cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1f4k3
title: Data from: Effects of mating order and male size on embryo survival in a pipefish

description: In species that provide parental care, individuals should invest
 adaptively in their offspring in relation to the pre- and post-zygotic
 care provided by their partners. In the broad-nosed pipefish, Syngnathus
 typhle L., females transfer large, nutrient-rich eggs into the male brood
 pouch during mating. The male broods and nourishes the embryos for several
 weeks before independent juveniles emerge at parturition. Given a choice,
 females clearly prefer large partners. Yet, females provide protein-richer
 eggs when the same individual mates with a smaller than a larger male. In
 the present study, we allowed each female to mate with one small and one
 large male, in alternated order. We found a strong effect of female mating
 order, with larger clutches and higher embryo mortality in first- than
 second-laid broods, which may suggest that eggs over-ripen in the ovaries
 or reflect the negative effects of high embryo density in the brood pouch.
 In either case, this effect should put constraints on the possibility of a
 female being selective in mate choice. We also found that small and large
 males produced embryos of similar size and survival, consistent with the
 reproductive compensation hypothesis, suggesting that, in this species,
 larger males provide better nourishment to the embryos than smaller males.
description: BragaGoncalvesetal_datafileThe file BragaGoncalvesetal_datafile.csv contains the data used for the analysis of the effects of male size and mate number on embryo mortality and body length in the pipefish Syngnathus typhle, associated with Braga Goncalves et al., 2015 in Biological Journal of the Linnean Society. The file BragaGoncalvesetal.txt provides the description of all column names.
DOI: 10.5061/dryad.f1t8m
title: Data from: Kinetic estimation of GFR improves prediction of dialysis and recovery after kidney transplantation

description: Background: The early prediction of delayed graft function (DGF) would
 facilitate patient management after kidney transplantation. Methods: In a
 single-centre retrospective analysis, we investigated kinetic estimated
 GFR under non-steady-state conditions, KeGFR, in prediction of DGF.
 KeGFRsCr was calculated at 4h, 8h and 12h in 56 recipients of deceased
 donor kidneys from initial serum creatinine (sCr) concentrations,
 estimated creatinine production rate, volume of distribution, and the
 difference between consecutive sCr values. The utility of KeGFRsCr for DGF
 prediction was compared with, sCr, plasma cystatin C (pCysC), and
 KeGFRpCysC similarly derived from pCysC concentrations. Results: At 4h,
 the KeGFRsCr area under the receiver operator characteristic curve (AUC)
 for DGF prediction was 0.69 (95% CI: 0.56–0.83), while sCr was not useful
 (AUC 0.56, (CI: 0.41–0.72). Integrated discrimination improvement analysis
 showed that the KeGFRsCr improved a validated clinical prediction model at
 4h, 8h, and 12h, increasing the AUC from 0.68 (0.52–0.83) to 0.88
 (0.78–0.99) at 12h (p = 0.01). KeGFRpCysC also improved DGF prediction. In
 contrast, sCr provided no improvement at any time point. Conclusions:
 Calculation of KeGFR from sCr facilitates early prediction of DGF within 4
 hours of renal transplantation.
description: Data
 KeGFRPatient demographic data
 available upon application from the New South Wales (Australia) Health
 South Eastern Sydney Local Health District Human Research Ethics Committee
 (HREC)
DOI: 10.5061/dryad.6d925
title: Data from: Estimation of contemporary effective population size and population declines using RAD sequence data

description: Large genomic datasets generated with restriction-site associated DNA
 sequencing (RADseq), in combination with demographic inference methods,
 are improving our ability to gain insights into the population history of
 species. We used a simulation approach to examine the potential for RADseq
 datasets to accurately estimate effective population size (Ne) over the
 course of stable and declining population trends, and we compare the
 ability of two methods of analysis to accurately distinguish stable from
 steadily declining populations over a contemporary time scale (20
 generations). Using a linkage disequilibrium-based analysis, individual
 sampling (i.e., n ≥ 30) had the greatest effect on Ne estimation and the
 detection of population-size declines, with declines reliably detected
 across scenarios approximately 10 generations after they began.
 Coalescent-based inference required fewer sampled individuals (i.e., n =
 15), and instead was most influenced by the size of the SNP dataset, with
 25,000 to 50,000 SNPs required for accurate detection of population trends
 and at least 20 generations after decline began. The number of samples
 available and targeted number of RADseq loci are important criteria when
 choosing between these methods. Neither method suffered any apparent bias
 due to the effects of allele dropout typical of RAD data. With an
 understanding of the limitations and biases of these approaches,
 researchers can make more informed decisions when designing their sampling
 and analyses. Overall, our results reveal that demographic inference using
 RADseq data can be successfully applied to infer recent population size
 change and may be important tools for population monitoring and
 conservation biology.
description: fscfastsimcoal2 analysis
 input filessimupop_modelsimupop population simulation script
DOI: 10.5061/dryad.n65r7p0
title: Data from: Maladaptive phenotypic plasticity in cardiac muscle growth is suppressed in high-altitude deer mice

description: How often phenotypic plasticity acts to promote or inhibit adaptive
 evolution is an ongoing debate among biologists. Recent work suggests that
 adaptive phenotypic plasticity promotes evolutionary divergence, though
 several studies have also suggested that maladaptive plasticity can
 potentiate adaptation. The role of phenotypic plasticity, adaptive or
 maladaptive, in evolutionary divergence remains controversial. We examined
 the role of plasticity in evolutionary divergence between two species of
 Peromyscus mice that differ in native elevations. We used cardiac mass as
 a model phenotype, since ancestral hypoxia-induced responses of the heart
 may be both adaptive and maladaptive at high-altitude. While left
 ventricle growth should enhance oxygen delivery to tissues, hypertrophy of
 the right ventricle can lead to heart failure and death. We compared left-
 and right-ventricle plasticity in response to hypoxia between captive-bred
 P. leucopus (representing the ancestral lowland condition) and P.
 maniculatus from high-altitude. We found that maladaptive ancestral
 plasticity in right ventricle hypertrophy is reduced in high-altitude deer
 mice. Analysis of the heart transcriptome suggests that changes in
 expression of inflammatory signaling genes, particularly interferon
 regulatory factors, contribute to the suppression of right ventricle
 hypertrophy. We found weak evidence that adaptive plasticity of left
 ventricle mass contributes to evolution. Our results suggest that
 selection to suppress ancestral maladaptive plasticity plays a role in
 adaptation.
description: Dryad_supp_heartdataRaw heart mass and body mass data for Peromyscus maniculatus and Peromyscus leucopus acclimated to normobaria (approximately sea level) and hypobaric hypoxia (60 kPa barometric pressure) for 20 weeks.
DOI: 10.5061/dryad.1rp4308
title: Data from: Ophrys annae and Ophrys chestermanii: an impossible love between two orchid sister species

description: The biological concept of species is founded on the presence of barriers
 that limit the gene flow and species delimitation represents a vivid topic
 in orchids. Studies on the reproductive isolation in mediterranean orchids
 often examine the gene flow between co-occuring species providing a
 relevant understanding of how species boundaries are maintained. In
 Ophrys, the role of post-mating boundaries are always been tought to be
 weak and, despite the relevant morphological and ethological differences,
 low phylogenetic diversity has been recorded. In contrast, not many
 studies are focused on the relevance of each barriers in close related
 species in island condition. Using a morphological approach and
 experimental crosses to evaluate post-mating barriers, here, we clarify
 the taxonomic position of two sardinian endemic orchid sister-species,
 Ophrys annae and Ophrys chestermanii, currently ascribed in the
 bornmuelleri group. In Ophrys, due their iper specialized pollination
 syndrome, premating barriers are often considered more relevant than post
 mating barriers. We found that the two endemisms differs sustantially in
 16 functional traits adopted. We further detected asymmetric results in
 manual crosses suggesting that post-mating barriers may act as
 reinforcement of the pre-mating barriers. Our results suggest that in
 close related orchid species of the genus Ophrys, gene flow is limited
 also by post-mating barriers which have a relevant act in keeping the two
 reproductively isolated.
description: Table
 2Floral morphometric
 analysis.Table
 3Mann
 Whitney U Test resultsTable
 4Percentage of fruits
 production, meand and standard deviation in interspecific and
 intraspecific crosses.Table
 1
DOI: 10.5281/zenodo.18385886
title: ESCAPING POVERTY THROUGH HOUSEHOLD EXPENSE OPTIMIZATION: A COMPREHENSIVE ANALYSIS OF FINANCIAL MANAGEMENT STRATEGIES
DOI: 10.5281/zenodo.18385887
title: ESCAPING POVERTY THROUGH HOUSEHOLD EXPENSE OPTIMIZATION: A COMPREHENSIVE ANALYSIS OF FINANCIAL MANAGEMENT STRATEGIES
DOI: 10.5061/dryad.g2m0j
title: Data from: Diet quality in a wild grazer declines under the threat of an ambush predator

description: Predators influence prey populations not only through predation itself,
 but also indirectly through prompting changes in prey behaviour. The
 behavioural adjustments of prey to predation risk may carry nutritional
 costs, but this has seldom been studied in the wild in large mammals.
 Here, we studied the effects of an ambush predator, the African lion
 (Panthera leo), on the diet quality of plains zebras (Equus quagga) in
 Hwange National Park, Zimbabwe. We combined information on movements of
 both prey and predators, using GPS data, and measurements of faecal crude
 protein, an index of diet quality in the prey. Zebras which had been in
 close proximity to lions had a lower quality diet, showing that
 adjustments in behaviour when lions are within short distance carry
 nutritional costs. The ultimate fitness cost will depend on the frequency
 of predator–prey encounters and on whether bottom-up or top-down forces
 are more important in the prey population. Our finding is the first
 attempt to our knowledge to assess nutritionally mediated risk effects in
 a large mammalian prey species under the threat of an ambush predator, and
 brings support to the hypothesis that the behavioural effects of predation
 induce important risk effects on prey populations.
description: Crude Protein content of
 Plains zebras in Hwange National Park, ZimbabweThis file contains the
 Crude Protein content of faeces of plains zebras and the data associated
 to this index of diet quality : Distance to lions (two classes : far and
 close from lions) ; Sex of of the individual ; Harem affiliation and
 Individual Identity of the zebra ; Date of faeces
 collection.Table_diet_quality.csv
DOI: 10.5061/dryad.70pt4
title: Data from: Why we do not expect dispersal probability density functions based on a single mechanism to fit real seed shadows

description: Bullock et al. (Journal of Ecology 105:6-19, 2017) have suggested that the
 theory behind the Wald Analytical Long Distance (WALD) model for wind
 dispersal from a point source needs to be re-examined. This is on the
 basis that an inverse Gaussian probability density function (pdf) does not
 provide the best fit to seed shadows around individual source plants known
 to be dispersed by wind. We present two reasons why we would not
 necessarily expect any of the standard mechanistically derived pdfs to fit
 real seed shadows any better than empirical functions. Firstly, the
 derivation of “off-the-shelf” pdfs such as the Gaussian, exponential and
 inverse Gaussian involves only one of the processes and factors that
 together generate a real seed shadow. It is implausible to expect that a
 single-process model, no matter how sophisticated in detail, will capture
 the behaviour of an entire, complex system, which may involve a number of
 sequential random processes, or a superposition of parallel random
 processes, or both. Secondly, even if there is only one process involved
 and we have a perfect model for that process, the basic parameters of the
 model would be difficult to pin down precisely. Moreover, these parameters
 are unlikely to remain constant over a dispersal season, so that
 effectively we observe the outcome of a linear combination of dispersal
 events with different parameter values, constituting a form of averaging
 over the parameters of the distribution. Simple examples show that
 averaging a pdf over its parameters can lead to a pdf from an entirely
 different class. Synthesis. The failure of the inverse Gaussian model to
 fit seed shadow data is not in itself a reason to doubt the validity of
 the Wald Analytical Long Distance model for movement of particles through
 the air under specified environmental conditions. A greater awareness is
 needed of the differences between the Wald Analytical Long Distance and
 the inverse Gaussian (or Wald) and the purposes for which they are used.
 The complexity of dispersing populations of seeds means that any of the
 standard mechanistically derived pdfs will actually be merely empirical in
 this context. Shape and flexibility of a pdf is far more important for
 adequately describing data than some perceived higher status.
description: Dispersal simulation
 codeMatlab code that was
 used in our paper to simulate numbers of seeds landing in quadrats along a
 transect based on empirical pdfs with randomly varying
 parameters.Sim_dispresal.m
DOI: 10.34894/kyxtft
title: Diamond factories in Amsterdam

description: Inventarisation of diamond factories in Amsterdam between 1840 - 1940. Based on original list compiled by Daniel Metz, checked and expanded by Micon Schorsij. Main sources are the Nijverheidsstatistiek Struve en Bekaar for North Holland, Delpher newspapers and magazines and various websites (see the inventarisation).
DOI: 10.5061/dryad.8h8t0
title: Data from: Ecotypic differences in the phenology of the tundra species Eriophorum vaginatum reflect sites of origin

description: Eriophorum vaginatum is a tussock-forming sedge that contributes
 significantly to the structure and primary productivity of moist acidic
 tussock tundra. Locally adapted populations (ecotypes) have been
 identified across the geographical distribution of E. vaginatum; however,
 little is known about how their growth and phenology differ over the
 course of a growing season. The growing season is short in the Arctic and
 therefore exerts a strong selection pressure on tundra species. This
 raises the hypothesis that the phenology of arctic species may be poorly
 adapted if the timing and length of the growing season change. Mature E.
 vaginatum tussocks from across a latitudinal gradient (65–70°N) were
 transplanted into a common garden at a central location (Toolik Lake,
 68°38′N, 149°36′W) where half were warmed using open-top chambers. Over
 two growing seasons (2015 and 2016), leaf length was measured weekly to
 track growth rates, timing of senescence, and biomass accumulation. Growth
 rates were similar across ecotypes and between years and were not affected
 by warming. However, southern populations accumulated significantly more
 biomass, largely because they started to senesce later. In 2016, peak
 biomass and senescence of most populations occurred later than in 2015,
 probably induced by colder weather at the beginning of the growing season
 in 2016, which caused a delayed start to growth. The finish was delayed as
 well. Differences in phenology between populations were largely retained
 between years, suggesting that the amount of time that these ecotypes grow
 has been selected by the length of the growing seasons at their respective
 home sites. As potential growing seasons lengthen, E. vaginatum may be
 unable to respond appropriately as a result of genetic control and may
 have reduced fitness in the rapidly warming Arctic tundra.
description: Toolik Lake Common
 garden Phenology DatasetECE-2017-02-00182.csv
DOI: 10.5061/dryad.gg3rn
title: Data from: Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea)

description: BACKGROUND: The shrimp Nematocarcinus lanceopes Bate, 1888 is found in the
 deep sea around Antarctica and sub-Antarctic islands. Previous studies on
 mitochondrial data and species distribution models provided evidence for a
 homogenous circum-Antarctic population of N. lanceopes. However, to
 analyze the fine-scale population genetic structure and to examine
 influences of abiotic environmental conditions on population composition
 and genetic diversity, a set of fast evolving nuclear microsatellite
 markers is required. FINDINGS: We report the isolation and
 characterization of nine polymorphic microsatellite markers from the
 Antarctic deep-sea shrimp species Nematocarcinus lanceopes (Crustacea:
 Decapoda: Caridea). Microsatellite markers were screened in 55 individuals
 from different locations around the Antarctic continent. All markers were
 polymorphic with 9 to 25 alleles per locus. The observed heterozygosity
 ranged from 0.545 to 0.927 and the expected heterozygosity from 0.549 to
 0.934. CONCLUSIONS: The reported markers provide a novel tool to study
 genetic structure and diversity in Nematocarcinus lanceopes populations in
 the Southern Ocean and monitor effects of ongoing climate change in the
 region on the populations inhabiting these.
description: msat_sequencesThis file contains the nucleotide sequence information for the described microsatellite markers. Primer sites are indicated in the sequences.
DOI: 10.5061/dryad.12773
title: Data from: Comparative genomics of Methicillin-resistant Staphylococcus aureus ST239: distinct geographical variants in Beijing and Hong Kong

description: Background: The ST239 lineage is a globally disseminated, multiply
 drug-resistant hospital-associated methicillin-resistant Staphylococcus
 aureus (HA-MRSA). We performed whole-genome sequencing of representative
 HA-MRSA isolates of the ST239 lineage from bacteremic patients in
 hospitals in Hong Kong (HK) and Beijing (BJ) and compared them with three
 published complete genomes of ST239, namely T0131, TW20 and JKD6008.
 Orthologous gene group (OGG) analyses of the Hong Kong and Beijing cluster
 strains were also undertaken. Results: Homology analysis, based on
 highest-percentage nucleotide identity, indicated that HK isolates were
 closely related to TW20, whereas BJ isolates were more closely related to
 T0131 from Tianjin. Phylogenetic analysis, incorporating a total of 30
 isolates from different continents, revealed that strains from HK
 clustered with TW20 into the ‘Asian clade’, whereas BJ isolates and T0131
 clustered closely with strains of the ‘Turkish clade’ from Eastern Europe.
 HK isolates contained the typical φSPβ-like prophage with the SasX gene
 similar to TW20. In contrast, BJ isolates contained a unique 15 kb
 PT1028-like prophage but lacked φSPβ-like and φSA1 prophages. Besides
 distinct mobile genetic elements (MGE) in the two clusters, OGG analyses
 and whole-genome alignment of these clusters highlighted differences in
 genes located in the core genome, including the identification of single
 nucleotide deletions in several genes, resulting in frameshift mutations
 and the subsequent predicted truncation of encoded proteins involved in
 metabolism and antimicrobial resistance. Conclusions: Comparative
 genomics, based on de novo assembly and deep sequencing of HK and BJ
 strains, revealed different origins of the ST239 lineage in northern and
 southern China and identified differences between the two clades at single
 nucleotide polymorphism (SNP), core gene and MGE levels. The results
 suggest that ST239 strains isolated in Hong Kong since the 1990s belong to
 the Asian clade, present mainly in southern Asia, whereas those that
 emerged in northern China were of a distinct origin, reflecting the
 complexity of dissemination and the dynamic evolution of this ST239
 lineage.
description: Figure 1. Maximum
 likelihood phylogenetic tree of ST239The phylogeny was based
 on the SNPs of the core genomes. The tree was rooted by using MRSA FPR3757
 USA300 as an outgroup.Figure1_tree_data.nex
DOI: 10.5281/zenodo.18385858
title: LINF_320009500

description: FAM210A/B-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.5061/dryad.q41jr576
title: Data from: Male offspring production by asexual Potamopyrgus antipodarum, a New Zealand snail

description: As only females contribute directly to population growth, sexual females
 investing equally in sons and daughters experience a two-fold cost
 relative to asexuals producing only daughters. Typically, researchers have
 focused on benefits of sex that can counter this ‘cost of males’ and thus
 explain its predominance. Here, we instead ask whether asexuals might also
 pay a cost of males by quantifying the rate of son production in 45
 experimental populations (‘lineages’) founded by obligately asexual female
 Potamopyrgus antipodarum. This New Zealand snail is a powerful model for
 studying sex because phenotypically similar sexual and asexual forms often
 coexist, allowing direct comparisons between sexuals and asexuals. After 2
 years of culture, 23 of the 45 lineages had produced males, demonstrating
 that asexual P. antipodarum can make sons. We used maximum-likelihood
 analysis of a model of male production in which only some lineages can
 produce males to estimate that ~50% of lineages have the ability to
 produce males and that ~5% of the offspring of male-producing lineages are
 male. Lineages producing males in the first year of the experiment were
 more likely to make males in the second, suggesting that some asexual
 lineages might pay a cost of males relative to other asexual lineages.
 Finally, we used a simple deterministic model of population dynamics to
 evaluate how male production affects the rate of invasion of an asexual
 lineage into a sexual population, and found that the estimated rate of
 male production by asexual P. antipodarum is too low to influence invasion
 dynamics.
description: HDY-11-OR0388R
 dryad
DOI: 10.5281/zenodo.18385857
title: LINF_320009500

description: FAM210A/B-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.34894/u8m3g1
title: ANDB-public-sample

description: This dataset contains a public sample of persons in the ANDB dataset, specifically those who appear to have visited the city of Hilversum in their lifetime.

This sample of the dataset is available under a CC-BY-SA license, meaning that any amendment, product, or service based on the dataset will be provided under the samen license. See: https://creativecommons.org/licenses/by-sa/4.0/