cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7j1q0
title: Data from: Evaluating patterns of convergent evolution and trans-species polymorphism at MHC immunogenes in two sympatric stickleback species

description: The immunologically important major histocompatibility complex (MHC)
 harbors some of the most polymorphic genes in vertebrates. These genes
 presumably evolve under parasite-mediated selection and frequently show
 inconsistent allelic genealogies, where some alleles are more similar
 between species than within species. This phenomenon is thought to arise
 either from convergent evolution under parallel selection or from the
 preservation of ancient allelic lineages beyond speciation events
 (trans-species polymorphism, TSP). Here we examine natural populations of
 two sympatric stickleback species (Gasterosteus aculeatus and Pungitius
 pungitius) to investigate the contribution of these two mechanisms to the
 evolution of inconsistent allelic genealogies at the MHC. Overlapping
 parasite taxa between the two host species in three different habitats
 suggest contemporary parallel selection on the MHC genes. Accordingly, we
 detected a lack of species-specific phylogenetic clustering in the
 immunologically relevant antigen-binding residues of the MHC IIB genes
 which contrasted with the rest of the coding and non-coding sequence.
 However, clustering was not habitat-specific and a codon-usage analysis
 revealed patterns of similarity by descent. In this light, common descent
 via TSP, in combination with intra-species gene conversion, rather than
 convergent evolution is the more strongly supported scenario for the
 inconsistent genealogy at the MHC.
description: Lenz_ParasiteDataIndividual parasite data for community comparison among habitats and host species.
DOI: 10.5061/dryad.5mg73
title: Data from: A new paleoecological look at the Dinwoody Formation (Lower Triassic, western U.S.): intrinsic versus extrinsic controls on ecosystem recovery after the end-Permian mass extinction

description: The Dinwoody Formation of the Western U.S. represents an important archive
 of Early Triassic ecosystems in the immediate aftermath of the end-Permian
 mass extinction. We present a systematic description and a quantitative
 paleoecological analysis of its benthic faunas in order to reconstruct
 benthic associations and to explore the temporal and spatial variations of
 diversity, ecological structure and taxonomic composition throughout the
 earliest Triassic of the western U.S. A total of 15 bivalve species, two
 gastropod species, and two brachiopod species are recognized in the study
 area. The paleoecological analysis shows that the oldest Dinwoody
 communities are characterized by low diversity, low ecological complexity
 and high dominance of few species. We suggest that this diversity-low most
 likely reflects the consequences of the mass extinction in the first place
 and not necessarily the persistence of environmental stress. Whereas this
 diversity pattern persists into younger strata of the Dinwoody Formation
 in outer shelf environments, an increase in richness, evenness and guild
 diversity occurred around the Griesbachian-Dienerian boundary in more
 shallow marine habitats. This incipient recovery towards the end of the
 Griesbachian is in accordance with observations from other regions and
 thus probably represents an interregional signal. In contrast to
 increasing richness within communities (alpha-diversity), beta-diversity
 remained low during the Griesbachian and Dienerian in the study area. This
 low beta-diversity reflects a wide environmental and geographical range of
 taxa during the earliest Triassic, indicating that the increase of
 within-habitat diversity has not yet led to significant competitive
 exclusion. We hypothesize that the well-known prevalence of generalistic
 taxa in post-extinction faunas is primarily an effect of reduced
 competition that allows species to exist through the full range of their
 fundamental niches, rather than being caused by unusual and uniform
 environmental stress.
description: Faunal data of the Lower
 Triassic Dinwoody FormationAbundance data, faunal
 lists, associations and diversity of marine macrofossils of the Dinwoody
 Formation (Lower Triassic, western U.S.) collected in the
 field.Electronic_supplement_Hofmann-Dinwoody.xls
DOI: 10.5061/dryad.mg249
title: Data from: Atlantic bluefin tuna spawn at suboptimal temperatures for their offspring

description: Life-history traits such as spawning migrations and timing of reproduction
 are adaptations to specific environmental constraints and seasonal cycles
 in many organisms’ annual routines. In this study we analyze how offspring
 fitness constrains spawning phenology in a large migratory apex predator,
 the Atlantic bluefin tuna. The reproductive schedule of Atlantic bluefin
 tuna varies between spawning sites suggesting plasticity to local
 environmental conditions. Generally, temperature is considered to be the
 main constraint on tuna spawning phenology. We combine evidence from
 long-term field data, temperature-controlled rearing experiments on eggs
 and larvae and a model of egg fitness, and show that Atlantic bluefin tuna
 do not spawn to optimize egg and larval temperature exposure. The timing
 of spawning leads to temperature exposure considerably lower than optimal
 at all spawning grounds across the Atlantic Ocean. The early spawning is
 constrained by thermal inhibition of egg hatching and larval growth rates,
 but some other factors must prevent later spawning. Matching offspring
 with ocean productivity and the prey peak might be an important driver for
 bluefin tuna spawning phenology. This finding is important for predictions
 of reproductive timing in future climate warming scenarios for bluefin
 tuna.
description: Temperature and fitness
 data for Atlantic bluefin tuna in their spawning groundsAverage daily
 temperature (ºC) records in the major spawning grounds for Atlantic
 bluefin tuna and the predicted egg fitness or probability of survival of
 eggs from hatching to the postflexion stage estimated from the model
 described in the main text.temperature_fitness_data.xlsx
DOI: 10.5061/dryad.68r7s
title: Data from: Evolution of virulence under intensive farming: salmon lice increase skin lesions and reduce host growth in salmon farms

description: Parasites rely on resources from a host and are selected to achieve an
 optimal combination of transmission and virulence. Human-induced changes
 in parasite ecology, such as intensive farming of hosts, might not only
 favor increased parasite abundances, but also alter the selection acting
 on parasites and lead to life history evolution. The trade-off between
 transmission and virulence could be affected by intensive farming
 practices such as high host density and the use of anti-parasitic drugs,
 which might lead to increased virulence in some host-parasite systems. To
 test this we therefore infected Atlantic salmon (Salmo salar) smolts with
 salmon lice (Lepeophtheirus salmonis) sampled either from wild or farmed
 hosts in a laboratory experiment. We compared growth and skin damage (i.e.
 proxies for virulence) of hosts infected with either wild or farmed lice
 and found that, compared to lice sampled from wild hosts in unfarmed
 areas, those originating from farmed fish were more harmful; they
 inflicted more skin damage to their hosts and reduced relative host weight
 gain to a greater extent. We advocate that more evolutionary studies
 should be done using farmed animals as study species, given the current
 increase in intensive food production practices that might be compared to
 a global experiment in parasite evolution.
description: JEBvirulencedata
DOI: 10.5061/dryad.pp2t3
title: Data from: Non-coaxiality of sand under bi-directional shear loading

description: This study aims to investigate the effect of consolidation shear stress
 magnitude on the shear behaviour and noncoaxiality of soils. In previous
 drained bi-directional simple shear test on Leighton Buzzard sand, it is
 showed that the level of non-coaxiality, which is indicated by the angle
 difference between the principal axes of stresses and the corresponding
 principal axes of strain rate tensors, is increased by increasing angle
 difference between the direction of consolidation shear stress and
 secondary shearing. This paper further investigated the relation, and
 includes results with higher consolidation shear stresses. Results agree
 with previous relation, and further showed that increasing consolidation
 shear stresses decreased the level of non-coaxiality in tests with angle
 difference between 0 to 90 degrees, and increased the level of
 non-coaxiality in tests with angle difference between 90 to 180 degrees.
description: data
DOI: 10.5061/dryad.1255834
title: Data from: Male stress response is related to ornamentation but not resistance to oxidative stress in a warbler

description: 1. Ornaments are thought to honestly signal individual quality to
 potential mates. Individual quality may include the ability to cope with
 stress through the production of glucocorticoids (GCs), which help to
 redirect resources from growth or reproduction to survival during an acute
 stress response. However, elevated levels of GCs may also increase
 oxidative stress and reduce immune function. Thus, an important question
 is whether high quality individuals, with more elaborate ornaments, signal
 their ability to produce a strong stress response and mitigate some of the
 negative effects of doing so through higher resistance to oxidative
 stress. 2. We tested whether ornamentation and resistance to oxidative
 stress were related to the magnitude of the increase in corticosterone
 (CORT), the main GC in birds, during an acute stress response in common
 yellowthroats (Geothlypis trichas). Males in this species have two plumage
 ornaments, a black (eumelanin-based) facial mask and a yellow
 (carotenoid-based) bib. We measured the increase in CORT in response to
 capture and handling. 3. Males with more elaborate ornaments (larger masks
 and more colourful bibs) had a greater increase in CORT during an acute
 stress response. However, the increase in CORT was not related to
 resistance to oxidative stress. 4. These results suggest that both
 melanin- and carotenoid-based plumage ornaments can signal the ability of
 a male to cope with stressors through a greater increase in CORT. Thus,
 the association between ornamentation and stress induced CORT is not
 likely due to a mechanism specific to a particular colour (melanin or
 carotenoid), but instead may result from more general interactions between
 CORT and health or condition.
description: Corticosterone,
 oxidative stress and ornament data for yellowthroatsCORT_data_for_Dryad.csv
DOI: 10.5061/dryad.60ns6
title: Data from: Specific leaf area predicts dryland litter decomposition via two mechanisms

description: 1. Litter decomposition plays important roles in carbon and nutrient
 cycling. In dryland both microbial decomposition and abiotic degradation
 (by UV light or other forces) drive variation in decomposition rates, but
 whether and how litter traits and position determine the balance between
 these processes is poorly understood. 2. We investigated relationships
 between litter quality and their decomposition rates among diverse plant
 species in a desert ecosystem in vertically contrasting positions
 representing distinct decomposition environments driven by different
 relative contributions of abiotic and microbial degradation. Thereto, leaf
 litter samples from 17 desert species were sealed into litterbags and
 placed on the soil surface under strong solar exposure versus shade
 conditions, or buried in the soil at 10 cm depth, for a whole year. 3.
 Litter decomposition rates were 21 and 17 % higher in burial and
 light-exposed treatments, respectively, than those in shade. Leaf traits,
 i.e. specific leaf area (SLA), litter C:N ratio and lignin concentration
 could predict litter decomposition to some degree, but their predictive
 power was dependent on litter position. However, multiple linear
 regression showed that SLA, litter C and P significantly affected k values
 for leaf litter decomposition besides litter position, with SLA standing
 out as a strong determinant of litter decomposition rate as related either
 to solar radiation or the environment below the soil surface. Furthermore,
 the interspecific differences in litter decomposition rate decreased over
 time, implying that afterlife effects of leaf traits on decomposition were
 attenuated. 4. Synthesis. These ﬁndings suggest that abiotic
 photodegradation and soil burial mediated microbial decomposition could be
 responsible for higher than expected litter turnover in dryland. They
 point to a dual role of specific leaf area as a promotor of decomposition
 rates: via relative exposure of the leaf surface to abiotic factors such
 as UV light versus to soil moisture and microbes under soil burial.
description: Leaf litter
 decomposition in dryland under different three litter
 postionsThere are three excel
 sheets. 1. Initial traits and k values in litter decomposition model
 across 17 desert species 2. The fraction of mass loss during three
 incubation times for each of three treatments 3. Litter concentration
 during different incubation times for each of threee
 treatmentJEcol-2017-0346data.xlsx
DOI: 10.5061/dryad.m028b
title: Data from: The role of founder effects on the evolution of reproductive isolation

description: Several theories argue that large changes in allele frequencies through
 genetic drift after a small founding population becomes allopatrically
 isolated can lead to significant changes in reproductive isolation and
 thus trigger the origin of new species. For this reason, founder
 speciation has been proposed as a potent force in the generation of new
 species. Nonetheless, the relative importance of such “founder effects”
 remains largely untested. In this report, I used experimental evolution to
 create one thousand replicates that underwent an extreme bottleneck and to
 study whether founder effects can lead to an increase in reproductive
 isolation in Drosophila yakuba. Even though the most common outcome of
 inbreeding is extinction, founder effects can lead to increased premating
 reproductive isolation in a very small proportion of cases. Changes in
 reproductive isolation after a founding population bottleneck are similar
 to changes in other phenotypic traits, in which inbreeding might displace
 the mean phenotypic value and substantially increase the phenotypic
 variance. This increase in phenotypic variance does not confer an increase
 in the response to selection for reproductive isolation in artificial
 selection experiments, indicating that the increased phenotypic variance
 is not caused by increases in additive genetic variance. These results
 also demonstrate that, similar to morphological and life history traits,
 behavioral traits can be affected by inbreeding and genetic drift.
description: Reproductive isolation
 measurements before and after inbreeding, Effect of color on mating
 choiceReproductive isolation
 measurements in the laboratory at 21ºC.raw_data_DRM_JEB.zip
DOI: 10.5061/dryad.457tt13
title: Data from: Of molecules, memories, and migration: M1 acetylcholine receptors facilitate spatial memory formation and recall during migratory navigation

description: Many animals use complex cognitive processes, including the formation and
 recall of memories, for successful navigation. However, the developmental
 and neurological processes underlying these cognitive aspects of
 navigation are poorly understood. To address the importance of the
 formation and recollection of memories during navigation, we
 pharmacologically manipulated turtles (Chrysemys picta) that navigate long
 distances using precise, complex paths learned during a juvenile critical
 period. We treated freely-navigating turtles both within and outside of
 their critical learning period with a specific M1 acetylcholine-receptor
 antagonist, a drug known to disrupt spatial cognition. Experienced adult
 turtles lost all navigational ability under the influence of the drug,
 while naïve juveniles navigated successfully. We retested these same
 juveniles the following year (after they had passed their critical
 period). The juveniles that initially navigated successfully under the
 influence of the antagonist (but were unable to form spatial memories)
 were unable to do so subsequently. However, the control animals (who had
 the opportunity to form memories previously) exhibited typical
 navigational precision. These results suggest that the formation of
 spatial memories for navigation occur during a critical period, and
 successful navigation after the critical period is dependent upon the
 recall of such memories.
description: Roth and Krochmal M1
 data for Dryad
DOI: 10.34740/kaggle/dsv/14634687
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.v5p71
title: Data from: Major radiations in the evolution of caviid rodents: reconciling fossils, ghost lineages, and relaxed molecular clocks

description: BACKGROUND: Caviidae is a diverse group of caviomorph rodents that is
 broadly distributed in South America and is divided into three highly
 divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and
 Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant
 and diverse since the late Miocene. Caviids belongs to Cavioidea sensu
 stricto (Cavioidea s.s.) that also includes a diverse assemblage of
 extinct taxa recorded from the late Oligocene to the middle Miocene of
 South America (“eocardiids”). RESULTS: A phylogenetic analysis combining
 morphological and molecular data is presented here, evaluating the time of
 diversification of selected nodes based on the calibration of phylogenetic
 trees with fossil taxa and the use of relaxed molecular clocks. This
 analysis reveals three major phases of diversification in the evolutionary
 history of Cavioidea s.s. The first two phases involve two successive
 radiations of extinct lineages that occurred during the late Oligocene and
 the early Miocene. The third phase consists of the diversification of
 Caviidae. The initial split of caviids is dated as middle Miocene by the
 fossil record. This date falls within the 95% higher probability
 distribution estimated by the relaxed Bayesian molecular clock, although
 the mean age estimate ages are 3.5 to 7 Myr older. The initial split of
 caviids is followed by an obscure period of poor fossil record (refered
 here as the Mayoan gap) and then by the appearance of highly
 differentiated modern lineages of caviids, which evidentially occurred at
 the late Miocene as indicated by both the fossil record and molecular
 clock estimates. CONCLUSIONS: The integrated approach used here allowed us
 identifying the agreements and discrepancies of the fossil record and
 molecular clock estimates on the timing of the major events in cavioid
 evolution, revealing evolutionary patterns that would not have been
 possible to gather using only molecular or paleontological data alone.
description: DatasetS1
DOI: 10.5061/dryad.jd6ff
title: Data from: Differences in developmental strategies between long-settled and invasion-front populations of the cane toad in Australia

description: Phenotypic plasticity can enhance a species’ ability to persist in a new
 and stressful environment, so that reaction norms are expected to evolve
 as organisms encounter novel environments. Biological invasions provide a
 robust system to investigate such changes. We measured the rates of early
 growth and development in tadpoles of invasive cane toads (Rhinella
 marina) in Australia, from a range of locations and at different larval
 densities. Populations in long-colonized areas have had the opportunity to
 adapt to local conditions, whereas at the expanding range edge, the
 invader is likely to encounter challenges that are both novel and
 unpredictable. We thus expected invasion-vanguard populations to exhibit
 less phenotypic plasticity than range-core populations. Compared to
 clutches from long-colonized areas, clutches from the invasion front were
 indeed less plastic (i.e. rates of larval growth and development were less
 sensitive to density). In contrast, those rates were highly variable in
 clutches from the invasion front, even among siblings from the same clutch
 under standard conditions. Clutches with highly variable rates of growth
 and development under constant conditions had lower phenotypic plasticity,
 suggesting a trade-off between these two strategies. Although these
 results reveal a strong pattern, further investigation is needed to
 determine whether these different developmental strategies are adaptive
 (i.e. adaptive phenotypic plasticity vs. bet-hedging) or instead are
 driven by geographic variation in genetic quality or parental effects.
description: SM dataset MS Ducatez et
 al. JEBdataset Rhinella marina Ducatez
 et al. JEB.xlsx
DOI: 10.5061/dryad.cj5fp
title: Data from: Assessing the relationship between quality of life and behavioral activation using the Japanese behavioral activation for depression scale-short form

description: Quality of life (QOL) is an important health-related concept. Identifying
 factors that affect QOL can help develop and improve health-promotion
 interventions. Previous studies suggest that behavioral activation fosters
 subjective QOL, including well-being. However, the mechanism by which
 behavioral activation improves QOL is not clear. Considering that QOL
 improves when depressive symptoms improve post-treatment and that
 behavioral activation is an effective treatment for depression, it is
 possible that behavioral activation affects QOL indirectly rather than
 directly. To clarify the mechanism of the influence of behavioral
 activation on QOL, it is necessary to examine the relationships between
 factors related to behavioral activation, depressive symptoms, and QOL.
 Therefore, we attempted to examine the relationship between these factors.
 Participants comprised 221 Japanese undergraduate students who completed
 questionnaires on behavioral activation, QOL, and depressive symptoms: the
 Japanese versions of the Behavioral Activation for Depression Scale-Short
 Form (BADS-SF), WHO Quality of Life-BREF (WHOQOL-26), and Center for
 Epidemiologic Studies Depression Scale (CES-D). The BADS-SF comprises two
 subscales, Activation and Avoidance, and the WHOQOL-26 measures overall
 QOL and four domains, Physical Health, Psychological Health, Social
 Relationships, and Environment. Mediation analyses were conducted with
 BADS-SF activation and avoidance as independent variables, CES-D as a
 mediator variable, and each WHO-QOL as an outcome variable. Results
 indicated that depression completely mediated the relationship between
 Avoidance and QOL, and partially mediated the relationship between
 Activation and QOL. In addition, analyses of each domain of QOL showed
 that Activation positively affected all aspects of QOL directly and
 indirectly, but Avoidance had a negative influence on only part of QOL
 mainly through depression. The present study provides behavioral
 activation strategies aimed at QOL enhancement.
description: RawDataThe Behavioral Activation for Depression Scale-Short Form (BADS-SF; Activation, Avoidance), Center for Epidemiologic Studies Depression Scale (CES-D), Japanese version of the WHO Quality of Life-BREF (WHOQOL-26; Mean total score, Physical Health, Psychological Health, Social Relationships, Environment, Overall QOL)S1_Dataset.xlsx