cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ns1rn8pq3
title: Data from: They like it cold, but only in winter: climate‐mediated effects on a hibernator

description: Variations in ambient temperature (Ta) profoundly influence energy
 consumption in endotherms and therefore their survival and fitness. But
 depending on whether endotherms are hibernating or active, the same
 changes in Ta may have opposing consequences for their energy
 consumption. The aim of this study was therefore to investigate how
 variations in Ta, occurring during hibernation and during the active
 period of a hibernator, affect different fitness relevant traits. To
 understand whether changes in Ta impact phenology, body mass and
 reproduction in a small mammalian hibernator, we analysed
 Ta variations and detailed capture-mark-recapture data on edible
 dormice (Glis glis) collected between 1993 and 2016 in South-West Germany.
 Results revealed that during hibernation a Ta increase of 1°C
 advanced the date of first capture after hibernation by 6 days, but only
 if food availability during the preceding year was low. In contrast, after
 years of comparatively high food availability, date of first capture was
 not affected by Ta, but dormice had a significantly lower body mass after
 emergence, if Ta during hibernation was elevated (3 to 6g per
 1°C). We presume that an earlier emergence as well as a lower body mass
 after emergence potentially reduce the chance to survive. During the
 active period of edible dormice, mean spring Ta a did not affect
 the date of birth but was positively associated with litter size,
 potentially improving reproductive success. Results of this study
 highlight that, depending on the physiological state of a hibernator, an
 increase in Ta can have positive and negative effects on fitness
 relevant traits.
description: Data were collected in a capture - mark - recapture
 study. Ambient temperature data are retrieved from the
 weather station Stuttgart-Echterdingen, DWD (Deutscher Wetterdienst;
 www.dwd.de)<i>.</i>
DOI: 10.5061/dryad.m905qftz9
title: Fifty years of European ungulate dietary studies: a synthesis

description: Over recent decades, ungulate populations across Europe have undergone a
 rapid recovery. While this constitutes a conservation success, there is
 increasing concern about their impacts on shared resources with humans.
 Understanding ungulate food choices is crucial for predicting such
 impacts. Numerous studies have focused on single species or communities at
 narrow spatial scales. Here, we used 265 published diets from 87 European
 studies to investigate patterns of resource use by four common deer
 species (moose Alces alces, red deer Cervus elaphus, roe deer Capreolus
 capreolus, and fallow deer Dama dama), and wild boar Sus scrofa at the
 continental scale. On average, deer diets separated mostly along a
 gradient from grass to browse. Fallow deer diets contained the most and
 moose diets the least amount of grass, but we also found large
 intraspecific variation among all deer species. Diets of roe deer, a
 presumed browser, frequently contained ≥ 25% grass. Wild boar diet
 contained grass in amounts similar to red deer but otherwise differed
 strongly from deer diets. All five ungulate species shifted to eating
 higher proportions of woody browse during winter. Habitat influenced
 variation in intraspecific diets, but the proportions of key forage types
 related to feeding type (i.e., grass for intermediate feeders red and
 fallow deer, and shrubs for the browsers moose and roe deer) remained
 fairly consisted across habitat types. In northern and central Europe,
 diet similarity between roe deer and red deer was highest during winter
 and spring and lowest during summer and autumn but remained constant
 across the seasons in southern Europe. We foresee that, as interspecific
 interactions driven by land-use and climatic changes increase across
 Europe, further monitoring and testing will be needed to understand the
 dynamics of dietary niche partitioning among ungulates.
description: The dataset contains 265 diet profiles of five ungulate species
 (moose, roe deer, red deer, fallow deer, and wild boar) which were
 extracted from the European literature and standardized into 11 food
 categories and annual seasons.
DOI: 10.5061/dryad.vt4b8gtpt
title: Ethylene signaling mediates host invasion by parasitic plants

description: Parasitic plants form a specialized organ, a haustorium, to invade host
 tissues and acquire water and nutrients. To understand the molecular
 mechanism of haustorium development, we performed a forward genetics
 screening to isolate mutants exhibiting haustorial defects in the model
 parasitic plant Phtheirospermum japonicum. We isolated
 two mutants that show prolonged and sometimes aberrant
 meristematic activity in the haustorium apex, resulting in severe defects
 on host invasion. Whole genome sequencing revealed that the two
 mutants respectively have point mutations in homologs of ETHYLENE
 RECEPTOR 1 (ETR1) and ETHYLENE INSENSITIVE
 2 (EIN2), signaling components in response to the gaseous
 phytohormone ethylene. Application of the ethylene signaling inhibitors
 also caused similar haustorial defects, indicating that ethylene
 signaling regulates cell proliferation and differentiation of parasite
 cells. Importantly, genetic disruption of host ethylene
 production also perturbs parasite invasion. We propose that parasitic
 plants utilize ethylene as a signal to invade host roots.
description: Whole genome sequence of a facultative parasitic plant
 Phtheirospermum japonicum (ecotype Okayama) was analysed by illumina
 paired-end and mate-pair sequencing, together with PacBio long read
 sequencing. The draft genome was assembly using allpaths-lg and PBJelly,
 and annotated using MakerP pipeline using P. japonicum
 transcriptome.
description: This dataset contains whole genome assembly
 (PjScaffold_ver1.fasta), predicted transcripts
 (Pj.v1.1_transcripts.fasta) and translated amino acid
 (Pj.v1.1_proteins.fasta) sequences in fasta format with gff3 annotation
 file (PjScaffold.v1.1.gff).
DOI: 10.5061/dryad.r7sqv9s8v
title: Ecological niche models for American black bear, Rafinesque's big-eared bat, and timber rattlesnake

description: This data set contains rasters that are predictive environmental
 suitability maps for three wildlife species: the American black
 bear (Ursus americanus), Rafinesque's big-eared bat (Corynorhinus
 rafinesquii), and Timber rattlesnake (Crotalus horridus). Rasters for each
 species include: individual prediction maps for each of 5 ENMs
 (GBM: generalized boosting model, GLM: generalized linear model,
 MARS: multivariate adaptive regression spline, MX: maximum
 entropy, and RF: random forest), as well as the ensemble prediction map
 from all five ecological niche models (ENMs).
description: The ENMs were created using the Biomod package in R. Input data
 included occurrence points for each species, along with environmental
 variables from recent land cover and climate data sets. Individual models
 were created via the five algorithms (GBM, GLM, MARS, MX, and RF) and then
 averaged to produce the ensemble ENM. The ensemble models were used to map
 habitat cores and least cost paths between cores for the three focal
 species. Least cost paths are posted here: https://doi.org/10.5061/dryad.z8w9ghx85<br> For more information on the purpose of these data and the methods used to create them, see:<br> Costanza et al. Preserving connectivity under climate and land-use change: no one-size-fits-all approach for focal species in similar habitats. <i>Biological Conservation</i>.
description: See the file naming conventions in the readme file (readme.txt)
 that has been uploaded with this data set.
DOI: 10.34740/kaggle/dsv/14644228
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.5mkkwh73d
title: The diversity of maternal-age effects upon pre-adult survival across animal species

description: Maternal senescence is the detrimental effect of increased maternal age on
 offspring performance. Despite much recent interest given to describing
 this phenomenon, its distribution across animal species is poorly
 understood. A review of the published literature finds that maternal age
 affects pre-adult survival in 252 of 272 populations (93%) representing 97
 animal species. Age effects tended to be deleterious in invertebrates and
 mammals, including humans, confirming the presence of senescence. However,
 bird species were a conspicuous exception, as pre-adult survival tended to
 increase with maternal age in surveyed populations. In all groups,
 maternal-age effects became more negative in older mothers. Invertebrates
 senesced faster than vertebrates, and humans aged faster than non-human
 mammals. Within invertebrates, lepidopterans demonstrated the most extreme
 rates of maternal-effect senescence. Among the surveyed studies,
 phylogeny, life history and environment (e.g. laboratory versus wild
 populations) were tightly associated; this made it difficult to make
 confident inferences regarding the causes of diversity for the phenomenon.
 However, we provide some testable suggestions, and we observe that some
 differences appear to be consistent with predictions from evolutionary
 theory. We discuss how future work may help clarify ultimate and proximate
 causes for this diversity.
description: The analysis file is annotated. Please see the
 ReadMe file for more information on data used.
DOI: 10.5061/dryad.bg79cnp8c
title: Data from: Exploring the biotic homogenisation and diversity resistance hypotheses: the understorey of non-native and native woodland canopies in three urban areas of Europe

description: Exploring the biotic homogenisation and diversity resistance hypotheses by
 assessing the effect of non-native black locust canopy on understorey
 species turnover. Location: Berlin, the Venetian metropolitan
 area, and Rome. We modelled the zeta (ζ) expression of diversity to
 compare the understorey species turnover between the non-native black
 locust and native woodland canopies across multiple sites and through
 predictors of anthropogenic pressure (road and built-up density) and
 interior conditions (tree basal area and mean height). In Rome black
 locust showed the lowest survivability and cover and did not produce any
 homogenisation of the understorey. In Berlin and in the Venetian
 metropolitan area, black locust caused understorey homogenisation,
 although with a low intensity in Berlin. Under black locust canopies,
 distance between sites and road density were more consistently associated
 with species turnover, across urban areas and multiple sites. Under native
 canopies in Berlin, factors prominently associated with species turnover
 were road and built-up density and mean tree height, while in the Venetian
 metropolitan area it was road density. Evidence in support of the biotic
 homogenisation in contrast to the diversity resistance hypothesis varied
 across urban areas. Species turnover was influenced by land use patterns
 more evidently under native tree canopies and where the non-native tree
 had higher survivability. Similar analyses in other urban areas could
 confirm these relationships with other types of landscapes.
DOI: 10.5061/dryad.gmsbcc2k3
title: Optimal resource allocation and prolonged dormancy strategies in herbaceous plants

description: 1. Understanding the fitness consequences of different life histories is
 critical for explaining their diversity and for predicting effects of
 changing environmental conditions. However, current theory on plant life
 histories relies on phenomenological, rather than mechanistic, models of
 resource production. 2. We combined a well-supported mechanistic model of
 ontogenetic growth that incorporates differences in the size-dependent
 scaling of gross resource production and maintenance costs with a dynamic
 optimization model to predict schedules of reproduction and prolonged
 dormancy (plants staying below ground for ≥ 1 growing season) that
 maximize lifetime offspring production. 3. Our model makes three novel
 predictions: First, maintenance costs strongly influence the conditions
 under which a monocarpic or polycarpic life history evolves and how
 resources should be allocated to reproduction by polycarpic plants.
 Second, in contrast to previous theory, our model allows plants to
 compensate for low survival conditions by allocating a larger proportion
 of resources to storage and thereby improving overwinter survival.
 Incorporating this ecological mechanism in the model is critically
 important because without it our model never predicts significant
 investment into storage, which is inconsistent with empirical
 observations. Third, our model predicts that prolonged dormancy may evolve
 solely in response to resource allocation tradeoffs. 4. Significance: Our
 findings reveal that maintenance costs and the effects of resource
 allocation on survival are primary determinants of the fitness
 consequences of different life history strategies, yet previous theory on
 plant life history evolution has largely ignored these factors. Our
 findings also validate recent arguments that prolonged dormancy may be an
 optimal response to costs of sprouting. These findings have broad
 implications for understanding patterns of plant life history variation
 and predicting plant responses to changing environments.
description: The data presented in this manuscript were generated using a
 stochastic dynamic programming (SDP) model. The R script containing the
 SDP model code is deposited here.
description: Some of the parameter names used in the R script differ from the
 names provided in the manuscript. A translation from the parameter
 names in the model code to those used in the manuscript is provided at the
 beginning of the R script.
DOI: 10.5061/dryad.ksn02v720
title: Data from: What doesn’t kill you makes you stronger: detoxification ability as mechanism of honesty in a sexually selected signal

description: These files contain the data to perform all analysis done for the
 submitted manuscript What doesn’t kill you makes you stronger:
 detoxification ability as mechanism of honesty in a sexually selected
 signal.
DOI: 10.5061/dryad.5mkkwh73g
title: Functional genetic diversity of domestic and wild American mink (Neovison vison )

description: The release of domestic organisms to the wild threatens biodiversity
 because the introduction of domestic genes through interbreeding can
 negatively impact wild conspecifics via outbreeding depression. In North
 America, farmed American mink (Neovison vison) frequently escape
 captivity, yet the impact of these events on functional genetic diversity
 of wild mink populations is unclear. We characterized domestic and wild
 mink in Ontario at 17 microsatellites located in functional genes and in a
 promoter region that is non-coding but thought to be associated with
 traits affected by domestication. We found low functional genetic
 diversity in both mink types, as only 4 of 17 genes were variable, and the
 number of alleles per locus were generally lower in captive mink than in
 wild mink. To determine if allele frequencies of wild populations were
 affected by domestic release events, we performed redundancy analysis and
 spatial analysis of principal components on four polymorphic loci (AR,
 ATN1, IGF-1, and TOB1). We found evidence to suggest domestic release
 events are affecting the functional genetic diversity of wild mink, as
 sPCA showed clear distinctions between wild individuals near mink farms
 and those located in areas without mink farms. This is further
 substantiated through RDA, where spatial location was associated with
 genetic variation of AR, ATN1, and IGF1.
description: Mink sampled from multiple farm and wild sites in Ontario
 were separated into five groups: Nova Scotia domestic black (NSB), Ontario
 domestic black (ONB), Ontario domestic brown (OND), wild (Wild), and
 free-ranging Ontario mink of mixed origin that cannot be classified as
 either fully domestic or fully wild (Hybrid) based on Bayesian assignment
 tests carried out in a previous study (Kidd et al., 2009). Individuals
 with a mean membership coefficient q ≥ 0.8 were assigned as wild, those
 with q ≤ 0.2 were domestic, and the remaining (0.2 &gt; q &lt;
 0.8) were considered hybrid though they may have been backcrossed to
 domestic or wild groups (Kidd et al., 2009). Samples were genotyped at
 microsatellite loci in four functional genes (AR, ATN1, IGF-1, and TOB1)
 and a set of neutral loci. We also sequenced AR and ATN1 alleles to test
 for sequence polymorphisms in same-sized alleles.
DOI: 10.5061/dryad.f4qrfj6td
title: Data from: Postglacial recolonization of North America by spadefoot toads: integrating niche and corridor modeling to study species’ range dynamics over geologic time

description: Understanding the factors that shape species’ distributions is a key topic
 in biogeography. As climates change, species can either cope with these
 changes through evolution, plasticity or by shifting their ranges to track
 the optimal climatic conditions. Ecological niche modeling (ENM) is a
 widespread technique in biogeography that estimates the niche of the
 organism by using occurrences and environmental data to estimate species’
 potential distributions. ENMs are often criticized for failing to take
 species’ dispersal abilities into consideration. Here, we attempt to fill
 this gap by combining ENMs with dispersal and corridor modeling to study
 the range dynamics of North American spadefoot toads (Scaphiopodidae) over
 the Holocene. We first estimated the current and past distributions of
 spadefoot toads and then estimated their past distributions from the Last
 Glacial Maximum (LGM) to the present day. Then, we estimated how each
 taxon recolonized North American by using dispersal and corridor modeling.
 By combining these two modeling approaches we were able to 1) estimate the
 LGM refugia used by the North American spadefoot toads, 2) further refine
 these projections by estimating which of the putative LGM refugia
 contributed to the recolonization of North America via dispersal, and 3)
 estimate the relative influence of each LGM refugium to the current
 species’ distributions. The models were tested using previously published
 phylogeographic data, revealing a high degree of congruence between our
 models and the genetic data. These results suggest that combining ENMs and
 dispersal modeling over time is a promising approach to investigate both
 historical and future species’ range dynamics.
description: Data used to create the ecological niche models and corridors
 models.
DOI: 10.5061/dryad.stqjq2c1h
title: Data from: Deep Divergence between Island Populations in Lichenized Fungi

description: Macaronesia is characterized by a high degree of endemism and represents a
 noteworthy system to study the evolutionary history of populations and
 species. Here, we compare the population-genetic structure in three
 lichen-forming fungi, the widespread Lobaria pulmonaria and two
 Macaronesian endemics, L. immixta and L. macaronesica, based on
 microsatellites. We utilize population genetic approaches to explore
 population subdivision and evolutionary history of these taxa on the
 Canary Islands, Madeira, Azores, and the western Iberian Peninsula. A
 common feature in all species was the deep divergence between populations
 on the Azores, a pattern expected by the large geographic distance among
 islands. For both endemic species, there was a major split between
 archipelagos. In contrast, in the widespread L. pulmonaria, divergent
 individuals were distributed across multiple archipelagos, suggesting a
 complex evolutionary history involving repeated migration between islands
 and mainland.
description: The genotyping of microsatellites followed Werth et al. (2014).
 Fragment analyses were run on an automated capillary sequencer (3730xl DNA
 Analyzer, Life Technologies, Rotkreuz). Alleles were genotyped with an
 internal size standard (LIZ500) using GeneMapper version 3.7 (Life
 Technologies, Rotkreuz).  
 <strong>Reference</strong> Werth
 S, Cheenacharoen S, Scheidegger C (2014) Propagule size is not a good
 predictor for regional population subdivision or fine-scale spatial
 structure in lichenized fungi. Fungal Biology 118:126-138.
 doi:10.1016/j.funbio.2013.10.009
description: Allele frequency data of <i>Lobaria immixta</i>,
 <i>L. macaronesica</i>, and<i> L. pulmonaria</i>
 for six fungal microsatellite loci (LPu09, LPu15, LPu23, LPu24, LPu25,
 LPu28, Walser et al. 2003; Widmer et al. 2010) in each of 51 populations.
 Each entry represents the frequency of a given allele (row) in each
 population (column). Population names as in Table S1. Colored shading
 above population names refers to geographic regions or countries. Alleles
 are named by a combination of the locus name and allele length. Grey
 shading indicates populations where the endemic species (<i>Lobaria
 immixta</i>, <i>L. macaronesica</i>) did not
 occur.
 <strong>References</strong> Walser
 JC, Sperisen C, Soliva M, Scheidegger C (2003) Fungus-specific
 microsatellite primers of lichens: application for the assessment of
 genetic variation on different spatial scales in <em>Lobaria
 pulmonaria</em>. Fungal Genetics and Biology 40 (1):72-82.
 doi:10.1016/S1087-1845(03)00080-X Widmer I, Dal Grande
 F, Cornejo C, Scheidegger C (2010) Highly variable microsatellite markers
 for the fungal and algal symbionts of the lichen <em>Lobaria
 pulmonaria</em> and challenges in developing biont-specific
 molecular markers for fungal associations. Fungal Biology 114:538-544.
 doi:10.1016/j.funbio.2010.04.003
DOI: 10.5061/dryad.hhmgqnkds
title: Genomic inbreeding and population structure of northern pike (Esox lucius) in Xinjiang, China

description: Northern pike (Esox lucius) is widely distributed in the high latitudes of
 the northern hemisphere. In Xinjiang of China, the original record only
 distributed the Irtysh River, which has now spread to the main water
 bodies in northern Xinjiang and Bosten Lake in Southern Xinjiang. The
 number, extent and source of introductions of pike into Xinjiang waterways
 besides Irtysh River remain currently unknown. Understanding the genetic
 diversity, population structure and connectivity of the various
 populations could help us better trace the spread pattern of northern pike
 in Xinjiang, China. A total of four populations were collected from north
 to south in Xinjiang, including Irtysh River (RIR), Ulungu Lake (LUL), a
 small lake nearby Ulungu River (LJD) and Bosten Lake (LBO). We estimated
 population genomic parameters, performed gene flow analysis, and estimated
 the effective population size of each population.
DOI: 10.5061/dryad.31zcrjdhq
title: A new two-fingered dinosaur sheds light on the radiation of Oviraptorosauria

description: Late Cretaceous trends in Asian dinosaur diversity are poorly understood,
 but recent discoveries have documented a radiation of oviraptorosaur
 theropods in China and Mongolia. However, little work has addressed the
 factors that facilitated this diversification. A new oviraptorid from the
 Late Cretaceous of Mongolia sheds light on the evolution of the forelimb,
 which appears to have played a role in the radiation of oviraptorosaurs.
 Surprisingly, the reduced arm has only two functional digits, highlighting
 a previously unrecognized occurrence of digit loss in theropods.
 Phylogenetic analysis shows that the onset of this reduction coincides
 with the radiation of heyuannine oviraptorids, following dispersal from
 southern China into the Gobi region. This suggests expansion into a new
 niche in the Gobi region, which relied less on the elongate, grasping
 forelimbs inherited by oviraptorosaurs. Variation in forelimb length and
 manus morphology provides another example of niche partitioning in
 oviraptorosaurs, which may have made possible their incredible diversity
 in the latest Cretaceous of Asia.
description: Methods for data collection, processing, and analysis are
 presented in Funston et al. (2020).
description: Methods for data collection, processing, and analysis are
 presented in Funston et al. (2020).