendix_S07_2018-01-08Input data and analysis scripts for Appendix S7Appendix_S08_2018-01-08Input data and analysis scripts for Appendix S8Appendix_S09_2018-01-08Input data and analysis scripts for Appendix S9Genotypes_as_used_2018-01-08MHC genotypes of fish in this experiment (P-generation, F1 and F2)MHC_genotypingRaw MHC sequencing data (IonTorrent PGM) and genotyping (AmpliSAS) of guppies that feature in this experiment (P-generation, F1, and F2)
DOI: 10.5061/dryad.788k6
title: Data from: Diploid hybrid origin of Ostryopsis intermedia (Betulaceae) in the Qinghai-Tibet Plateau triggered by Quaternary climate change

description: Despite the well known effects that Quaternary climate oscillations had on
 shaping intraspecific diversity, their role in driving homoploid hybrid
 speciation is less clear. Here we examine their importance in the putative
 homoploid hybrid origin and evolution of Ostryopsis intermedia, a diploid
 species occurring in the Qinghai-Tibet Plateau (QTP), a biodiversity
 hotspot. We investigated interspecific relationships between this species
 and its only other congeners, O. davidiana and O. nobilis, based on four
 sets of nuclear and chloroplast population genetic data and tested
 alternative speciation hypotheses. All nuclear data distinguished the
 three species clearly and supported a close relationship between O.
 intermedia and the disjunctly distributed O. davidiana. Chloroplast DNA
 sequence variation identified two tentative lineages, which distinguished
 O. intermedia from O. davidiana, however both were present in O. nobilis.
 Admixture analyses of genetic polymorphisms at 20 SSR loci and sequence
 variation at 11 nuclear loci and Approximate Bayesian Computation (ABC)
 tests supported the hypothesis that O. intermedia originated by homoploid
 hybrid speciation from O. davidiana and O. nobilis. We further estimated
 that O. davidiana and O. nobilis diverged 6-11 million years ago while O.
 intermedia originated 0.5-1.2 million years ago when O. davidiana is
 believed to have migrated southward, contacted and hybridized with O.
 nobilis possibly during the largest Quaternary glaciation that occurred in
 this region. Our findings highlight the importance of Quaternary climate
 change in the QTP in causing hybrid speciation in this important
 biodiversity hotspot.
description: DataAccessibility
DOI: 10.5061/dryad.sp21b
title: Data from: Legacy effects of diversity in space and time driven by winter cover crop biomass and nitrogen concentration

description: Plant diversity can increase nitrogen cycling and decrease soil-borne
 pests, which are feedback mechanisms influencing subsequent plant growth.
 The relative strength of these mechanisms is unclear, as is the influence
 of preceding plant quantity and quality. Here, we studied how plant
 diversity in space and time influences subsequent crop growth. During 2
 years, we rotated two main crops (Avena sativa, Cichorium endivia) with
 four winter cover crop (WCC) species in monocultures and mixtures. We
 hypothesized that, relative to monocultures, WCC mixtures promote WCC
 biomass (quantity) and nitrogen concentration (quality), soil mineral
 nitrogen, soil organic matter, and reduce plant-feeding nematode
 abundance. Additionally, we predicted that preceding crops modified WCC
 legacies. By structural equation modelling (SEM), we tested the relative
 importance of WCC shoot biomass and nitrogen concentration on succeeding
 crop productivity directly and indirectly via nitrogen cycling and
 root-feeding nematode abundance. WCC shoot biomass, soil properties and
 succeeding Avena productivity were affected by first-season cropping,
 whereas subsequent Cichorium only responded to the WCC treatments. WCC
 mixtures’ productivity and nitrogen concentration showed over- and
 under-yielding, depending on mixture composition. Soil nitrogen and
 nematode abundance did not display WCC mixture effects. Soil organic
 matter was lower than expected after Raphanus sativus + Vicia sativa
 mixture. Subsequent Avena productivity depended upon mixture composition,
 whereas final Cichorium productivity was unresponsive to WCC mixtures. SEM
 indicated that WCC legacy effects on subsequent Avena (R2 = 0.52) and
 Cichorium (R2 = 0.59) productivity were driven by WCC biomass and nitrogen
 concentration, although not by the quantified soil properties. Synthesis
 and applications. Through understanding plant–soil feedback, legacy
 effects of plant species and species mixtures can be employed for
 sustainable management of agro-ecosystems. Biomass and nitrogen
 concentration of plants returned to the soil stimulate subsequent plant
 productivity. Winter cover crop quantity and quality are both manipulable
 with mixtures. The specificity of spatial and temporal diversity effects
 warrants consideration of plant species choice in mixtures and rotations
 for optimal employment of beneficial legacy effects.
description: Soil legacies of winter
 cover crop mixturesExcel data file with
 legacy effects of a two year rotation (2014-2015), including winter cover
 crop monocultures and mixtures. Contains variable description,
 experimental design, data on winter cover crop biomass and N, soil organic
 matter, mineral N, potential N mineralisation, plant feeding nematode
 abundance, biomass of response plants Avena sativa and Cichorium
 endivia.Barel-JAPPL-2017-00007.xlsx