cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kwh70rz00
title: Desert-like badlands and surrounding (semi-)dry grasslands of Central Germany promote small-scale phenotypic and genetic differentiation in Thymus praecox

description: Environmental heterogeneity among sites can generate phenotypic and
 genetic variation facilitating differentiation and microevolution of plant
 populations. Badlands are desert-like, predominantly vegetation-poor
 habitats often embedded in (semi-)dry grasslands. The desert-like
 conditions of badlands demand extreme adaptation of plants, i.e.,
 phenotypic modifications in short-term and/or natural adaptation in
 long-term. However, detailed knowledge is missing about both plant
 phenotypic and genetic differentiation in this unique and widely occurring
 habitat type. The present study focused on the largest known badlands
 systems in Central Europe located in the ‘Drei Gleichen’ region, a
 designated nature conservation area in Central Germany. Locations were
 suitable for this study in terms of having co-occurring badlands and
 (semi-)dry grassland habitats (sites) occupied by the pioneer plant Thymus
 praecox. Here, we studied the environmental preferences, morphological and
 functional trait variation, and genetic variation using microsatellite
 markers of T. praecox. Results revealed significant, mainly site-dependent
 environmental, phenotypic and genetic differentiation. In general,
 individuals in badlands are shorter in height, have lower patch sizes
 (length x width), relative growth rates, and smaller stomata. The PCA
 additionally unveiled slightly increased leaf robustness, trichome
 density, decreased stomatal conductance, fewer females, and earlier
 phenology in badlands. We interpret differentiation patterns as adaptive
 responses to light, temperature, drought and nutrient stress conditions
 supported by reviewed literature. Genetic differentiation was strongest
 between local badlands and grassland sites, and clearly weaker among
 locations and between sites (in total) as indicated by GST, AMOVA, PCoA
 and population structure. Our study supports the importance of small-scale
 microhabitat conditions as a driver of microevolutionary processes, and
 the population´s need for sufficient phenotypic plasticity and genetic
 resources to deal with environmental changes. We demonstrated that
 badlands are an appropriate model system for testing plant response to
 extreme habitats and that more research is needed on these fascinating
 landscapes.
DOI: 10.5061/dryad.xsj3tx99n
title: Extinct plants of North America north of Mexico

description: The recent study by Humphreys et al., reporting extinction of almost 600
 plant species globally, represents a groundbreaking effort at compiling
 direct data on seed plants. We applaud Humphreys et al. for quantifying
 plant extinctions because they formulate an important and testable
 hypothesis. However, their study missed many extinctions and rediscoveries
 of seed plants in the United States and Canada. Our team of experts has
 been compiling a list of extinct plants of North America north of Mexico.
 This work is challenging and time-consuming, given the complexities
 inherent in botanical diversity, the incomplete status of taxonomic
 understanding, vagaries of reporting, and complexities of phytogeography.
DOI: 10.5061/dryad.1jwstqjqm
title: Reproduction affects immune defenses in the guinea pig even under ad libitum food

description: Reproduction is one of the most costly processes in the life of an animal.
 Life history theory assumes that when resources are limiting allocation to
 reproduction will reduce allocation to other essential processes thereby
 inducing costs of reproduction. The immune system is vital for survival.
 If reproduction reduces investment in immune function, this could increase
 the risk of disease, morbidity and mortality. We here test in the guinea
 pig, if even under ad libitum food conditions, pregnancy and lactation
 reduce the activity of the adaptive and innate immune system compared to
 the reaction of non-reproducing animals. In response to a challenge with
 keyhole limpet haemocyanin the antibody-mediated adaptive immunity during
 pregnancy and lactation was reduced. Pregnant and lactating females showed
 higher levels of bacterial killing activity, an integrated measure of
 innate immunity, than non-reproducing females. However, two major
 effectors of the innate immunity, the natural antibody and the complement
 of pregnant and lactating females showed lower levels than in
 non-reproducing females. Pregnant and lactating females did not differ
 significantly in the expressed levels of innate immunity. Our results
 indicate that changes in the immune response during reproduction are
 physiological adjustments to predictable allocation problems, because they
 happen even under ad libitum food availability.
DOI: 10.5061/dryad.0gb5mkkww
title: Data from: Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent

description: Species delimitation is ever more critical for assessing biodiversity in
 threatened regions of the world, especially when undescribed lineages may
 be at risk from habitat loss. Mouse lemurs (Microcebus) are an example of
 a rapid radiation of morphologically cryptic species that are distributed
 throughout Madagascar in its rapidly vanishing forested habitats. Here, we
 focus on two pairs of sister lineages that occur in a region in
 northeastern Madagascar that shows high levels of microendemism. We
 revisit previous hypotheses of species diversity by filling geographic
 sampling gaps and by generating new genomic data for three named species,
 as well as an undescribed lineage previously identified to be of interest
 due to its highly divergent mtDNA. We analyzed RADseq data with multiple
 species delimitation methods based on the multispecies coalescent (MSC)
 model while accounting for introgression. Non-sister lineages occur
 sympatrically in two instances, despite an estimated divergence time of
 less than 1 Ma, thus suggesting rapid evolution of reproductive isolation
 in the mouse lemur clade. We note, however, that the divergence time
 estimates reported here are based on the MSC and calibrated with
 pedigree-based primate mutation rates. These dates are considerably more
 recent than previous analyses that used traditional relaxed clock methods
 and distant fossil calibrations. One pair of sister lineages passed all
 species delimitation tests while the other pair failed most, largely due
 to differences in Ne between the two pairs of lineages. Nevertheless,
 delimitation results were also supported by differences in levels of gene
 flow and patterns of isolation-by-distance between the two pairs. We
 conclude that MSC-based species delimitation methods are valuable tools
 for evaluating cryptic species, even though these methods can be strongly
 affected by variable Ne. We suggest that this result has general
 implications for species delimitation studies of other recently diverged
 lineages.
description: In the tarball, there are four folders describing analyses,
 metadata, scripts, and the sequence data. Each folder and their
 subdirectories have readme files describing the contents.
DOI: 10.5281/zenodo.18394074
title: Base de datos para el análisis de supervivencia del abandono educativo en la Universidad Nacional de Costa Rica
DOI: 10.5281/zenodo.18394073
title: Base de datos para el análisis de supervivencia del abandono educativo en la Universidad Nacional de Costa Rica
DOI: 10.5061/dryad.v9s4mw6qw
title: Trophic selectivity in aquatic isopods increases with the availability of resources

description: 1. Trophic selectivity has major influences on consumers’ fitness,
 stability of predator and prey populations, and nutrient fluxes in food
 webs. Trophic selectivity occurs when the relative abundances of resources
 in a consumer's diet differ from their relative abundances in the
 environment. This discrepancy between resources abundance and use has been
 predicted to increase with the availability of resources in the
 environment. Trophic selectivity has also been predicted to increase with
 the heterogeneity of resources quality in the environment. Despite their
 ecological and evolutionary implications, conclusive in situ tests of
 these predictions are still lacking. 2. We challenged these two
 predictions by studying 15 closely related species of isopods distributed
 along a wide range of resource availability (from 1.3 to 57.6 grams of
 organic carbon per square meter). Our dataset ranged from deep cave
 systems, considered as some of the most resource-limited environments on
 Earth, to highly-productive surface streams. 3. For each species, we
 quantified the relative abundance of all available resources in the
 environment and estimated the heterogeneity in the stoichiometric quality
 of these resources. Isopod diet was determined using C and N stable
 isotopes and a Bayesian mixing model. The degree of trophic selectivity
 was then calculated for each species. 4. By coupling a standardized
 quantification of trophic resources with a fine determination of diets
 using stable isotopes, we uncovered a positive relationship between
 resource availability and trophic selectivity. Contrary to our second
 prediction, trophic selectivity did not correlate with the heterogeneity
 of resources quality. 5. Our results have important implications in terms
 of trophic competition among organisms inhabiting low-resource
 environments. Our findings call for further evaluation of the mechanisms
 causing the positive relationship between trophic selectivity and resource
 availability, as these mechanisms could be closely linked to those
 generating the documented relationship between species richness and
 productive energy.
description: - SuppTables_S1-4_FE-2019-00460: data for supplemental tables
 1-4 - isotopic_data: raw isotopic data. Sites as
 described in the Table 1 of the corresponding article
DOI: 10.5061/dryad.9p8cz8wbs
title: Phylogenetic relatedness among Cladosporium leaf endophytes predicts their ability to reduce the severity of a poplar leaf rust disease

description: More closely related organisms are expected to function more similarly
 than distantly related organisms due to shared ancestry and functional
 trait heritability. However, there have been few tests of this hypothesis
 for fungal leaf endophytes, which can modify host plant disease severity
 by a variety of mechanisms. We tested whether phylogenetic relatedness
 within Cladosporium, a genus including many common fungal leaf endophyte
 species, predicts endophyte effects on cottonwood leaf rust disease
 severity caused by Melampsora × columbiana. First, we used multilocus
 sequence typing to infer phylogenetic relationships among 96 Cladosporium
 isolates collected from wild cottonwood trees growing in Pacific Northwest
 of North America. Next, we conducted a double-inoculation leaf-disk assay
 (endophyte inoculated first, then rust pathogen) for a subset of 50
 Cladosporium isolates to characterize disease modification for the
 endophyte isolates; data on endophytes parasitizing rust was collected
 simultaneously for each isolate. We used generalized linear models to link
 disease modification and mycoparisitic ability to endophyte phylogeny,
 while accounting for endophyte geographic origin. We recognized 17
 distinct species of Cladosporium; all fifty isolates of Cladosporium
 reduced rust disease severity in our leaf disk assay (by as much as 79%
 and as little as 45%). Cladosporium phylogeny was a significant predictor
 of rust disease severity and was also correlated with
 mycoparasitism.  The geographic origin of the isolates explained
 only a small amount of the overall variation in disease reduction. Our
 results demonstrate that fungal endophyte phylogenetic relatedness can
 help predict differences in endophyte function.
DOI: 10.15468/dl.y3gk4t
title: Occurrence Download

description: A dataset containing 213 records in GBIF matching the query:
SELECT
 '418' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 37.42857426825602
 AND decimalLatitude &lt;= 41.89415215079384
 AND decimalLongitude &gt;= 86.346182691082
 AND decimalLongitude &lt;= 95.90519603780048
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 213 records were derived from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002003-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.xgxd254c0
title: West Nile Virus evolves at the pace of its avian hosts’ life-history

description: Disease resistant hosts are central in the spread, persistence, adaptation
 and diversification of infectious pathogens. In theory, resistant hosts
 must compromise on reproduction and invest more energy in self maintenance
 and immune defence. Here we investigated these hypotheses on the emergence
 of West Nile Virus (WNV) from 1999 to 2012 in the United States, when the
 virus caused mass mortality in some bird species. Our study comprehends
 two steps: First, we used regression tree meta-analysis on 233 reports of
 dead birds from 90 species, to test correlations between WNV-linked
 mortality and the birds’ life history and ecological traits. Second, we
 tested links between diversification of WNV and the reproductive
 investment and self-maintenance of its avian hosts, by analysing the
 phylogeography of 520 genome sequences of WNV from 1999 to 2012.
 Statistical analyses revealed less WNV-linked mortality in both, species
 that incubate their eggs for few days (&gt;17) and large species
 (&gt;235g). The evolutionary trajectory of the virus suggests that
 there was no special viral strain infecting the most and the less
 vulnerable species. However, by 2012 the WNV strains found in large birds
 like American crows (Corvus brachyrhynchos) diversified and evolved
 separately from the rest. Together, our findings support that hosts’
 reproductive investment impairs disease resistance, and hosts investing in
 self-maintenance may lead WNV diversification.
DOI: 10.5061/dryad.0rxwdbrvf
title: Data from: Numerical ordinality in a wild nectarivore

description: Ordinality is a numerical property that nectarivores may use to remember
 the specific order in which to visit a sequence of flowers, a foraging
 strategy also known as traplining. In this experiment, we tested whether
 wild, free-living rufous hummingbirds (Selasphorus rufus) could use
 ordinality to visit a rewarded flower. Birds were presented with a series
 of linear arrays of 10 artificial flowers; only one flower in each array
 was rewarded with sucrose solution. During training, birds learned to
 locate the correct flower independent of absolute spatial location. The
 birds showed no significant decrease in accuracy depending on which
 ordinal position (1st, 2nd, 3rd or 4th) was rewarded, which suggests that
 they used an object-indexing mechanism of numerical processing, rather
 than a magnitude-based system. When distance cues between flowers were
 made irrelevant during test trials, birds were still able to locate the
 correct flower. The distribution of errors during both training and
 testing indicates that the birds may have used a so-called ‘working up’
 strategy to locate the correct ordinal position. These results provide the
 first demonstration of numerical ordinal abilities in a wild vertebrate
 and suggest that such abilities could be used during foraging in the wild.
description: We recorded the visits to all flowers during training and during
 tests. We recorded the distance between flowers during tests. Both
 training and test data from the combined visits of all birds to a
 particular location were analysed using one-sample and paired t-tests to
 determine the significance of percentage probes to each flower in all
 arrays for a given position. The effect that position of the flower had on
 the number of mistakes was analysed with a factorial repeated measures
 ANOVA. A Repeatability test was used to assess if the number of visits
 during each training phase was repeatable within a bird. A Friedman’s
 ANOVA was used to compare the number of trials the birds took to learn the
 four different ordinal positions. A chi-square test was used to determine
 whether during the four training trials birds were equally likely to visit
 the correct flower as to visit the adjacent flowers. We used Spearman’s
 correlations to test whether the total number of trials or the number of
 trials when F4 was rewarded were correlated with the test performance of
 the hummingbirds. We used a binomial test to determine if the birds
 visited F4 more often than expected by chance at 0.10. All analyses were
 conducted using R version 3.3.2.
DOI: 10.5061/dryad.1zcrjdfnh
title: Interleukin-6 (IL-6) activates the NOTCH1 signaling pathway through E-proteins in endometriotic lesions

description: Context: NOTCH signaling is activated in endometriotic lesions but the
 exact mechanisms remains unclear. Interleukin-6 (IL-6), which is increased
 in the peritoneal fluid of women with endometriosis, induces NOTCH1
 through E-proteins including E2A and HEB in cancer development. Objective:
 To study the role of E-proteins in inducing NOTCH1 expression under the
 regulation of IL-6 in endometriosis. Setting and Design: The expression of
 E2A, HEB and NOTCH1 was first investigated in endometrium of women with
 endometriosis and the baboon model of endometriosis. Regulation of
 E-proteins and NOTCH1 expression was examined after IL-6 stimulation and
 siRNA mediated inhibition of E2A or/and HEB in human endometriotic
 epithelial cells (12Z) in vitro, and subsequent following in vivo IL-6
 treatment in the mouse model of endometriosis in vivo. Results: E2A, HEB
 and NOTCH1 were significantly upregulated in glandular epithelium (GE) of
 ectopic endometrium compared to eutopic endometrium in both women and
 baboon model. IL-6 treatment upregulated the expression of NOTCH1
 together with E2A and HEB in 12Z cells. siRNA inhibition of E2A and HEB or
 HEB alone decreased NOTCH1 expression. Binding efficiency of both E2A and
 HEB was significantly higher at the binding sites on the human NOTCH1
 promoter after IL-6 treatment. Finally, IL-6 treatment resulted in a
 significantly increased number of endometriotic lesions along with the
 increased expression of E2A, HEB and NOTCH1 in GE of the lesions compared
 with the vehicle treated group in an endometriosis mouse model.
 Conclusions: IL-6 induced NOTCH1 expression is mediated by E-proteins in
 the ectopic GE cells, which may promote endometriotic lesion development.
DOI: 10.5061/dryad.jh9w0vt6s
title: Belowground competition can influence the evolution of root traits

description: Although root traits play a critical role in mediating plant-plant
 interactions and resource acquisition from the soil environment, research
 examining if and how belowground competition can influence the evolution
 of root traits remains largely unexplored. Here we examine the potential
 that root traits may evolve as a target of selection from interspecific
 competition using Ipomoea purpurea and I. hederacea, two closely related
 morning glory species that commonly co-occur in the United States as a
 model system. We show that belowground competitive interactions between
 the two species can alter the pattern of selection on root traits in each
 species. Specifically, competition with I. purpurea changes the pattern of
 selection on root angle in I. hederacea, and competitive interactions with
 I. hederacea changes the pattern of selection on root size in I. purpurea.
 However, we did not uncover evidence that intraspecific competition
 altered the pattern of selection on any root traits within I. hederacea.
 Overall, our results suggest that belowground competition between closely
 related species can influence the phenotypic evolution of root traits in
 natural populations. Our findings provide a microevolutionary perspective
 of how competitive belowground interactions may impact plant fitness,
 potentially leading to patterns of plant community structure.
DOI: 10.5061/dryad.fqz612jp6
title: Data from: Rapid and Repeatable Host Plant Shifts Drive Reproductive Isolation Following a Recent Human-Mediated Introduction of the Apple Maggot Fly, Rhagoletis pomonella

description: Ecological speciation via host-shifting is often invoked as a mechanism
 for insect diversification, but the relative importance of this process is
 poorly understood. The shift of Rhagoletis pomonella in
 the 1850s from the native downy hawthorn, Crataegus
 mollis, to introduced apple, Malus pumila, is a classic
 example of sympatric host race formation, a hypothesized early stage of
 ecological speciation. The accidental human-mediated introduction
 of R. pomonella into the Pacific Northwest (PNW) in the
 late-1970’s allows us to investigate how novel ecological opportunities
 may trigger divergent adaptation and host race formation on a rapid
 timescale. Since the introduction, the fly has spread in the PNW, where in
 addition to apple, it now infests native black hawthorn, C.
 douglasii, and introduced ornamental hawthorn, C. monogyna. We
 use this “natural experiment” to test for genetic differentiation among
 apple, black and ornamental hawthorn flies co-occurring at three sympatric
 sites. We report evidence that populations of all three host-associations
 are genetically differentiated at the local level, indicating that partial
 reproductive isolation has evolved in this novel habitat. Our results
 suggest that conditions suitable for initiating host-associated divergence
 may be common in nature, allowing for the rapid evolution of new host
 races when ecological opportunity arises.  
description: These data are genotypes for 28 microsatellite loci (originally
 described in Velez et a. 2005, Molecular Ecology Resources) for
 <em>Rhagoletis</em> flies collected from three different host
 associations (apple- <em>Malus pumila</em>, black hawthorn -
 <em>Crataegus douglasii</em>, and ornamental hawthorn -
 <em>Crateagus monogyna</em>) in each of three different
 sympatric sites Washington State University, Burnt Bridge Creek Greenway,
 and St. Cloud Park. Details about collection locations, host-plant
 associations, and insect collection and rearing methods can be found in
 the associated manuscript. DNA extraction, PCR
 conditions including primer pairs, genotyper conditions (using a
 Beckaman-Coulter CEQ 8000), and allele calling protocols are described in
 the associated manuscript.  
description: Genotypes are provided in the "Convert" format, which
 allows for easy file conversion for different population genetics software
 formats using PGDSpider (http://www.cmpg.unibe.ch/software/PGDSpider/). Population designations are as follows: File designation Host-association Site WSU_A Apple Washington State University WSU_B Black hawthorn Washington State University WSU_O Ornamental hawthorn Washington State University BBG_A Apple Burnt Bridge Creek Greenway BBG_B Black hawthorn Burnt Bridge Creek Greenway BBG_O Ornamental hawthorn Burnt Bridge Creek Greenway StC_A Apple St. Cloud Park StC_B Black hawthorn St. Cloud Park StC_O Ornamental hawthorn St. Cloud Park Missing data are indicated with "?"