cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bzkh1894s
title: Long-term warming affects ecosystem functioning through species turnover and intraspecific trait variation

description: Effects of climate change on natural ecosystems can be mediated by
 ecological processes, but also by rapid evolutionary adaptations and/or
 non-heritable trait changes in organisms. So far, most studies testing the
 importance of inter- vs. intraspecific changes for how communities and
 their functioning responds to climate change are either short-term
 laboratory experiments in highly controlled (artificial) environments, or
 long-term field surveys suffering from lack of experimental manipulation.
 Here, we quantified how community composition and functioning has changed
 in response to long-term warming, including the potential direct and
 indirect effects via immediate and delayed physiological, non-heritable
 plastic, ecological, evolutionary and eco-evolutionary responses. We used
 a space-for-time approach, sampling sites in an artificially heated basin
 and a nearby area to quantify how &gt;30 years of experimental warming
 in situ affects benthic grazer communities and traits of grazer taxa, as
 well as their contribution to a key ecosystem function: grazing on
 filamentous algae. The community composition shifted with warming, because
 a non-native species was highly common, and taxa with higher mobility,
 became more common in the heated areas compared to the control sites.
 Warming altered community functioning but the underlying mechanisms varied
 between traits: increased metabolism was caused by intraspecific trait
 change, while increased grazing rate was mainly driven by species
 turnover. Our results suggest that both population- and community-level
 processes mediate the responses of natural communities to long-term
 environmental change, and that the ongoing warming of coastal waters is
 likely to alter the functioning of key marine ecosystems.
DOI: 10.5061/dryad.37pvmcvfc
title: Data from: An X-linked meiotic drive allele has strong, recessive fitness costs in female Drosophila pseudoobscura

description: Selfish ‘meiotic drive’ alleles are transmitted to &gt;50% of
 offspring, allowing them to rapidly invade populations even if they reduce
 the fitness of individuals carrying them. Theory predicts that drivers
 should either fix or go extinct, yet some drivers defy these predictions
 by persisting at low, stable frequencies for decades. One possible
 explanation for this discrepancy is that drivers are especially costly
 when homozygous, although empirical tests of this idea are rare and
 equivocal. Here, we measure the fitness of female Drosophila pseudoobscura
 carrying zero, one, or two copies of the X-linked driver Sex-Ratio (SR).
 SR had strong negative effects on female offspring production and the
 probability of reproductive failure, and these effects were largely
 similar across four genetic backgrounds. SR was especially costly when
 homozygous. We used our fitness measurements to parameterise a population
 genetic model, and found that the female fitness costs observed here can
 explain the puzzlingly low allele frequency of SR in nature. We also use
 the model to show how spatial variation in female mating behaviour,
 fitness costs of SR, and the reduced siring success of SR males can
 jointly explain the North-South cline in SR frequencies across North
 America.
description: Excel spreadsheet showing the number of offspring produced by
 females carrying 0 (ST/ST), 1 (SR/ST), or 2 (SR/SR) driving X chromsomes
 introgressed into 4 genetic backgrounds (Lew 13, Lew 17, Slo7, Slo13),
 with female age and body size as covariate = main data
 Separate excel spreadsheet showing the total number of sons and
 daughters produced across the 3 genotypes and 4 genetic backgrounds = sex
 ratio
DOI: 10.5061/dryad.3j9kd51d1
title: Data from: Environmental DNA surveys help to identify winter hibernacula of a temperate freshwater turtle

description: Background and aims Overwintering is a critical part of the annual cycle
 of animals living at high latitudes, and selection of overwintering sites
 (hibernacula) is important to population persistence. Identifying the
 overwintering sites of aquatic species is challenging in areas where water
 bodies are frozen for significant parts of the year. We tested whether
 environmental DNA (eDNA) approaches could help to locate them. Materials
 and methods We conducted environmental DNA surveys of underwater
 overwintering sites of the northern map turtle (Graptemys geographica), a
 species of conservation concern in Canada. We collected water samples
 under the ice in winter across a mid‐sized temperate lake and used
 quantitative PCR with a species‐specific probe to quantify concentrations
 of map turtle eDNA. Results and discussion We found localized eDNA signals
 consistent with known overwintering sites and one previously suspected
 site. The latter was further confirmed using underwater remote operated
 vehicle (ROV) visual surveys. Conclusions Our study confirms that eDNA can
 offer insights on a critical part of the annual cycle of aquatic species,
 for which we know very little.
DOI: 10.5061/dryad.h44j0zpfj
title: Data from: Predators’ consumption of unpalatable prey does not vary as a function of bitter taste perception

description: Many prey species contain defensive chemicals that are described as
 tasting bitter. Bitter taste perception is therefore assumed to be
 important when predators are learning about prey defenses. However, it is
 not known how individuals differ in their response to bitter taste, and
 how this influences their foraging decisions. We conducted taste
 perception assays in which wild-caught great tits (Parus major) were given
 water with increasing concentrations of bitter-tasting chloroquine
 diphosphate until they showed an aversive response to bitter taste. This
 response threshold was found to vary considerably among individuals,
 ranging from chloroquine concentrations of 0.01 mmol/l to 8 mmol/l. We
 next investigated whether the response threshold influenced the
 consumption of defended prey during avoidance learning by presenting birds
 with novel palatable and defended prey in a random sequence until they
 refused to attack defended prey. We predicted that individuals with taste
 response thresholds at lower concentrations would consume fewer defended
 prey before rejecting them, but found that the response threshold had no
 effect on birds’ food choices. Instead, willingness to consume defended
 prey was influenced by birds’ body condition. This effect was age and sex
 dependent, with adult males attacking more defended prey when their body
 condition was poor, whereas body condition did not have an effect on the
 foraging choices of juveniles and females. Together, our results suggest
 that even though taste perception might be important for recognizing prey
 toxicity, other factors, such as predators’ energetic state, drive the
 decisions to consume chemically defended prey.
DOI: 10.5061/dryad.2rbnzs7hz
title: Data from: Timing of arrival in the breeding area is repeatable and affects reproductive success in a non-migratory population of blue tits

description: Events in one part of the annual cycle often affect the performance (and
 subsequently fitness) of individuals later in the season (carry-over
 effects). An important aspect of this relates to the timing of activities.
 For example, many studies on migratory birds have shown that relatively
 late spring arrival in the breeding area reduces both the likelihood of
 getting a mate or territory and reproductive success. In contrast,
 relatively little is known about movements of individuals in non-migratory
 populations during the non-breeding season. Few studies have investigated
 the timing of arrival at the breeding area in such species, possibly due
 to the assumption that most individuals remain in the area during the
 non-breeding season. In this study, we used four years of data from a
 transponder-based automated recording system set up in a non-migratory
 population of blue tits (Cyanistes caeruleus) to describe individual
 variation in arrival at the breeding site. We investigated whether this
 variation can be explained by individual characteristics (sex, body size,
 or status), and we assessed its effect on aspects of reproductive success
 in the subsequent breeding season. We found substantial variation in
 arrival date and demonstrate that this trait is individual-specific
 (repeatable). Females arrived later than males, but the arrival dates of
 social pair members were more similar than expected by chance, which
 suggests that individuals may mate assortatively depending on their
 arrival in the breeding area. Arrival predicted both whether an individual
 would end up breeding that season, and several aspects of its breeding
 success. Our study suggests that individuals of non-migratory species
 leave the breeding area during the non-breeding season. Hence, it may be
 useful to consider variation in the scale of movements between breeding
 and non-breeding sites, rather than using a simple dichotomy between
 “resident” and “migratory” species. We conclude that the timing of
 pre-breeding events, in particular arrival date, may be an overlooked, but
 important, fitness-relevant trait in non-migratory species.
DOI: 10.5061/dryad.tx95x69sv
title: Niches and radiations: A case study on the Andean Sapphire-vented Puffleg (Eriocnemis luciani) and Coppery-naped Puffleg (E. sapphiropygia) (Aves, Trochilidae)

description: The interaction between ecology and evolution, particularly with regard to
 speciation processes, remains a main topic of scientific research. Andean
 hummingbirds have undergone a remarkable radiation, with many species
 exhibiting patchy distributions and, in some cases, taxonomic controversy.
 An example is the Sapphire-vented Puffleg (Eriocnemis luciani; ssp.
 baptistae, luciani, and meridae), which some authors merge with the
 Coppery-naped Puffleg (E. sapphiropygia; ssp. catharina and
 sapphiropygia). Each group is distributed either north or south from the
 Huancabamba Depression, the major biogeographical barrier within the
 tropical Andes. We investigated whether these subspecies share some niche
 characteristics despite their geographical separation and determined their
 meaning in the context of the speciation process of trochilids in the
 tropical Andes. For each subspecies, we performed geographical predictions
 and paired tests of niche conservatism in environmental space.
 Geographical predictions included separate regions for subspecies
 catharina and sapphiropygia, while the predicted regions for
 subspecies luciani and baptistae greatly overlapped. The
 E. l. luciani model predicted a single pixel near to the
 potential area of E. l. meridae, known only from a unique, old record.
 Subspecies luciani and baptistae exhibited the greatest
 niche overlap among the pairs of taxa for most variables. However, our
 results clearly indicated niche divergence for the four members of the E.
 luciani-sapphiropygia complex, independent of the similarities or
 slight dissimilarities in their respective backgrounds, indicating that
 other forces in addition to variation in environmental parameters, such as
 natural selection or genetic drift, are driving the radiation of these
 hummingbirds. This finding coincides with the unusually high speciation
 rates reported for Andean hummingbirds. Thus, the currently accepted
 taxonomy within the E. luciani-sapphiropygia complex may be even
 more convoluted than indicated by previous studies. Hence, the results of
 our study are a wakeup call to include the exploration of lineage
 diversification in biodiversity-related efforts.
DOI: 10.5061/dryad.fqz612jp8
title: Recent evolutionary history predicts population but not ecosystem level patterns

description: In the face of rapid anthropogenic environmental change, it is
 increasingly important to understand how ecological and evolutionary
 interactions affect the persistence of natural populations. Augmented gene
 flow has emerged as a potentially effective management strategy to
 counteract negative consequences of genetic drift and inbreeding
 depression in small and isolated populations. However, questions remain
 about the long-term impacts of augmented gene flow and whether changes in
 individual and population fitness are reflected in ecosystem structure,
 potentiating eco-evolutionary feedbacks. In this study, we used
 Trinidadian guppies (Poecilia reticulata) in experimental outdoor
 mesocosms to assess how populations with different recent evolutionary
 histories responded to a scenario of severe population size reduction
 followed by expansion in a high-quality environment. We also investigated
 how variation in evolutionary history of the focal species affected
 ecosystem dynamics. We found that evolutionary history (i.e., gene flow
 versus no gene flow) consistently predicted variation in individual
 growth. In addition, gene flow led to faster population growth in
 populations from one of the two drainages, but did not have measurable
 impacts on the ecosystem variables we measured: zooplankton density, algal
 growth, and decomposition rates. Our results suggest that benefits of gene
 flow may be long-term and environment-dependent. Although small in
 replication and duration, our study highlights the importance of
 eco-evolutionary interactions in determining population persistence and
 sets the stage for future work in this area.
DOI: 10.15468/dl.6q2hdf
title: Occurrence Download

description: A dataset listing the 2883 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is UCM Fossil Vertebrate Specimens (Arctos)"
 ]
}

 The dataset's 2883 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002013-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fn2z34tpx
title: Data from: Games academics play and their consequences: how authorship, h-index, and journal impact factors are shaping the future of academia

description: Research is a highly competitive profession where evaluation plays a
 central role; journals are ranked and individuals are evaluated based on
 their publication number, the number of times they are cited, and their
 h-index. Yet, such evaluations are often done in inappropriate ways that
 are damaging to individual careers, particularly for young scholars, and
 to the profession. Furthermore, as with all indices, people can play games
 to better their scores. This has resulted in the incentive structure of
 science increasingly mimicking economic principles, but rather than a
 monetary gain, the incentive is a higher score. To ensure a diversity of
 cultural perspectives and individual experiences, we gathered a team of
 academics in the fields of ecology and evolution from around the world and
 at different career stages. We first examine how authorship, h-index of
 individuals, and journal impact factors are being used and abused. Second,
 we speculate on the consequences of the continued use of these metrics
 with the hope of sparking discussions that will help our fields move in a
 positive direction. We would like to see changes in the incentive systems
 rewarding quality research and guaranteeing transparency. Senior faculty
 should establish the ethical standards, mentoring practices, and
 institutional evaluation criteria to create the needed changes.
description: The number of authors on research articles in six journals
 through time. The area of each circle corresponds to the number of
 publications with that publication number for that year. To aid in visual
 interpretation of the data, a generalized additive model was fitted to the
 data. For ease of interpretation, the number of authors is truncated at
 100, meaning that publications with &gt;100 coauthors are plotted here
 as just including 101 coauthors.
DOI: 10.5061/dryad.qnk98sfbq
title: Data from: Leaf drought tolerance cannot be inferred from classic leaf traits in a tropical rainforest

description: Plants are enormously diverse in their traits and ecological adaptation,
 even within given ecosystems, such as tropical rainforests. Accounting for
 this diversity in vegetation models poses serious challenges. Global plant
 functional trait databases have highlighted general trait correlations
 across species that have considerably advanced this research program.
 However, it remains unclear whether trait correlations found globally hold
 within communities, and whether they extend to drought tolerance traits.
 For 134 individual plants spanning a range of sizes and life forms (tree,
 liana, understory species) within an Amazonian forest, we measured leaf
 drought tolerance (leaf water potential at turgor loss point, πtlp),
 together with 17 leaf traits related to various functions, including leaf
 economics traits and nutrient composition (leaf mass per area, LMA; and
 concentrations of C, N, P, K, Ca, and Mg per leaf mass and area), leaf
 area, water use efficiency (carbon isotope ratio), and time-integrated
 stomatal conductance and carbon assimilation rate per leaf mass and area.
 We tested trait coordination and the ability to estimate πtlp from the
 other traits through model selection. Performance and transferability of
 the best predictive model were assessed through cross-validation. πtlp was
 positively correlated with leaf area, and with N, P and K concentrations
 per leaf mass, but not with LMA or any other studied trait. Five axes were
 needed to account for &gt;80% of trait variation, but only three of
 them explained more variance than expected at random. The best model
 explained only 30% of the variation in πtlp, and out-sample predictive
 performance was variable across life forms or canopy strata, suggesting a
 limited transferability of the model. Synthesis. We found a weak
 correlation among leaf drought tolerance and other leaf traits within a
 forest community. We conclude that higher trait dimensionality than
 assumed under the leaf economics spectrum may operate among leaves within
 plant communities, with important implications for species coexistence and
 responses to changing environmental conditions, and also for the
 representation of community diversity in vegetation models.
description: All methods and analyses are explicitely described and provided
 in the corresponding paper.
description: Please refer to the corresponding paper published in Journal of
 Ecology for further details.
DOI: 10.5061/dryad.ksn02v70g
title: Haplotype-resolved genome analyses of a heterozygous diploid potato

description: Potato (Solanum tuberosum L.) is the most important tuber crop
 worldwide. An effort is underway to transform the crop from a clonally
 propagated tetraploid into a diploid seed-propagated, inbred line-based
 hybrid, which requires a better understanding of its highly heterozygous
 genome of potato. Here, we report the 1.67 Gb haplotype-resolved assembly
 of a diploid potato, RH89-039-16, using the combination of multiple
 sequencing and mapping strategies, including circular consensus
 sequencing. Comparison of the two haplotypes revealed ~2.1% intra-genome
 diversity, including 22,134 predicted deleterious mutations in 10,642
 annotated genes. In a total of 20,583 pairs of allelic genes, 16.6% and
 30.8% exhibited differential expression and methylation between alleles,
 respectively. Deleterious mutations and differentially expressed alleles
 were dispersed throughout both haplotypes, complicating strategies to
 eradicate deleterious alleles or stacking of beneficial alleles, via
 meiotic recombination. Further cataloguing of functional haplotypes, in
 diploid potato, could enable exploitation of heterosis using genotypes
 with complementary haplotypes. This study offers a holistic view of the
 genome organization of a clonally propagated diploid species, as well as
 provides insights into technological evolution in resolving complex
 genomes.
DOI: 10.5061/dryad.mpg4f4qv3
title: Data from: Bee pollinator functional responses and functional effects in restored tropical forests

description: Wild pollinators are necessary for ensuring plant reproduction not only
 among crop fields but also remnant and restored ecosystems. Restoration
 activities should, therefore, lead to wild pollinator recovery, and thus
 be monitored to evaluate effects on pollinator diversity and
 functionality. We assessed bee pollinator functional responses in
 restoration plantings by creating functional groups (traits: body size,
 nesting location, sociality and foraging strategy), comparing their
 abundance and diversity to that of other habitats (i.e. conserved and
 degraded primary forest fragments, anthropogenic wetlands and sugarcane
 fields), and testing for an effect of source habitat (i.e., primary forest
 fragments) isolation. We analyzed functional effects on pollen
 transportation by identifying the pollen grains attached on the bodies of
 bees; creating plant functional groups with the identified species
 (traits: habit, successional class, geographic origin and pollination
 mode); comparing their frequency, diversity and interaction network
 structure among habitats; and searching for key interactions in network
 modules. In general, the abundance and diversity of bee communities and
 the frequency and diversity of the interacting plant species in
 restoration plantings were lower than those in primary forest fragments
 but higher than those in anthropogenic wetlands and sugarcane fields,
 suggesting that restoration plantings better enhance bee community
 recovery and functionality than other disturbed habitats. The interacting
 bees and plants were also negatively affected by habitat isolation,
 demonstrating the importance of primary forest fragments to supply bee
 populations to restored sites. The structure of interaction networks was
 little affected by habitat change and isolation, but the composition and
 diversity of functional groups varied significantly. There were more
 effects on larger bee species with more restricted nesting and floral
 requirements, and the woody species with which they interact most
 frequently. We identified key functional groups of bee pollinators that
 deserve priority for conservation because they play an important role in
 the pollen transportation of some the most relevant species in remnant
 forests and restoration plantings, and also respond more negatively to
 habitat disturbances. Restoration efforts should include provisioning of
 nesting resources and management and conservation of primary forest
 remnant fragments that represent source habitats for them.
DOI: 10.15468/dl.2jmzpd
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus carteri"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002026-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.