cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fttdz08qb
title: Data from: Positive associations with native shrubs are intense and important for an exotic invader but not the native annual community across an aridity gradient

description: AIM AND LOCATION: Positive interactions influence the assembly of plant
 communities globally, particularly in stressful environments like
 deserts.  However, few studies have measured the intensity and
 relative importance of positive interactions involving native and invasive
 species along aridity gradients.  These measures are essential
 for predicting how dryland communities will respond to biological
 invasions and environmental change.  Here, we measured the
 intensity and importance of positive associations formed between native
 shrubs and the annual plant community, which included highly invasive
 Bromus madritensis ssp. rubens (“B. rubens”) and native neighbours, along
 an aridity gradient across the Mojave and San Joaquin Deserts. METHODS:
 Along the gradient, we sampled metrics of abundance and performance for
 invasive B. rubens, native annual species (pooled), exotic annual species
 (pooled), and all annual species (pooled) during peak flowering at 120
 pairs of shrub and open microsites. RESULTS: Across the gradient, B.
 rubens occurred at far greater abundance, cover, biomass, and fitness near
 shrubs than away from shrubs.  When Larrea tridentata was the
 focal shrub, positive effects on B. rubens abundance and cover were
 weakest (though never negative) at the most arid sites under the shortest
 shrubs.  The native annual community occurred at greater
 abundance, cover, and species richness away from shrubs, regardless of
 relative aridity or shrub traits.  Community-level species
 richness was greatest away from shrubs, but exotic species richness was
 similar in shrub and open microsites. MAIN CONCLUSIONS: Across two
 deserts, B. rubens formed intense and important positive
 associations with native shrubs that consistently imporoved its abundance,
 cover, biomass, and fitness; and for abundance and cover, the intensity
 of B. rubens-L. tridentata associations depended upon
 relative aridity and shrub height.  By strongly facilitating a
 dominant invader but not native- or community-level biodiversity, native
 shrubs provided the wrong kind of help to the annual plant
 community.
DOI: 10.5061/dryad.1zcrjdfpt
title: Data from: Warming alters plant phylogenetic and functional community structure

description: Climate change is known to affect many facets of the Earth’s ecosystems.
 However, little is known about its impacts on phylogenetic and functional
 properties of ecological communities. Here we studied the responses of
 plant communities in an alpine grassland on the Tibetan Plateau to
 environmental warming across taxonomic, phylogenetic, and functional
 levels in a six-year multiple-level warming experiment. While low-level
 warming did not alter either plant species richness or
 phylogenetic/functional community structure, high-level warming
 significantly decreased species richness. Higher-level warming more
 strongly reduced soil moisture and caused stronger environmental
 filtering, consequently changing species composition and community
 structure. At the plant functional trait level, high-level warming
 promoted species turnover through altering the effects of traits such as
 plant height on species extinction and specific leaf area on species
 colonization. As a result, high-, but not low-level warming drove
 phylogenetic/functional community structure from overdispersion to
 randomness, by filtering out species that were functionally dissimilar and
 distantly related to the resident species. Synthesis. Our study provides
 evidence that the responses of plant phylogenetic and functional community
 structure to low warming differ from those in the future scenarios of
 increasing temperature. Importantly, the extinction of species that were
 functionally dissimilar and distantly related to the resident species
 contributed to alterations in plant community structure under high
 warming. Our study underscores the need to incorporate the phylogenetic
 and functional perspectives to gain a more complete understanding of
 community responses to climate warming.
DOI: 10.5061/dryad.5tb2rbp27
title: Data from: The coevolution of male and female genitalia in a mammal: a quantitative genetic insight

description: Male genitalia are among the most phenotypically diverse morphological
 traits, and sexual selection is widely accepted as being responsible for
 their evolutionary divergence. Studies of house mice suggest that the
 shape of the baculum (penis bone) affects male reproductive fitness and
 experimentally imposed postmating sexual selection has been shown to drive
 divergence in baculum shape across generations. Much less is known of the
 morphology of female genitalia and its coevolution with male genitalia. In
 light of this, we used a paternal half-sibling design to explore patterns
 of additive genetic variation and covariation underlying baculum shape and
 female vaginal tract size in house mice (Mus musculus domesticus). We
 applied a landmark-based morphometrics approach to measure baculum size
 and shape in males and the length of the vaginal tract and width of the
 cervix in females. Our results reveal significant additive genetic
 variation in house mouse baculum morphology and cervix width, as well as
 evidence for genetic covariation between male and female genital measures.
 Our data thereby provide novel insight into the potential for the
 coevolutionary divergence of male and female genital traits in a
 mammal. 
description: <strong>Baculum_Landmark_Data</strong>: Landmarks
 were placed around the periphery of the baculum (36 sliding, 4 fixed) and
 relative warps (RWs) and centroid size were extracted. Landmark placement
 conducted using tpsDig 232 developed by Rohlf. TPS file with baculum raw
 landmarks for each specimen. Specimen numbers/ID can be matched with ID at
 the quantitative genetics data excel spreadsheet.
 <strong>Baculum_Repeatibility_Landmark_Data</strong>: Landmarks were placed around the periphery of the baculum (36 sliding, 4 fixed) and relative warps (RWs) and centroid size were extracted. Landmark placement conducted using tpsDig 232 developed by Rohlf. TPS file with baculum raw landmarks of a subset of the individuals. For the same individual, we have two sets of landmarks. Used to assess the repeatability of landmark placement. Specimen numbers/ID can be matched with ID at the quantitative genetics data excel spreadsheet. <strong>Female_Repeatibility_Data</strong>: Excel spreadsheet containing the vaginal measurements data for repeatability analysis, plus the identifiers of each individual. For the same individual, we have three measurements per variable measured. Used to assess the repeatability of measurement. Specimen numbers/ID can be matched with ID at the quantitative genetics data excel spreadsheet. <strong>Quantitative _Genetics _Data</strong>: Excel spreadsheet containing the male and female body weight, genital measurements, female oestrous stage, plus the identifiers of each individual and information on each individual parentage (sire and dam).
DOI: 10.5061/dryad.zgmsbcc80
title: Undersampling correction methods to control γ-dependence for comparing β-diversity between regions

description: Measures of β-diversity are known to be highly constrained by the
 variation in γ-diversity across regions (i.e., γ-dependence), making it
 challenging to infer underlying ecological processes. Undersampling
 correction methods have attempted to estimate the actual β-diversity in
 order to minimize the effects of γ-dependence arising from the problem of
 incomplete sampling. However, no study has systematically tested their
 effectiveness in removing γ-dependence, and examined how well
 undersampling-corrected β-metrics reflect true β-diversity patterns that
 respond to ecological gradients. Here, we conduct these tests by comparing
 two undersampling correction methods with the widely used individual-based
 null model approach, using both empirical data and simulated communities
 along a known ecological gradient across a wide range of γ-diversity and
 sample sizes. We found that undersampling correction methods using
 diversity accumulation curves were generally more effective than the null
 model approach in removing γ-dependence. In particular, the
 undersampling-corrected β-Shannon diversity index was most independent on
 γ-diversity and was the most reflective of the true β-diversity pattern
 along the ecological gradient. Moreover, the null model-corrected
 Jaccard-Chao index removed γ-dependence more effectively than either
 approach alone. Our validation of undersampling correction methods as
 effective tools for accommodating γ-dependence greatly facilitates the
 comparison of β-diversity across regions.
description: The data were generated using the simulation code in the
 dataset.
description: Please cite the paper if anyone use this dataset or R code.
DOI: 10.5061/dryad.g1jwstqnt
title: Data from: Sustained immune activation is associated with susceptibility to the amphibian chytrid fungus

description: The disease chytridiomycosis caused by the fungus Bd has devastated
 amphibian populations worldwide. Functional genomic contributions to host
 susceptibility remain enigmatic and vary between species and populations.
 We conducted experimental Bd infections in Rana yavapaiensis, a species
 with intraspecific variation in chytridiomycosis susceptibility, to assess
 the skin and spleen transcriptomic response to infection over time. We
 predicted that increased immune gene expression would be associated with a
 positive disease outcome, but we instead found that surviving frogs had
 significantly reduced immune gene expression compared to susceptible frogs
 and to uninfected controls. MHC class II gene expression was also
 significantly higher in susceptible frogs compared to surviving frogs.
 Furthermore, susceptible frogs expressed a significantly larger number of
 distinct class II alleles, demonstrating a negative correlation between
 class II expression, functional diversity, and survival. Expression of
 the MHC class II locus previously associated with Bd disease outcomes was
 a significant predictor of Bd infection intensity at early infection
 stages but not at late infection stages, suggesting initial MHC-linked
 immune processes are important for ultimate disease outcomes. We infer
 through disease association and phylogenetic analysis that certain MHC
 variants are linked to the immune expression that was negatively
 associated with survival, and we hypothesize that frogs that did not
 express these alleles could better survive infections. Our study finds
 that MHC expression at early and late infection stages predicts Bd
 infection intensity, and suggests that generating a sustained immune
 response against Bd may be counterproductive for surviving
 chytridiomycosis in this partially susceptible species.
description: This dataset presents replicate qPCR pathogen quatification
 values for control and Bd-exposed individuals that were lab-reared from
 egg masses through metamorphosis and tracked for a 55 day exposure
 experiement. All control and Bd-exposed individuals
 were housed in separate cages and swabbed weekly, as well as swabbed at
 the time of euthanasia when RNAseq tissues were also collected. DNA was
 extracted from swabs and standard Bd qPCR protocols were used to run each
 sample in duplicate. Serial dilutions of known quantities of the pathogen
 were included as stadards, enabling absolute pathogen
 quantification.
DOI: 10.34740/kaggle/dsv/14644079
title: Bacteria_Confer_Protection
DOI: 10.5061/dryad.2547d7wnh
title: Transcriptomic signatures of ageing vary in solitary and social forms of an orchid bee

description: Eusocial insect queens are remarkable in their ability to maximise both
 fecundity and longevity, thus escaping the typical trade-off between these
 two traits. Several mechanisms have been proposed to underlie the
 remoulding of the trade-off, such as reshaping of the juvenile hormone
 pathway, or caste-specific susceptibility to oxidative stress. However, it
 remains a challenge to disentangle the molecular mechanisms underlying the
 remoulding of the trade-off in eusocial insects from caste-specific
 physiological attributes that have subsequently arisen. The socially
 polymorphic orchid bee Euglossa viridissima represents an excellent model
 to address the role of sociality per se in longevity as it allows direct
 comparisons of solitary and social individuals within a common genetic
 background. We investigated gene expression and juvenile hormone levels in
 young and old bees from both solitary and social nests. We found 902 genes
 to be differentially expressed with age in solitary females, including
 those involved in oxidative stress, versus only 100 genes in social
 dominant females, and 13 genes in subordinate females. A weighted gene
 co-expression network analysis further highlights pathways related to
 ageing in this species, including the target of rapamycin pathway. Eleven
 genes involved in translation, apoptosis and DNA repair show concurrent
 age-related expression changes in solitary but not in social females,
 representing potential differences based on social status. Juvenile
 hormone titres did not vary with age or social status. Our results
 represent an important step in understanding the proximate mechanisms
 underlying the remodelling of the fecundity/longevity trade-off that
 accompanies the evolutionary transition from solitary life to eusociality.
DOI: 10.5061/dryad.xksn02vch
title: Data from: Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryagrasses

description: Background Cultivated grasses are an important source of food for domestic
 animals worldwide. Better knowledge of their genomes can speed up the
 development of new cultivars with better quality and resistance to biotic
 and abiotic stresses. The most widely grown grasses are tetraploid
 ryegrass species ( Lolium spp.) and diploid and hexaploid fescue species
 (Festuca spp.). In this work, we characterized repetitive DNA sequences
 and their contribution to genome size in five fescue and two ryegrass
 species, as well as one fescue and two ryegrass cultivars. Results Partial
 genome sequences produced by Illumina technology were used for genome-wide
 comparative analyses using RepeatExplorer pipeline. Retrotransposons were
 found to be the most abundant repeat types in all seven grass species.
 Athila element of Ty3/gypsy family showed the most striking differences in
 copy number between fescues and ryegrasses. The sequence data enabled the
 assembly of an LTR element Fesreba, which is highly enriched in
 centromeric and (peri)centromeric regions in all species. A combination of
 FISH with a probe specific to Fesreba element and immunostaining with
 CENH3 antibody showed their colocalization and indicated a possible role
 of Fesreba in centromere function. Conclusions Comparative repeatome
 analysis in a set of fescues and ryegrasses provided new insights into
 their genome organization and divergence, including the assembly of LTR
 element Fesreba. A new LTR element Fesreba was identified and found
 abundant in centromeric regions of the fescues and ryegrasses. It may have
 a role in the function of their centromeres.
description: Partial genome sequences produced by Illumina technology were
 used for genome-wide comparative analyses using RepeatExplorer pipeline.
 DNA repeat were assembled and further characterized based on the homology
 searches and other tools useful for repeat characterization (e.g. BLASTN
 and BLASTX programs, phylogenetic analysis). Tandem organized repeats were
 identified using Dotter.
description: Dataset (multifasta file) contains contigs of DNA repeats
 identified in ten representatives of fescues and ryegrasses.
DOI: 10.6078/d1dh52
title: Technical appendices from: Affordable housing without public subsidies: rent-setting practices in small rental properties

description: Rental housing affordability is a severe problem for low- and
 moderate-income families across the US. While some renters benefit from
 subsidies or rent-regulation, most low-income renters live in
 unsubsidized, unregulated units, particularly in low-cost 1- to 4-unit
 properties. Some of these small rental properties are low-cost because
 they are low quality or are in low-demand neighborhoods, but there has
 long been speculation that many of these units are low-cost because their
 owners set rents below market. However the extent to which owners set rent
 below market, which owners do so, and why, is unknown. I conducted a
 nationwide survey with follow-up interviews of the owners of small rental
 properties to understand below-market rent-setting. I find that nearly
 half of small rental owners choose to set rents below market. These
 discounts are substantial, averaging 16% below market. Owner's
 rent-setting strategies are diverse and there do not appear to be sharp
 distinctions between owners who set rent below market and those who do
 not. However there is evidence that some owners' lack of knowledge of
 market conditions contributes to discounts, as does owners'
 impression of their tenant's income. Most municipalities likely have
 large stocks of good quality below-market rental housing in small rental
 properties. Supporting below-market small rentals could be a means for
 municipalities to realize their housing affordability goals. However the
 right policies to support this part of the stock are unclear and likely
 vary by jurisdiction. Planners could examine the owners and tenants of
 small rentals in their area to understand their needs and respond
 accordingly. Supporting this stock will raise new equity questions,
 particularly regarding who gets to rent these units, and practical issues
 about how the public sector can productively engage with non-professional
 landlords. These two technical appendices to the article "Affordable
 Housing Without Public Subsidies: Rent-Setting Practices in Small Rental
 Properties" describe the generalizeability of the survey and the
 detailed results of the regressions in the article.
DOI: 10.5061/dryad.g4f4qrfn2
title: Cognitive map-based navigation in wild bats revealed by a new high-throughput tracking system

description: Seven decades of research on the “cognitive map”, the allocentric
 representation of space, have yielded key neurobiological insights, yet we
 still lack field evidence from free-ranging wild animals. Using a system
 capable of tracking dozens of animals simultaneously at high accuracy and
 resolution, we assembled a large dataset of 172 foraging Egyptian fruit
 bats comprising &gt;18M localizations collected over 3,449 bat-nights
 across 4 years. Detailed track analysis, combined with translocation
 experiments, revealed that wild bats seldom exhibit random search but
 instead repeatedly forage in goal-directed, long and straight flights that
 include frequent shortcuts. Alternative non-map-based strategies were
 ruled out by simulations, time-lag embedding and other trajectory
 analyses. Our results are consistent with expectations from cognitive
 map-like navigation and support previous neurobiological evidence from
 captive bats. 
description: All bat procedures were approved by the Hebrew University of
 Jerusalem Animal Care and Use Committee (permit NS-15-14660-2). Bats were
 mist-netted on fruit trees or cave entrances and tagged with ATLAS in 38
 capture sessions spanning all seasons between 2015-2019. Bats were tagged
 with ATLAS – a reverse-GPS system that localizes extremely light-weight,
 low-cost tags. Each ATLAS tag transmits a unique radio signal detected by
 a base-station network distributed in the study area. Tag localization is
 computed using nanosecond-scale differences in signal time-of-arrival to
 each station, enabling nearly real-time tracking and alleviating the need
 to retrieve the tag or to have some power-consuming remote-download
 capability. Bats were tagged by gluing the tag to their back (138
 individuals) or by a custom-made collar (34 individuals). We applied a
 simple 10-second median filter to eliminate localization errors and
 smoothen the data.
description: The data are in a comma-delimited text file. Each row is a single
 localization of a single tag. There are 10 columns, as follows:
 1) Tag (bat) number 2) X-coordinate (metric,
 ITM coordinate system) 3) Y-coordinate (metric, ITM
 coordinate system) 4) Timestamp (Unix epoch time) in
 UTC 5-10) Time in human-readable format: Year, Month,
 Day, Hour, Minute, Second
DOI: 10.5061/dryad.3r2280gd6
title: Genetic diversity in the threatened freshwater mussel Lampsilis powellii

description: North America is home to the greatest share of the world’s freshwater
 mussel diversity; however, over 70% of its ~300 species are endangered or
 threatened. Lampsilis powellii, the Arkansas Fatmucket, is endemic to
 Arkansas and now restricted to upstream reaches of the Ouachita and Saline
 rivers, but the species is declining within this small range. Conservation
 actions such as augmenting or reintroducing populations may be necessary,
 but they require knowledge of the distribution of genetic variation within
 and among extant populations. We analyzed population structure between the
 South Fork Ouachita River and Saline River using a 607 base pair region of
 the mitochondrial COI gene and 14 microsatellites designed for Lampsilis
 abrupta. COI sequences showed little variation and the most common
 haplotype was present in both rivers. Our mtDNA sequences were
 indistinguishable from those of L. siliquoidea deposited on GenBank, but
 we were unable to make conclusions about the taxonomic distinctiveness of
 L. powellii. Microsatellites showed heterozygote deficiency for most loci
 and revealed little evidence of population structure between the two
 rivers. Overall, our results show low genetic diversity in L. powellii,
 which may reflect its small population size due to its long history of
 geographic isolation compounded by anthropogenic habitat destruction and
 fragmentation. Further genetic analyses of lampsiline taxa is needed to
 establish species limits for Lampsilis in the Interior Highlands.
description: Fourteen of fifteen microsatellite primers designed for
 <i>Lampsilis abrupta</i> (Eackles and King 2002) were
 successfully optimized in <i>L. powellii. </i>Forward primers
 for each PCR were labeled with a 5’ fluorescent tag (6-FAM, NED, PET, or
 VIC) for visualization.<i>  </i>Microsatellite loci were
 amplified in 10 μL reactions using GoTaq Master Mix (Promega Corp.), 0.5
 μM of fluorescently-labeled forward and reverse primer, and 10 ng of DNA
 template carried out under the following conditions: initial denaturing at
 94 °C for 2 min; 35 cycles of 94 °C for 40 s, variable annealing
 temperature for 40 s (Appendix A1), 72 °C for 1 min; and a final extension
 at 72 °C for 5 min. Fragment analysis was performed on an ABI 3730 Genetic
 Analyzer with LIZ600 size standard (Applied Biosystems, Inc).