cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7272/q6fj2f2n
title: SAFER: Safer conception strategies to prevent HIV transmission among HIV sero-different couples desiring pregnancy

description: Safer conception strategies are needed to minimize HIV transmission among
 HIV sero-different couples desiring pregnancy. Few studies have evaluated
 the choices couples make when offered multiple safer conception methods,
 or method acceptability. We piloted a comprehensive safer conception
 program for HIV-sero-different couples planning pregnancy in Zimbabwe,
 measuring feasibility, method uptake, acceptability, pregnancy, and HIV
 transmission. Couples in this prospective study were given a
 choice of one or more safer conception methods: antiretroviral therapy
 (ART) with monthly viral load (VL) monitoring for the HIV-positive partner
 (ART/VL), pre-exposure prophylaxis (PrEP) for the HIV-negative partner,
 vaginal insemination (VI) for couples with an HIV-positive woman, and
 semen washing (SW) for couples with an HIV-positive man. Couples were
 followed monthly for up to 12 months of pregnancy attempts, quarterly
 during pregnancy, and 12 weeks post-partum.  At each
 visit, data on method use, urine for pregnancy testing, and blood for HIV
 antibody testing, or viral load if HIV-positive, were obtained. Infants
 born to HIV-positive women were tested for HIV at 6 and 12
 weeks.  
description: The data are made available as .csv files. They can be imported
 into open-source and proprietary software analysis packages.
DOI: 10.5061/dryad.qz612jmj3
title: Data from: Acclimation in ants: Interference of communication and waterproofing through cuticular hydrocarbons in a multifunctional trait

description: Organismal traits may experience conflicting selection pressures if they
 fulfil different functions simultaneously. This can require trade-offs
 between functions or alternatively functional separation between elements
 of the trait. An important multifunctional trait in insects is the
 cuticular hydrocarbon (CHCs) layer. CHCs cover the body of nearly all
 insects, protect against desiccation and serve as a communication signal.
 In social insects like ants, they provide cues for nestmate recognition.
 To maintain their waterproofing function, insects have to adjust CHC
 composition to current temperatures. These changes might affect
 information content and interfere with communication, which would be
 especially detrimental in social insects. Here, we studied how acclimation
 affects nestmate recognition in two sister species of the ant genus
 Lasius. Colony fragments were exposed to three climate regimes. We
 analysed behaviour towards same and differently acclimated conspecifics,
 and determined which CHCs were related to acclimatory changes, colony
 differences, and inter-individual aggression. Differential acclimation led
 to higher aggression and chemical distances among former nestmates. We
 identified small CHC subsets, which only differed among colonies or among
 acclimation treatments. Moreover, few compounds sufficed to explain
 inter-individual aggression, suggesting that ants do not use the entire
 CHC profile for nestmate recognition and that colony identity is encoded
 in a redundant way. Across individual CHCs, their contribution to colony
 differences and to differences among acclimatory treatments was negatively
 correlated, indicating that there is some degree of functional separation.
 However, CHC classes could not be clearly assigned to one or another
 function, indicating that the role of each CHC is idiosyncratic and may
 differ among species. Acclimatory effects and colony differences were more
 independent from each other in L. platythorax than in L. niger, indicating
 that functional separation can differ even among sister species. Our
 results show that CHC functions are more intertwined than previously
 assumed, suggesting that insects cannot optimise all functions
 independently. The main constraint might be the need to maintain a certain
 phase behaviour of the CHC layer, which depends on CHC composition and
 affects functionality. The need to separate functions might depend on
 species-specific ecological and life-history parameters.
DOI: 10.5061/dryad.pc866t1rm
title: Low winter temperatures and divergent freezing resistance set the cold range limit of widespread alpine graminoids

description: Aim: “Where and why does a species exist” is a fundamental
 question in ecology. However, the actual range limits of alpine plant
 species are largely unexplored and unexplained. We aim at identifying the
 low temperature range limits of the two most abundant alpine graminoid
 species on acidic soils that intermingle in mosaics of high-elevation
 habitats across the European Alps. Location: Alpine grasslands in
 the Swiss Alps. Taxon: Carex
 curvula (Cyperaceae) and Nardus
 stricta (Poaceae), named by the genus name hereafter.
 Results: Carex and Nardus clearly
 segregated across different microsites. Season length, growing degree
 hours and soil chemistry (pH, C/N-ratio, phosphorus) did not demarcate the
 two species’ ranges, while their distribution was strongly affected by
 soil minimum temperature in winter. Carex occurred at
 sites with and without protecting snow cover and resisted low soil
 temperatures (-13 °C). Nardus was absent at microsites
 with snow cover duration less than 5 months and soil minimum temperatures
 below -5 °C. During the growing season, leaves
 of Carex had a higher freezing resistance with LT50 of
 -16.1 °C than those of Nardus with LT50 of -13.3 °C
 (LT50: lethal temperature for 50% of the tissue). Tetrazolium staining in
 shoots also revealed a higher freezing resistance
 in Carex compared to Nardus, and shoot apices
 tolerated lowest temperatures: Carex -30
 °C, Nardus -24 °C. Though, a vital shoot apex alone did
 not ensure regrowth after winter. Regrowth after severe frost events
 requires intact vessels and roots, all less freezing tolerant than apical
 meristems and young leaves. Main conclusions: The cold range
 limits of these widespread alpine graminoid species are evidently set by
 thermal extremes in winter. Microtopography, thus snow distribution
 pattern, in concert with the species’ freezing resistance explains the
 cold edge of the fundamental niche of these two species.
description: We year-round assessed the temperature 3 cm below ground, closest
 to the plant meristems as well as snow cover duration, soil chemistry and
 vegetation characteristics at high spatio-temporal resolution, resulting
 in 115 well-characterized microsites. Field data were combined with the
 freezing resistance analyses (electrolyte leakage, tetrazolium vital
 staining, regrowth capability) in plant individuals at 38 microsites by
 employing mixed regression models.
DOI: 10.15468/dl.nx8e6v
title: Occurrence Download

description: A dataset containing 789 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Algeria",
 "OccurrenceStatus is Present",
 "TaxonKey is Chiroptera"
 ]
}

 The dataset includes 789 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003135-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g79cnp5s3
title: No evidence that conifer biochar impacts soil functioning by serving as microbial refugia in boreal soils

description: It is well established that application of biochar to soils can promote
 soil fertility, which ultimately may enhance plant growth. While many
 mechanisms have been proposed to explain this, one specific mechanism, the
 “microbial refugia hypothesis” suggests that biochar may provide physical
 protection for soil microbe from soil micro-fauna that otherwise exert
 top-down control on microbial biomass and activity. We tested the
 microbial refugia hypothesis by incubating two boreal soils with and
 without biochar derived from a wood mixture of boreal tree species (Picea
 abies and Pinus sylvestris), and with and without soil nematodes. We
 measured phospholipid fatty acids (PLFA) as a relative measure of
 microbial biomass, and several variables indicative of microbial activity,
 including extractable nutrient concentrations (NH4+, NO3-, and PO4-),
 heterotrophic N2-fixation, and soil respiration. Contrary to our
 expectations, we found that biochar by itself did not stimulate microbial
 biomass or activity. Further, we found that nematode addition to soil
 stimulated rather than depressed the biomass of several bacterial PLFA
 groups. Finally, interactive effects between the nematode treatment and
 biochar never worked in a way that supported the microbial refugia
 hypothesis. Our findings suggests that a typical boreal biochar applied to
 boreal soils may not have the same stimulatory effect on microbial biomass
 and activity that has been shown in some other ecosystems, and that
 enhanced plant growth in response to biochar addition sometimes observed
 in boreal environments is likely due to other mechanisms, such as direct
 nutrient supply from biochar, or amelioration of soil pH.
DOI: 10.5061/dryad.sbcc2fr8t
title: Data from: A tiny cuckoo: risk-dependent interspecific brood parasitism in a predatory mite

description: Many animal species protect their eggs against predators while others do
 not. When these species share the same habitat, the latter species may
 profit by adding their eggs to those of the protecting species. We show
 that one tiny predatory mite species protects its own eggs only to a
 limited extent, and instead adds them to those of another predatory mite
 species that does guard its eggs, resulting in reduced egg predation. This
 cuckoo behaviour comes with a cost, and therefore only occurs when egg
 predators are present. Furthermore, the parasites only add eggs to those
 of the guarding host species, not to those of another mite species that
 does not guard its eggs. To the best of our knowledge, this is the first
 study to show that facultative brood parasitism is more effective than
 brood care, in increasing offspring survival in the presence of egg
 predators.
DOI: 10.5061/dryad.8cz8w9gtf
title: Ninety years of coastal monitoring reveals baseline and extreme ocean temperatures are increasing off the Finnish coast

description: Global marine heatwave assessments often rely on satellite-derived sea
 surface temperature. However, these data have low accuracy in coastal
 areas, are unable to measure sub-surface temperatures and have only been
 available since the 1980s. Here, we analyse 90 years of in situ surface
 and bottom (30 m) water temperature data from a Finnish coastal monitoring
 site. Water temperatures were significantly higher between 1991–2020 than
 1931–1960 and 1961–1990. We find strong differences between
 satellite-derived and in situ temperatures, with in situ temperatures
 being lower in autumn and winter and higher in spring. Measurements at the
 seafloor indicate marine heatwaves occurred during all seasons between
 2016 and 2020, with intensities and durations exceeding previous records.
 Since the 1990s, we find an upward shift of the baseline temperature and
 increasingly frequent occurrences of temperatures previously considered as
 an extreme. Our findings highlight the importance of long-term in situ
 data and choice of climatological reference periods for assessing change.
DOI: 10.5061/dryad.xd2547dk7
title: Data from: Predicting range shifts of the giant pandas under future climate and land use scenarios

description: Aim: Understanding and predicting how species will respond to
 global environmental change (i.e., climate and land use change) is
 essential to efficiently inform conservation and management strategies for
 authorities and managers. Here, we assessed the combined effect of future
 climate and land use change on the potential range shifts of the giant
 pandas (Ailuropoda melanoleuca).  Location: Sichuan
 Province, China. Methods: We used ensemble species distribution
 models (SDMs) to forecast range shifts of the giant pandas by the 2050s
 and 2070s under four combined climate and land use change scenarios. We
 also compared the differences in distributional changes
 of giant pandas among the five mountains in the study area. 
 Results: Our ensemble SDMs exhibited good model performance in
 terms of both AUC (0.931) and TSS (0.747), and suggested that
 precipitation seasonality, annual mean temperature, the proportion of
 forest cover and total annual precipitation are the most important factors
 in shaping the current distribution patterns for the giant pandas. Our
 projections of future species distribution also suggested a range
 expansion under an optimistic greenhouse gas emission, while suggesting a
 range contraction under a pessimistic greenhouse gas emission. Moreover,
 we found that there is considerable variation in the projected range
 change patterns among the five mountains in the study area. Especially,
 the suitable habitat of the giant panda is predicted to increase under all
 scenarios in Minshan mountains, while is predicted to decrease under all
 scenarios in Daxiangling and Liangshan mountains, indicating the
 vulnerability of the giant pandas at low latitudes.  Main
 conclusions: Our findings highlight the importance of an
 integrated approach that combines climate and land use change to predict
 the future species distribution and the need for a spatial explicit
 consideration of the projected range change patterns of target species for
 guiding conservation and management strategies.
DOI: 10.5061/dryad.6djh9w13s
title: Deep-sequencing of viral genomes from treatment-naive HIV-infected persons shows positive association between intrahost genetic diversity and viral load

description: Background: Infection with human immunodeficiency virus type 1 (HIV)
 typically results from transmission of a small and genetically uniform
 viral population. Following transmission, the virus population becomes
 more diverse because of recombination and acquired mutations through
 genetic drift and selection. Viral intrahost genetic diversity remains a
 major obstacle to the cure of HIV; however, there is a disagreement
 whether intrahost viral genetic diversification associates positively or
 negatively with disease progression and progression markers. Viral load is
 a key progression marker and understanding its relationship to viral
 intrahost genetic diversity could help design future strategies for HIV
 monitoring and treatment. Methods: We analyzed deep-sequenced viral
 genomes from 2,650 treatment-naive HIV-infected persons to measure the
 intrahost genetic diversity of 2,447 genomic codon positions as calculated
 by Shannon entropy. We tested for associations between viral load (VL) and
 amino acid (AA) entropy accounting for sex, age, race, duration of
 infection, and HIV population structure. Results: We confirmed that the
 intrahost genetic diversity is highest in the env gene. Furthermore, we
 showed that mean Shannon entropy is significantly associated with VL,
 especially in infections of &gt;24 months duration. We identified 16
 significant associations between VL (p-value&lt;2.0x10-5) and Shannon
 entropy at AA positions which in our association analysis explained 13% of
 the variance in VL. Conclusions: Our results elucidate that viral
 intrahost genetic diversity is associated with VL and could be used as a
 better disease progression marker than HIV consensus sequence variants,
 especially in infections of longer duration. We emphasize that viral
 intrahost diversity should be considered when studying viral genomes and
 infection outcomes.
DOI: 10.5061/dryad.wdbrv15rj
title: Natural disease history of a canine model of oligogenic RPGRIP1-cone-rod dystrophy establishes variable effects of previously and newly mapped modifier loci

description: Canine model of RPGRIP1-cone-rod dystrophy (CRD) was originally identified
 as a monogenic autosomal recessive disease characterized by early-onset
 blindness in a research colony. However, subsequent studies in the broader
 canine population revealed extensive variability in disease onset among
 RPGRIP1 mutants. Further studies led to the identification of a genetic
 modifier, a MAP9 variant that gave rise to earlier disease onset among
 RPGRIP1 mutants. We now describe the mapping of L3, an additional modifier
 locus, based on phenotypic variation specific to cone photoreceptor
 function. A genome-wide association study and haplotype analysis mapped L3
 to a 4.1-Mb locus on canine chromosome 30, and containing 49 genes, at
 least 38 of which were indicated in retinal expression. RNA-seq and whole
 genome sequencing did not find critical disease-causing genetic variant.
 However, filtering of moderate variants resulted in 11 missense variants
 as candidates for L3. We then established the natural disease history of
 RPGRIP1 -CRD in a purpose-bred colony of 58 dogs including 44 RPGRIP1
 mutants that were grouped into four cohorts based on the modifier status
 of MAP9 and L3. Functional and structural retinal phenotypes were
 evaluated in dogs up to nearly 9 years of age using electroretinography
 and vision-guided navigation, ophthalmoscopy, spectral-domain optical
 coherence tomography, and transmission electron microscopy. RPGRIP1
 mutants affected by both MAP9 and L3 modifiers exhibited the most severe
 disease phenotypes with rapid progression. MAP9 alone acted as an overall
 accelerator of rod and cone diseases, while L3 had a cone-specific effect.
 Ultrastructural analysis of photoreceptors revealed varying degrees of rod
 and cone destruction, while the connecting cilia appeared structurally
 preserved in all groups. We conclude that at least three loci contribute
 to the pathogenesis of oligogenic RPGRIP1 -CRD. While the RPGRIP1 variant
 is required for disease, both MAP9 and L3 modifiers exacerbate the
 phenotype, individually and cumulatively. The oligogenic RPGRIP1 -CRD
 canine model demonstrates the impact of multiple genetic modifiers on
 disease phenotype under a controlled environment, and thus may contribute
 to the identification of new targets for broad-spectrum therapies in
 oligogenic or polygenic forms of inherited retinal diseases.
description: Libraries of 300 bp insert size was prepared, llumina HiSeq2500
 paired-end reads, (2 × 100 bp, one lane per sample); Casava was used for
 the fastq preparation
 (https://bioweb.pasteur.fr/packages/pack@casava@1.8.2, v 1.8.2).
DOI: 10.5061/dryad.d51c5b060
title: Evolutionary gain and loss of a pathological immune response to parasitism

description: Parasites impose fitness costs on their hosts. Biologists often assume
 that natural selection favors infection-resistant hosts. Yet, when the
 immune response itself is costly, theory suggests selection may instead
 favor loss of resistance. Intraspecific variation in immune costs are
 rarely surveyed in a manner that tests evolutionary patterns, and there
 are few examples of adaptive loss of resistance. Here, we show that when
 marine threespine stickleback colonized freshwater lakes they gained
 resistance to the freshwater-associated tapeworm, Schistocephalus solidus.
 Extensive peritoneal fibrosis and inflammation is a commonly observed
 phenotype that contributes to suppression of cestode growth and viability,
 but also impose a substantial cost of reduced fecundity. Combining genetic
 mapping and population genomics, we find that opposing selection generates
 immune system differences between tolerant and resistant populations,
 consistent with divergent optimization.
description: Data were collected as described in Weber et al (https://www.biorxiv.org/content/10.1101/2021.08.04.455160v1). The repository includes diverse datasets involving laboratory experimental infections, flow cytometry, gene expression, population genomics, and multiple field samples of infection rates and immune traits.
DOI: 10.5061/dryad.5qfttdz83
title: Supplementary data for: From genomics to integrative taxonomy? The case study of Pocillopora corals

description: With the advent of genomics, sequencing thousands of loci from hundreds of
 individuals now appears feasible at reasonable costs, allowing complex
 phylogenies to be resolved. This is particularly relevant for cnidarians,
 for which insufficient data due to the small number of currently available
 markers, coupled with difficulties in inferring gene trees and
 morphological incongruences, encrypts species boundaries, thereby blurring
 the study and conservation of these organisms. Yet, can genomics alone be
 used to delimit species in an integrative taxonomic context? Here,
 focusing on the coral genus Pocillopora, which plays key roles in
 Indo-Pacific reef ecosystems but has challenged taxonomists for decades,
 we explored and discussed the usefulness of multiple criteria (genetics,
 morphology, biogeography and symbiosis ecology) to delimit species of this
 genus. Phylogenetic inferences, clustering approaches and species
 delimitation methods based on genome-wide single-nucleotide polymorphisms
 (SNPs) were first used to resolve Pocillopora phylogeny and propose
 genomic species hypotheses from 356 colonies sampled across the
 Indo-Pacific (western Indian Ocean, tropical southwestern Paciﬁc and
 south-east Polynesia). These species hypotheses were then compared to
 previous genetic evidences, as well as to evidences based on morphology,
 biogeography and symbiosis. Genomics allowed to delimit 21 species
 hypotheses where only seven are currently recognised based on current
 taxonomy. Moreover, 13 species were strongly supported by all approaches,
 either confirming their currently recognised species status, or supporting
 the presence of new species that need to be formally described. Some of
 the other genomic species hypotheses were supported by biogeographic or
 symbiosis evidences, but additional investigations are needed to state on
 their species status. Altogether, our results support (1) the obsolescence
 of macromorphology (i.e., overall colony and branches shape) but the
 relevance of micromorphology (i.e., corallite structures) to refine
 Pocillopora species limits, (2) the need to identify molecularly species
 prior to their study, as morphology can blur species identification on the
 field, (3) the relevance of the mtORF (coupled with other markers in some
 cases) as a diagnostic marker of most species, and (4) the need for a
 taxonomical revision in the Pocillopora genus. These results give new
 insights into the usefulness of multiple criteria for resolving
 Pocillopora species limits and will ultimately provide helpful insights
 for the conservation of the species from this scleractinian genus.