cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vmcvdncph
title: Data from: Great spotted cuckoos show dynamic patterns of host selection during the breeding season

description: Avian brood parasites depend entirely on their hosts to raise their
 nestlings until independence. Thus, parasite females should select
 suitable host nests for egg laying according to traits that enhance
 offspring survival. Availability of nests of certain characteristics
 influencing survival of parasitic offspring is however temporally dynamic
 and, thus, patterns of host selection should be evaluated considering
 characteristics of available host nests the day of parasitism. This allows
 detecting possible seasonal changes and, therefore, a more realistic
 picture of host selection by brood parasites. In this paper, we adopt such
 a new approach, and consider daily availability of magpie (Pica pica) host
 nests at different breeding stage that were or were not parasitized by the
 great spotted cuckoo (Clamator glandarius). Theory predicts that cuckoos
 should select host nests at the laying stage. Accordingly, we detected
 that cuckoos preferred to parasitize magpie nests at the laying stage,
 but, mainly those that already harboured one or two cuckoo eggs, which may
 seem counter-intuitive. We also showed that patterns of host selection by
 cuckoos varied during the breeding season, which implies that brood
 parasites-hosts interaction is dynamic depending on phenology. These
 patterns are hidden when not considering the temporally dynamic nature of
 availability of host nests of characteristics of interest. We discuss the
 importance of such patterns and considering diary hosts nests availability
 for detecting them.
DOI: 10.15468/dl.muda65
title: Occurrence Download

description: A dataset containing 1291895 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Russian Federation",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is May"
 ]
}

 The dataset includes 1291895 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002076-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1g1jwstrb
title: Data from: Comparative analysis of the shape and size of the middle ear cavity of turtles reveals no correlation with habitat ecology

description: The middle ear of turtles differs from other reptiles in being separated
 into two distinct compartments. Several ideas have been proposed as to why
 the middle ear is compartmentalized in turtles, most suggesting a
 relationship with underwater hearing. Extant turtle species span fully
 marine to strictly terrestrial habitats, and ecomorphological hypotheses
 of turtle hearing predict that this should correlate with variation in the
 structure of the middle ear due to differences in the fluid properties of
 water and air. We investigate the shape and size of the air-filled middle
 ear cavity of 56 extant turtles using 3D data and phylogenetic comparative
 analysis to test for correlations between habitat preferences and the
 shape and size of the middle ear cavity. Only weak correlations are found
 between middle ear cavity size and ecology, with aquatic taxa having
 proportionally smaller cavity volumes. The middle ear cavity of turtles
 exhibits high shape diversity among species, but we found no relationship
 between this shape variation and ecology. Surprisingly, the estimated
 acoustic transformer ratio, a key functional parameter of
 impedance-matching ears in vertebrates, also shows no relation to habitat
 preferences (aquatic/terrestrial) in turtles. We suggest that middle ear
 cavity shape may be controlled by factors unrelated to hearing, such as
 the spatial demands of surrounding cranial structures. A review of the
 fossil record suggests that the modern turtle ear evolved during the Early
 to Middle Jurassic in stem turtles broadly adapted to freshwater and
 terrestrial settings. This, combined with our finding that evolutionary
 transitions between habitats caused only weak evolutionary changes in
 middle ear structure, suggests that tympanic hearing in turtles evolved as
 a compromise between subaerial and underwater hearing.
DOI: 10.5061/dryad.rr4xgxd5c
title: Data from: Genetic diversity of Helosciadium repens (Jacq.) W.D.J. Koch (Apiaceae) in Germany, a Crop Wild Relative of celery

description: Helosciadium repens (Jacq.) W.D.J. Koch is threatened by genetic erosion.
 It is a Crop Wild Relative (CWR) of celery and celeriac and a potentially
 valuable genetic resource for plant breeding. The objective of this study
 was the analysis of distribution of genetic diversity with a set of
 selected populations in Germany. The results of the genetic analysis and
 data obtained during the site visits were used to identify a subset which
 was chosen to best represent the genetic diversity of H. repens in
 Germany. The chance of long‐term conservation by securing the identified
 populations in genetic reserves is distinctly possible. Seven hundred and
 fifteen individuals from 27 sites were assessed using six simple sequence
 repeat markers. Discriminant analysis of principal components was used to
 identify six clusters of genetically similar individuals. The
 complementary compositional genetic differentiation Δj was calculated to
 designate a subset of populations chosen to best represent the overall
 genetic diversity. Entry 18R (Δ18R = 0.2498) represented its pooled
 remainder the best, while entry 22R (Δ22R= 0.4902) differed the most from
 its complement. Based on the results of the genetic analysis and
 information regarding the current conservation status, 14 most appropriate
 wild populations for potential genetic reserve were identified. The used
 markers display a low level of genetic variation between the analyzed
 populations, and a split between Northern and Southern populations was
 observed. CWR species are essential genetic resources for plant breeding
 and food security. However, 11.5% of the European CWRs are threatened.
 Therefore, it is of utmost importance to determine their genetic
 compositions. These insights will provide the fundamental basis for making
 crucial decisions concerning future conservation strategies for H. repens.
description: Explanations for SSR_datamatrix_H_repens.xlsx
 Primer set - name of the primer set used
 Population - Population code in the GeSell Project
 Individual - code of the individual Low -
 lowest bp length of the allele High - highest bp
 length of the allele
DOI: 10.5061/dryad.9cnp5hqdr
title: Data from: Is evolution predictable? quantitative genetics under complex genotype-phenotype maps

description: A fundamental aim of post-genomic 21st century biology is to understand
 the genotype-phenotype map (GPM) or how specific genetic variation relates
 to specific phenotypic variation. Quantitative genetics approximates such
 maps using linear models, and has developed methods to predict the
 response to selection in a population. The other major field of research
 concerned with the GPM, developmental evolutionary biology or evo-devo,
 has found the GPM to be highly nonlinear and complex.  Here we
 quantify how the predictions of quantitative genetics are affected by the
 complex, nonlinear maps found in developmental biology. We found that the
 disagreements between predicted and observed responses to selection are
 common, roughly in a third of generations, systematic and due to 
 nonlinear nature of the genotype-phenotype map. They occur at all time
 scales, even from one generation to the next. Our results are a step
 towards integrating the fields studying the GPM.
description: Simulated data for the manuscript "Is evolution predictable?
 Quantitative genetics under complex genotype-phenotype maps"
 published in Evolution. Data includes the evolution+development program,
 the complete evolutionary runs for the core parameter sets, as well as the
 observed and predicted changes. Observed changes are calculated using the
 "repetitions" methods and predicted changes are calculated from
 a halfsib breeding design.
DOI: 10.5061/dryad.mkkwh70vn
title: Moving towards a better understanding of iterative evolution: an example from the late Silurian Monograptidae (Graptolithina) of the Baltic Basin

description: Iterative evolution has proved a difficult evolutionary phenomenon to
 study and interpret. Inferences of causality vary from study to study and
 quantitatively based phylogenetic reconstruction has never been attempted.
 In an effort to better understand iterative evolution we employed
 stratocladistics, gap analysis and disparity analysis to study the case of
 the Monograptidae in the aftermath of the late
 Silurian Cyrtograptus lundgreni extinction event. Our
 combination of gap analytical and stratocladistic techniques allowed us to
 elucidate the evolutionary relationships between the studied taxa. Based
 on our stratocladistic results we recommend the generic reassignment of
 five monograptid taxa. The stratocladistic results, in conjunction with
 morphological disparity analysis suggest the presence of a persistent
 developmental potential for the emergence of iteratively evolving
 characters. This persistent potential appears to be limited by extrinsic
 ecological constraints, which would have relaxed in the aftermath of
 the C. lundgreni extinction event. Our findings
 indicate that iterative evolution in the late Silurian Monograptidae is a
 product of the interaction of both intrinsic and extrinsic constraints on
 the acquisition of the iteratively evolving character, with the exact
 causality being dependent on the particular character.
description: - Supporting material 1: The function called
 ancestor.descendant.gaps which estimates joint gap between ancestor and
 descendant when we have pessimistic stratigraphical scenario when ancestor
 is immediately succeeded by the descendant (either by gradualism or
 punctuation) - Supporting material 2: Productive
 graptolite samples from the Viduklė-61 core -
 Supporting material 3: Straticladistics Matrix, Disparity Matrix
DOI: 10.5061/dryad.p5hqbzkkx
title: The implications of different approaches to define AT(N) in Alzheimer's disease

description: Objective: To compare different amyloid-β (A),
 tau (T) and neurodegeneration (N) [AT(N)] variants within the
 Swedish BioFINDER studies. Methods: A total of490 participants
 were classified into AT(N) groups. These include  53
 cognitively unimpaired (CU) and 48 cognitively impaired (CI)
 participants (14 mild cognitive impairment [MCI] and 34 AD
 dementia) from BioFINDER-1 and 389 participants from BioFINDER-2 (245 CU
 and 144 CI subjects [138 MCI and six AD
 dementia]).Biomarkers for “A” were CSF Aβ42 and Amyloid-PET
 ([18F]flutemetamol); for “T” CSF P-tau and Tau-PET ([18F]flortaucipir);
 and for “(N)” hippocampal volume, temporal cortical thickness and CSF
 neurofilament light (NfL). Binarization of biomarkers was
 achieved using cut-offs defined in other cohorts. The relationship between
 different AT(N) combinations and cognitive trajectories (longitudinal Mini
 Mental State Examination (MMSE) scores) was examined using linear mixed
 modelling and coefficient of variation. Results: Among CU
 subjects, A-T-(N)- or A+T-(N)- variants were most common. However, more T+
 cases were seen using P-tau than Tau-PET. Among CI subjects,A+T+(N)+ was
 more common; however, more (N)+ cases were seen for MRI-measures relative
 to CSF NfL. Tau-PET best predicted longitudinal cognitive decline in CI
 and P-tau in CU
 subjects. Among CI subjects, continuous T (especially Tau-PET) and (N) measures improved the prediction of cognitive decline compared to binary measures.   Conclusions: Our findings show that different AT(N) variants are not interchangeable, and that optimal variants differ by clinical stage. In some cases, dichotomizing biomarkers may result in loss of important prognostic information.
DOI: 10.5061/dryad.kwh70rz0b
title: Dramatic decline of northern bat Eptesicus nilssonii in Sweden over 30 years

description: We monitored northern bat Eptesicus nilssonii (Keyserling &
 Blasius, 1839) acoustically along a 27 km road transect at weekly
 intervals in 1988, 1989, and 1990, and again in 2016 and 2017. The
 methodology of data collection and the transect were the same throughout,
 except that the insect-attracting mercury-vapour streetlights along parts
 of the road were replaced by sodium lights between the two survey periods.
 Counts along sections of the transect with and without streetlights were
 analyzed separately. The frequency of bat encounters in unlit sections
 showed an average decline of 3.0% (± 0.4 SE) per year, corresponding to a
 reduction of 59% between 1988 and 2017. Sections with streetlights showed
 an 85% decline over the same period (6.3% ± 0.4 SE per year). The decline
 represents a real reduction in the abundance of bats rather than an
 artefact of changed distribution of bats away from roads, following the
 disuse of insect-attracting mercury-vapour streetlights. Our results
 conform with another long-term survey of the same species on the Baltic
 island of Gotland. This decline agrees with predictions based on climate
 change models, and may also be explained by increased competition from
 pipistrelle bats (Pipistrellus spp.) expanding from the south. However,
 the decline may also be due to changed availability of preferred prey
 (moths), a likely effect of the change in streetlighting. In the 1980´s,
 E. nilssonii was considered the most common bat in Sweden, but the
 subsequent decline would rather qualify it for vulnerable or endangered
 status in the national Red List of Threatened Species.
DOI: 10.15468/dl.nwssxy
title: Occurrence Download

description: A dataset containing 26415 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Podarcis siculus"
 ]
}

 The dataset includes 26415 records from 149 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002092-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jm63xsj6f
title: Vertical distribution of epiphytic lichens on Quercus laurina Humb. & Bonpl. in a remnant of cloud forest in the state of Veracruz, México

description: It is considered that in the tropics, lichen richness and cover tend to
 increase from the trunk base to the top of the crown of trees. In this
 study we calculate total beta diversity of the lichen community along a
 vertical gradient on Quercus laurina. By comparing the richness and cover
 of the lichens by zone, we will be able to prove that the foliose and
 fruticose forms will be the minor component of the total lichen species
 richness; but with the highest cover with respect to the crustose lichens.
 Five zones were identified in each phorophyte (n=15) with a diameter at
 breast height &gt; 40 cm. A total of 92 species were identified, of
 these, 38% were found only in a single zone, 51% were shared between the
 different zones, 11% occurred across all zones. Species richness and cover
 increased from the lowest to the highest zones of phorophytes.
 Dissimilarity in species composition between the zones, can be explained
 by species replacement. The Indicator Species Analysis revealed that only
 a few species such as Hypotrachyna vexans, H. cf. sublaevigata and
 Ramalina cf. sinaloensis preferred a particular zone. The results obtained
 to date show that the lichen community associated with Quercus laurina
 phorophytes is highly diverse. There is a high replacement of species
 across the different zones. Our results suggest that species richness and
 cover of the corticolous lichen community are related to the zone and the
 diverse growth forms.
DOI: 10.5061/dryad.m0cfxpnzx
title: Influence of socio-economic, demographic and climate factors on the regional distribution of dengue in the United States and Mexico

description: Climate change, urbanization, and global trade have contributed to the
 recent spread of dengue viruses. In this study, we investigate the
 relationship between dengue occurrence in humans, climate factors
 (temperature and minimum quarterly rainfall), socio-economic factors (such
 as household income, regional rates of education, regional unemployment,
 housing overcrowding, life expectancy, and medical resources), and
 demographic factors (such as migration flows, age structure of the
 population, and population density). From a geographical perspective, this
 study focuses on Mexico and parts of the United States to exploit
 similarity in climate conditions and differences in socio-economic and
 demographic factors, so as to try to isolate the role of the latter. Areas
 at risk of dengue are first selected based on the predicted presence of at
 least one of the two mosquito vectors responsible for dengue's
 transmission: Aedes aegypti and Aedes albopictus. The presence of the
 mosquito in a region is predicted by the above mentioned climate
 variables. In those regions where the vectors had a high probability of
 presence, we assess the impact of one composite socio-economic indicator
 (derived through factor analysis to account for collinearity), and three
 composite demographic indicators (also derived from factor analysis) on
 the regional distribution of dengue cases, controlling for climate, and
 allowing for spatial correlation. We found that an increase of one unit in
 the socio-economic indicator is related to a drop in the occurrence of
 dengue, whereas the demographic indicators showed no significant impact
 after taking climate into account. The significant impact of the
 socio-economic indicator also persists when looking at differences in the
 occurrence of dengue in Mexico only.
DOI: 10.5061/dryad.00000000j
title: Hepatic estrogen sulfotransferase distantly sensitizes mice to hemorrhagic shock-induced acute lung injury

description: Hemorrhagic shock (HS) is a potential life-threatening condition that may
 lead to injury to multiple organs, including the lung. The estrogen
 sulfotransferase (EST, or SULT1E1) is a conjugating enzyme that sulfonates
 and deactivates estrogens. In this report, we showed that the expression
 of Est was markedly induced in the liver, but not in the lung of female
 mice subject to hemorrhagic shock and resuscitation (HS/R). Genetic
 ablation or pharmacological inhibition of Est effectively protected female
 mice from HS-induced acute lung injury (ALI), including interstitial
 edema, neutrophil mobilization and infiltration, and inflammation. The
 pulmonoprotective effect Est ablation or inhibition was sex-specific,
 because the HS-induced ALI was not affected in male Est-/- mice.
 Mechanistically, the pulmonoprotective phenotype in female Est-/- mice was
 accompanied by increased lung and circulating levels of estrogens,
 attenuated pulmonary inflammation, and inhibition of neutrophil
 mobilization from the bone marrow and infiltration to the lung, whereas
 the pulmonoprotective effect was abolished upon ovariectomy, suggesting
 that the pulmonoprotective effect was estrogen dependent. The
 pulmonoprotective effect of Est ablation was also tissue-specific, as loss
 of Est had little effect on HS-induced liver injury. Moreover, transgenic
 reconstitution of human EST in the liver of global Est-/- mice abolished
 the pulmonoprotective effect, suggesting that it is the EST in the liver
 that sensitizes mice to HS-induced ALI. Taken together, our results
 revealed a sex- and tissue-specific role of EST in HS-induced ALI.
 Pharmacological inhibition of EST may represent an effective approach to
 manage HS-induced ALI.
description: Supplementary figures and table
DOI: 10.5061/dryad.zpc866t5b
title: Body size, sampling completeness, and extinction risk in the marine fossil record

description: Larger body size has long been assumed to correlate with greater risk of
 extinction, helping to shape body size distributions across the tree of
 life, but lack of comprehensive size data for fossil taxa have left this
 hypothesis untested for most higher taxa across the vast majority of
 evolutionary time. Here we assess the relationship between body size and
 extinction using a dataset comprising the body sizes, stratigraphic
 ranges, and occurrence patterns of 9,408 genera of fossil marine animals
 spanning eight Linnaean classes across the past 485 million years. We find
 that preferential extinction of smaller-bodied genera within classes is
 substantially more common than expected due to chance and that there is
 little evidence for preferential extinction of larger-bodied genera. Using
 a capture-mark-recapture analysis, we find that this size bias of
 extinction persists even after accounting for a pervasive bias against the
 sampling of smaller-bodied genera within classes. The size bias in
 extinction also persists after including geographic range as an additional
 predictor of extinction, indicating that correlation between body size and
 geographic range does not provide a simple explanation for the association
 between size and extinction. Regardless of the underlying causes, the
 preferential extinction of smaller-bodied genera across many higher taxa
 and most of geological time indicates that the selective loss of
 large-bodied animals is the exception, rather than the rule, in the
 evolution of marine animals.
DOI: 10.5061/dryad.wm37pvmhm
title: Rapid colour shift by reproductive character displacement in Cupido butterflies

description: Reproductive character displacement occurs when competition for successful
 breeding imposes a divergent selection on the interacting species, causing
 a divergence of reproductive traits. Here, we show that a disputed
 butterfly taxon is actually a case of male wing colour shift, apparently
 produced by reproductive character displacement. Using double digest
 restriction-site associated DNA sequencing and mitochondrial DNA
 sequencing we studied four butterfly taxa of the subgenus Cupido
 (Lepidoptera: Lycaenidae): Cupido minimus and the taxon carswelli, both
 characterized by brown males and females, plus C. lorquinii and C. osiris,
 both with blue males and brown females. Unexpectedly, taxa carswelli and
 C. lorquinii were close to indistinguishable based on our genomic and
 mitochondrial data, despite displaying strikingly different male
 colouration. In addition, we report and analysed a brown male within the
 C. lorquinii range, which demonstrates that the brown morph occurs at very
 low frequency in C. lorquinii. Such evidence strongly suggests that
 carswelli is conspecific with C. lorquinii and represents populations with
 a fixed male brown colour morph. Considering that these brown populations
 occur in sympatry with or very close to the blue C. osiris, and that the
 blue C. lorquinii populations never do, we propose that the taxon
 carswelli could have lost the blue colour due to reproductive character
 displacement with C. osiris. Since male colour is important for
 conspecific recognition during courtship, we hypothesize that the observed
 colour shift may eventually trigger incipient speciation between blue and
 brown populations. Male colour seems to be an evolutionarily labile
 character in the Polyommatinae, and the mechanism described here might be
 at work in the wide diversification of this subfamily of butterflies.