cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f1898rb
title: Data from: Do slower movers have lower reproductive success and higher mutation load?

description: Deleterious mutations occur frequently in eukaryotes, resulting in
 individuals carrying multiple alleles that decrease their fitness. At a
 population level, if unchecked, accumulation of this mutation load can
 ultimately lead to extinction. How selection counters the accumulation of
 mutation load, limiting declines in population fitness, is not well
 understood. Here, we use manipulative experiments in zebrafish (Danio
 rerio) to investigate the opportunities for selection on mutation load.
 Inducing high mutation load through mutagenesis, we applied one generation
 of within-family selection on locomotor performance, and characterised
 both the direct response to this selection and the indirect response of
 reproductive success. Offspring of slow swimming parents exhibited
 age-dependent declines in swimming speed, while their cousins, with faster
 swimming parents, did not. This pattern mimics previously documented
 differences between high and low mutation load populations of zebrafish,
 suggesting that slow swimming siblings inherited (and transmitted) more
 mutations than their faster swimming siblings. Crosses among offspring of
 slow swimming fish had, on average, &lt;75% of the reproductive
 success of crosses among offspring of fast swimming parents, or crosses of
 offspring of slow swimmers with offspring of fast swimmers. This evidence
 of mutationally correlated swimming speed and reproductive success reveals
 the potential for concordant selection on mutation load through different
 fitness components. There was no evidence that crosses within families
 (where parents potentially shared the same mutations inherited from their
 common ancestor) had lower reproductive success than crosses among
 families, suggesting that viability selection was not acting predominantly
 through lethal recessive homozygotes. Rather, patterns of reproductive
 success are suggestive of effects of mutation number per se on embryo
 viability. Overall, our results highlight the potential for early life
 mortality to remove deleterious mutations, and the need to account for
 this mortality when investigating the evolutionary dynamics of mutation
 load.
description: Selection
 appliedIn the F1 offspring of
 ENU treated males, divergent selection was applied within each family to
 generate fast swimming and slow swimming selection treatments. This file
 contains the information to calculate selection applied, and also
 underpins the analysis of speed in viable versus inviable
 families.Selection_Applied.csvSelection_responseThis file contains information on swimming speed and body size of all individual F2 fish assayed. The response to the divergent selection applied to their F1 parents was determined through analysis of the tank means calculated from this data.ViabilityData file containing information on the proportion of surviving embryos of crosses within and among F2 families of ENU treated males, divided into fast versus slow selection treatments.
DOI: 10.5061/dryad.q1t87
title: Data from: Post-glacial habitat release and incipient speciation in the genus Delphinus

description: The role of ecological and changing environmental factors in the radiation
 of species diversity is a fundamental question in evolutionary biology. Of
 particular interest is the potential for these factors to determine the
 boundary between what we would consider differentiation among populations
 and incipient speciation. Dolphins in the genus Delphinus provide a useful
 test case, exhibiting morphological variation in beak length, coloration
 and body size across their wide geographic distribution, and in particular
 among coastal and more pelagic habitats. Two species have been proposed,
 D. delphis and D. capensis, but morphologically similar allopatric
 populations are not monophyletic, indicating that the mostly coastal
 ‘long-beaked’ D. capensis form is not a single globally distributed
 species. However, the sympatric populations in the Eastern North Pacific
 currently designated as these two species are both morphologically and
 genetically differentiated. Here we use microsatellite DNA and
 mitochondrial DNA markers to investigate the evolutionary mechanisms that
 led to this incipient speciation event. We used coalescent and assignment
 methods to investigate the timing and extent of reproductive isolation.
 Our data indicate that although there is some level of on-going gene flow,
 the putative species found in the Eastern North Pacific are reciprocally
 monophyletic. The timing of isolation appears to be associated with
 regional changes in paleoceanographic conditions within the Holocene
 timeframe.
description: Common dolphins
 microsatellite genotypesThis data file contains
 long-beaked and short-beaked common dolphin genotypes for 16
 microsatellite loci.Segura-Garcia_Heredity_072016_DsppGenotypes.txt
DOI: 10.5061/dryad.v5m8v
title: Data from: High-resolution chemical dissection of a model eukaryote reveals targets, pathways and gene functions

description: Due to evolutionary conservation of biology, experimental knowledge
 captured from genetic studies in eukaryotic model organisms provides
 insight into human cellular pathways and ultimately physiology. Yeast
 chemogenomic profiling is a powerful approach for annotating cellular
 responses to small molecules. Using an optimized platform, we provide the
 relative sensitivities of the heterozygous and homozygous deletion
 collections for nearly 1800 biologically active compounds. The data
 quality enables unique insights into pathways that are sensitive and
 resistant to a given perturbation, as demonstrated with both known and
 novel compounds. We present examples of novel compounds that inhibit the
 therapeutically relevant fatty acid synthase and desaturase (Ole1p and
 Fas1p), and demonstrate how the individual profiles facilitate
 hypothesis-driven experiments to delineate compound mechanism of action.
 Importantly, the scale and diversity of tested compounds yields a dataset
 where the number of modulated pathways approaches saturation. This
 resource can be used to map novel biological connections, and also
 identify functions for unannotated genes. We validated hypotheses
 generated by global 2-way hierarchical clustering of profiles for (i)
 novel compounds with a similar mechanism of action acting upon
 microtubules or vacuolar ATPases, and (ii) an un-annotated ORF, YIL060w,
 that plays a role in respiration in the mitochondria. Finally, we identify
 and characterize background mutations in the widely used yeast deletion
 collection which should improve the interpretation of past and future
 screens throughout the community. This comprehensive resource of cellular
 responses enables the expansion of our understanding of eukaryotic pathway
 biology.
description: Table
 S1Compounds used in this
 studyTable_S1.xlsTable_S2Hit frequencies of HIP and HOP strainsTable_S3v-ATPase inhibitor correlation listTable_S4microtubule inhibitor compounds as identified by HIP HOPTable_S5Summary of identified HIP strains with common background mutationsTable_S6Signature hits for inhibition of non-proteinaceous targetsHIP_scores-benomylTab delimited text file with the data of all performed Benomyl experimentsHOP_scores-benomylTab delimited text file with the data of all performed Benomyl experimentsHIP_scoresTab-delimited text file with MADL and z-scores for all approx. 1800 compounds tested in this studyHOP_scoresTab-delimited text file with MADL and z-scores for all approx. 1800 compounds tested in this study
DOI: 10.5061/dryad.9kj41f0
title: Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance

description: 1. Hosts can alter their strategy towards pathogens during their lifetime,
 i.e., they can show phenotypic plasticity in immunity or life history.
 Immune priming is one such example, where a previous encounter with a
 pathogen confers enhanced protection upon secondary challenge, resulting
 in reduced pathogen load (i.e. resistance) and improved host survival.
 However, an initial encounter might also enhance tolerance, particularly
 to less virulent opportunistic pathogens that establish persistent
 infections. In this scenario, individuals are better able to reduce the
 negative fitness consequences that result from a high pathogen load.
 Finally, previous exposure may also lead to life history adjustments, such
 as terminal investment into reproduction. 2. Using different Drosophila
 melanogaster host genotypes and two bacterial pathogens, Lactococcus
 lactis and Pseudomonas entomophila, we tested if previous exposure results
 in resistance or tolerance and whether it modifies immune gene expression
 during an acute-phase infection (one day post-challenge). We then asked if
 previous pathogen exposure affects chronic-phase pathogen persistence and
 longer-term survival (28 days post-challenge). 3. We predicted that
 previous exposure would increase host resistance to an early stage
 bacterial infection while it might come at a cost to host fecundity
 tolerance. We reasoned that resistance would be due in part to stronger
 immune gene expression after challenge. We expected that previous exposure
 would improve long-term survival, that it would reduce infection
 persistence, and we expected to find genetic variation in these responses.
 4. We found that previous exposure to P. entomophila weakened host
 resistance to a second infection independent of genotype and had no effect
 on immune gene expression. Fecundity tolerance showed genotypic variation
 but was not influenced by previous exposure. However, L. lactis persisted
 as a chronic infection, whereas survivors cleared the more pathogenic P.
 entomophila infection. 5. To our knowledge, this is the first study that
 addresses host tolerance to bacteria in relation to previous exposure,
 taking a multi-faceted approach to address the topic. Our results suggest
 that previous exposure comes with transient costs to resistance during the
 early stage of infection in this host-pathogen system and that infection
 persistence may be bacterium-specific.
description: Kutzer et al data
 filesData files are labelled
 according to the experiment and model number(s). Full details on the
 statistical models and model numbers can be found in Appendix 1, which is
 a supplementary file for the paper.Kutzer_et_al_data_files.zip
DOI: 10.5061/dryad.f2mk6
title: Data from: Seasonally varying predation behaviour and climate shifts are predicted to affect predator-prey cycles

description: The functional response of some predator species changes from a pattern
 characteristic for a generalist to that for a specialist according to
 seasonally varying prey availability. Current theory does not address the
 dynamic consequences of this phenomenon. Since season length correlates
 strongly with altitude and latitude and is predicted to change under
 future climate scenarios, including this phenomenon in theoretical models
 seems essential for correct prediction of future ecosystem dynamics. We
 develop and analyze a two-season model for the great horned owl (Bubo
 virginialis) and snowshoe hare (Lepus americanus). These species form a
 predator-prey system in which the generalist to specialist shift in
 predation pattern has been documented empirically. We study the
 qualitative behavior of this predator-prey model community as summer
 season length changes. We find that relatively small changes in summer
 season length can have a profound impact on the system. In particular,
 when the predator has sufficient alternative resources available during
 the summer season, it can drive the prey to extinction, there can be
 coexisting stable states, and there can be stable large-amplitude limit
 cycles coexisting with a stable steady state. Our results illustrate that
 the impacts of global change on local ecosystems can be driven by internal
 system dynamics and can potentially have catastrophic consequences.
description: AmNat_codeThis tar file contains the Matlab m-files that generate solutions to the averaged and seasonal models published in the paper.
DOI: 10.5061/dryad.kj51b
title: Data from: Mollusc-shell debris can mitigate the deleterious effects of organic pollution on marine sediments

description: Organic pollution is widespread in coastal areas and can have profound
 impacts on the seabed. Coastal sediments play an important role at a
 global scale in the recycling of organic matter, and this process is
 influenced by the habitat complexity of the sediments, among other
 factors. Mollusc shells are produced as a waste product from a range of
 anthropogenic activities, but we demonstrate that they can be used to
 increase the habitat complexity of sediments. We studied the effect of
 mussel-shell debris (shell-hash) on the biogeochemical processes of marine
 sediments affected by organic pollution, using a mesocosm experiment
 simulating the bioturbation effects of macrofauna. We found that
 shell-hash improved the ecological status of organically polluted
 sediments by reducing the accumulation of sulphide from anaerobic
 metabolic pathways. Additionally, when shell-hash was present in an
 organically polluted sediment, there was a decrease in ammonium release to
 the water column, thus preventing the negative ecological consequences of
 eutrophication. Synthesis and applications. Our study indicates that
 shell-hash debris can be used as a potential tool to mitigate the effects
 of organic enrichment on marine sediments. A density of shell-hash debris
 of 1900 g m−2 in the sediment can diminish toxic by-products (sulphides
 and ammonium) derived from the stimulation of anaerobic metabolic pathways
 by organic pollution, at levels that are biologically relevant. The
 mitigation effect of shell-hash is more pronounced in sediments where
 macrofauna is not present.
description: Casado-Coy et. al.,
 2016. DataBiogeochemical fluxes
 and derived products.Casado-Coy et. al. 2016.
 Data.xls
DOI: 10.5061/dryad.f9h43b0
title: Data from: X-ray computed tomography and its potential in ecological research: a review of studies and optimization of specimen preparation

description: Imaging techniques are a cornerstone of contemporary biology. Over the
 last decades, advances in micro-scale imaging techniques have allowed
 fascinating new insights into cell and tissue morphology and internal
 anatomy of organisms across kingdoms. However, most studies so far
 provided snapshots of given reference taxa, describing organs and tissues
 under “idealized” conditions. Surprisingly, there is an almost complete
 lack of studies investigating how an organism´s internal morphology
 changes in response to environmental drivers. Consequently, ecology as a
 scientific discipline has so far almost neglected the possibilities
 arising from modern micro-scale imaging techniques. Here, we provide an
 overview of recent developments of x-ray computed tomography as an
 affordable, simple method of high spatial resolution, allowing insights
 into three-dimensional anatomy both in vivo and ex vivo. We review
 ecological studies using this technique to investigate the
 three-dimensional internal structure of organisms. In addition, we provide
 practical comparisons between different preparation techniques for maximum
 contrast and tissue differentiation. In particular, we consider the novel
 modality of phase contrast by self-interference of the x-ray wave behind
 an object (i.e. phase contrast by free space propagation). Using the
 cricket Acheta domesticus (L.) as model organism, we found that the
 combination of FAE fixative and iodine staining provided the best results
 across different tissues. The drying technique also affected contrast and
 prevented artefacts in specific cases. Overall, we found that for the
 interests of ecological studies, x-ray computed tomography is useful when
 the tissue or structure of interest has sufficient contrast that allows
 for an automatic or semi-automatic segmentation. In particular, we show
 that reconstruction schemes which exploit phase contrast can yield
 enhanced image quality. Combined with suitable specimen preparation and
 automated analysis, x-ray CT can therefore become a promising quantitative
 3D imaging technique to study organisms´ responses to environmental
 drivers, in both ecology and evolution.
description: Acheta domesticus -
 abdomenmicro computed
 tomography of the abdomen of a female house cricket (Acheta domesticus).
 Tissue fixed in FAE, stained with Iodine and subjected to critical point
 driedabdomen.7zAcheta domesticus - Headmicro computed tomography of the head of a female house cricket (Acheta domesticus). Tissue fixed in FAE, stained with Iodine and subjected to critical point driedHead.7z
DOI: 10.5061/dryad.jh174st3
title: Data from: Catching-up but telomere loss: half-opening the black box of growth and ageing trade-off in wild king penguin chicks

description: One of the reasons for animals not to grow as fast as they potentially
 could is that fast growth has been shown to be associated with reduced
 lifespan. However, we are still lacking a clear description of the reality
 of growth-dependent modulation of ageing mechanisms in wild animals. Using
 the particular growth trajectory of small king penguin chicks naturally
 exhibiting higher-than-normal growth rate to compensate for the winter
 break, we tested whether oxidative stress and telomere shortening are
 related to growth trajectories. Plasma antioxidant defences, oxidative
 damages levels and telomere length were measured at the beginning and the
 end of the post-winter growth period in three groups of chicks (small
 chicks which either passed away or survived the growth period, and large
 chicks). Small chicks that died early during the growth period had the
 highest level of oxidative damage and the shortest telomere lengths prior
 to death. Here, we show that small chicks that grew faster did it at the
 detriment of body maintenance mechanisms as shown by (i) higher oxidative
 damage and (ii) accelerated telomere loss. Our study provides the first
 evidence for a mechanistic link between growth and ageing rates under
 natural conditions.
description: king-penguins2011Excel file describing body mass, oxidative stress and telomere dynamics of chicks after the winter time
DOI: 10.5061/dryad.k67kf
title: Data from: Is famine exposure during developmental life in rural Bangladesh associated with a metabolic and epigenetic signature in young adulthood? A historical cohort study

description: Objectives Famine exposure in utero can ‘programme’ an individual towards
 type 2 diabetes and obesity in later life. We sought to identify, (1)
 whether Bangladeshis exposed to famine during developmental life are
 programmed towards diabetes and obesity, (2) whether this programming was
 specific to gestational or postnatal exposure windows and (3) whether
 epigenetic differences were associated with famine exposure. Design A
 historical cohort study was performed as part of a wider cross-sectional
 survey. Exposure to famine was defined through birth date and historical
 records and participants were selected according to: (A) exposure to
 famine in postnatal life, (B) exposure to famine during gestation and (C)
 unexposed. Setting Matlab, a rural area in the Chittagong division of
 Bangladesh. Participants Young adult men and women (n=190) recruited to a
 historical cohort study with a randomised subsample included in an
 epigenetic study (n=143). Outcome measures Primary outcome measures of
 weight, body mass index and oral glucose tolerance tests (0 and 120 min
 glucose). Secondary outcome measures included DNA methylation using
 genome-wide and targeted analysis of metastable epialleles sensitive to
 maternal nutrition. Results More young adults exposed to famine in
 gestation were underweight than those postnatally exposed or unexposed. In
 contrast, more young adults exposed to famine postnatally were overweight
 compared to those gestationally exposed or unexposed. Underweight adults
 exposed to famine in gestation in utero were hyperglycaemic following a
 glucose tolerance test, and those exposed postnatally had elevated fasting
 glucose, compared to those unexposed. Significant differences in DNA
 methylation at seven metastable epialleles (VTRNA2-1, PAX8, PRDM-9, near
 ZFP57, near BOLA, EXD3) known to vary with gestational famine exposure
 were identified. Conclusions Famine exposure in developmental life
 programmed Bangladeshi offspring towards diabetes and obesity in adulthood
 but gestational and postnatal windows of exposure had variable effects on
 phenotype. DNA methylation differences were replicated at previously
 identified metastable epialleles sensitive to periconceptual famine
 exposure.
description: beta_normalised_bmiqContains normalised beta values for each CpG which passed QC from 450K array. Each column is a sample and each row is CpG. The first column contains CpG identifiers.
DOI: 10.5061/dryad.rs82m
title: Data from: Revision of the first therocephalian, Theriognathus Owen (Therapsida: Whaitsiidae), and implications for cranial ontogeny and allometry in nonmammaliaform eutheriodonts

description: Historically, the whaitsiid therocephalian Theriognathus Owen was one of
 the earliest described nonmammalian therapsids, its morphology helping to
 link phylogenetically the Paleozoic synapsids of North America and
 southern Africa to their mammalian successors. However, decades of
 taxonomic over-splitting and superficial descriptions obscured the
 morphologic diversity of the genus, hindering its utility as a study
 system for the evolution of synapsid cranial function as well as its
 biostratigraphic significance in the Late Permian of southern Africa.
 Here, we revise the status and provenance of all the known specimens of
 Theriognathus from South Africa, Tanzania, and Zambia. We present both
 qualitative and quantitative support for the presence of a single
 morphospecies as proposed by some authors. Proportional differences in
 skulls that were previously ascribed to different morphotypes
 (‘Aneugomphius,’ ‘Notosollasia,’ ‘Moschorhynchus,’ and ‘Whaitsia’) are
 largely size-related and allometric trends are considered here in the
 context of jaw function and prey prehension. Our results suggest that the
 single species, Theriognathus microps, represented one of the most
 abundant Late Permian therocephalians in southern Africa and is
 consequently a potentially useful biostratigraphic marker for the upper
 Cistecephalus-lower Dicynodon Assemblage Zone transition (i.e., late
 Wuchiapingian). The wide range of preserved sizes in conjunction with
 recent paleohistological evidence supports that individuals spent much of
 their lives in an actively-growing, subadult phase. Later Dicynodon
 Assemblage Zone records (e.g., upper Balfour Formation) are unconfirmed as
 the genus was likely replaced by other theriodont predators (e.g.,
 Moschorhinus) leading up to the Permo-Triassic boundary in the Karoo Basin
 of South Africa.
description: HuttenlockerAbdalaSupplementalDataFileTable of measurements for whaitsiid holotypes and other referred specimens used in the allometric analysis.2471_0_supp_12_n6tlf5.xls