cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n9h1g
title: Data from: From past to future: impact of climate change on range shifts and genetic diversity patterns of circumboreal plants

description: Climate change is projected to influence the genetic resources of plant
 species. Recent research has examined genetic diversity patterns under
 current climate conditions, with little attention to the future genetic
 consequences for species. In this study, we combined ecological niche
 modeling and population genetic approaches to project future changes in
 genetic diversity using plastid and nuclear DNA and reconstructed
 distribution patterns of three circumboreal plants (Chamaedaphne
 calyculata, Linnaea borealis ssp. borealis, and Pedicularis
 sceptrum-carolinum ssp. sceptrum-carolinum) in the last glacial maximum.
 We found that circumboreal plants could potentially lose their geographic
 ranges in the future (2070; 35–52% in RCP 4.5 (representative
 concentration pathways), 37–53% in RCP 6.0, and 56–69% in RCP 8.5), only
 slightly compensated by a predicted range gain of 18–33% (across the three
 RCPs). It is expected that future genetic diversity level could remain
 similar or lower than the present level. On the other hand, the
 homogeneity of the genetic background—a lack of admixture and domination
 of one gene pool in most populations of C. calyculata and L. borealis ssp.
 borealis—was predicted to become more pronounced in the future. Combining
 the paleoecological niche modeling and genetic data revealed, more
 precisely, the climate refugia for circumboreal plants in the Alps,
 central Asia, Beringia, and southern North America and the macrorefugia
 more restricted to the northern part of Eurasia and North America,
 reaching the arctic zone.
description: AFLP_chamaedaphne
 calyculataAFLP_linnaea borealis
 ssp. borealisAFLP_pedicularis
 sceptrum carolinum ssp. sceptrum carolinumPedicularis
 sceptrum-carolinum ssp. sceptrum-carolinum_MaxEnt input
 locationsLinnea borealis ssp.
 borealis_MaxEnt input locationsChamedaphne
 calyculata_MaxEnt input locationsPedicularis
 sceptrum-carolinum sspChamaedaphne_POPSChamaedaphne calyculata_NE North America_results_POPSMaxEnt_Chamaedaphne calyculata_Linnaea borealis ssp. borealis_Pedicularis sceptrum-carolinum ssp. sceptrum-carolinum_results
DOI: 10.15468/dl.jjd9j3
title: Occurrence Download

description: A dataset containing 2339 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Observation, Human Observation, Living Specimen, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Amaranthus blitoides",
 "Year 2000-2026"
 ]
}

 The dataset includes 2339 records from 125 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000578-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.57n57
title: Data from: From β- to α-proteobacteria: the origin and evolution of rhizobial nodulation genes nodIJ

description: Although many α- and some β-proteobacterial species are symbiotic with
 legumes, the evolutionary origin of nitrogen-fixing nodulation remains
 unclear. We examined α- and β-proteobacteria whose genomes were sequenced
 using large-scale phylogenetic profiling and revealed the evolutionary
 origin of two nodulation genes. These genes, nodI and nodJ (nodIJ), play
 key roles in the secretion of Nod factors, which are recognized by legumes
 during nodulation. We found that only the nodulating β-proteobacteria,
 including the novel strains isolated in this study, possess both nodIJ and
 their paralogous genes (DRA-ATPase/permease genes). Contrary to the widely
 accepted scenario of the a-proteobacterial origin of rhizobia, our
 exhaustive phylogenetic analysis showed that the entire nodIJ clade is
 included in the clade of Burkholderiaceae DRA-ATPase/permease genes, i.e.,
 the nodIJ genes originated from gene duplication in a lineage of the
 β-proteobacterial family. After duplication, the evolutionary rates of
 nodIJ were significantly accelerated relative to those of homologous
 genes, which is consistent with their novel function in nodulation. The
 likelihood analyses suggest that this accelerated evolution is not
 associated with changes in either nonsynonymous/synonymous substitution
 rates or transition/transversion rates, but rather, in the GC content.
 Although the low GC content of the nodulation genes has been assumed to
 reflect past horizontal transfer events from donor rhizobial genomes with
 low GC content, no rhizobial genome with such low GC content has yet been
 found. Our results encourage a reconsideration of the origin of nodulation
 and suggest new perspectives on the role of the GC content of bacterial
 genes in functional adaptation.
description: nodI_seq_larger_data_setnodI_seq_smaller_data_set.nexnodI_seq_smaller_data_setnodJ_seq_larger_data_setnodJ_seq_smaller_data_setnodIJ_tree_larger_data_set_LogDet_NJnodIJ_tree_smaller_data_set_nonhomogeneous_ML
DOI: 10.5061/dryad.58k34
title: Data from: Dissecting functional components of reproductive isolation among closely related sympatric species of the Anopheles gambiae complex

description: Explaining how and why reproductive isolation evolves and determining
 which forms of reproductive isolation have the largest impact on the
 process of population divergence are major goals in the study of
 speciation. By studying recent adaptive radiations in incompletely
 isolated taxa, it is possible to identify barriers involved at early
 divergence before other confounding barriers emerge after speciation is
 complete. Sibling species of the Anopheles gambiae complex offer
 opportunities to provide insights into speciation mechanisms. Here we
 studied patterns of reproductive isolation among three taxa, An. coluzzii,
 An. gambiae s.s. and An. arabiensis, to compare its strength at different
 spatial scales, to dissect the relative contribution of pre- versus
 post-mating isolation, and to infer the involvement of ecological
 divergence on hybridization. Because F1 hybrids are viable, fertile, and
 not uncommon, understanding the dynamics of hybridization in this trio of
 major malaria vectors has important implications for how adaptations arise
 and spread across the group, and in planning studies of the safety and
 efficacy of gene drive as a means of malaria control. We first performed a
 systematic review and meta-analysis of published surveys reporting on
 hybrid prevalence, showing strong reproductive isolation at a continental
 scale despite geographically restricted exceptions. Second, we exploited
 our own extensive field datasets collected at a regional scale in two
 contrasting environmental settings, in order to assess: i) levels of
 pre-mating isolation; ii) spatio/temporal and frequency-dependent dynamics
 of hybridization, iii) relationship between reproductive isolation and
 ecological divergence, and iv) hybrid viability penalty. Results are in
 accordance with ecological speciation theory predicting a positive
 association between the strength of reproductive isolation and degree
 ecological divergence, and indicate that post-mating isolation does
 contribute to reproductive isolation among these species. Specifically,
 only post-mating isolation was positively associated with ecological
 divergence, whereas pre-mating isolation was correlated with phylogenetic
 distance.
description: AR x GA East
 AfricaData from systematic
 review concerning the numbers of Anopheles gambiae s.s., An. arabiensis
 and relative hybrids in different localities of East
 AfricaBF CxG hybrids -
 adultsData on numbers of adult
 Anopheles gambiae s.s., An. coluzzii, An. arabiensis and relative hybrids
 collected during surveys in Burkina Faso.CM CxG hybrids -
 larvaeData on numbers of
 larvae Anopheles gambiae, An. coluzzii, An. arabiensis collected during
 surveys in Cameroon.systematic
 reviewData retrieved from
 systematic review of relative presence of Anopheles coluzzii, An. gambiae
 s.s., An. arabiensis and their relative hybrids in continental
 Africa
DOI: 10.5061/dryad.54n60
title: Data from: Effects of school-based intervention by emergency medical technicians on students and their parents: a community-based prospective study of the Akashi Project

description: Objective: Stroke lessons for youth provided by emergency medical
 technicians (EMTs) may be an effective strategy to facilitate early
 intervention for patients with stroke. The aim of this study was to
 examine how effective EMT-led lessons on stroke awareness for
 schoolchildren were at disseminating stroke information. Setting,
 participants and outcome measures: The study was performed in the city of
 Akashi, Hyogo, Japan (Akashi project). Children (aged 9−10 years old) at
 11 public elementary schools and their parents were enrolled in this
 study. EMTs from the firefighting headquarters provided lessons on stroke
 to the children using our educational materials between September 2014 and
 October 2015. Each child was given our educational materials to take home
 and discuss stroke with their parents. The children and their parents
 answered questionnaires on stroke knowledge before, immediately, and at
 3months after the lesson. Results: A total of 763children and 489parents
 were enrolled (i.e., 64% of children). The scores of either stroke
 symptoms or risk factors were significantly higher immediately and at 3
 months after the lesson, compared to before the lesson, both in children
 and the parents (P&lt;0.01). Compared to the baseline in both groups
 (58% in children, 83% in parents), the meaning of the FAST mnemonic at
 3months (88%, 94%), as well as at immediately after the lesson (90%, 89%),
 were significantly higher (P &lt;0.001). Conclusion: Stroke education
 by EMTs was effective in increasing stroke awareness in elementary school
 children, as well as their parents.
description: original data
 childrenResults of
 questionnaires from the childrenoriginal data
 parentsResults of
 questionnaires from parents
DOI: 10.5061/dryad.2hk19
title: Data from: Mixed evidence for the erosion of inter-tactical genetic correlations through intralocus tactical conflict

description: Alternative reproductive tactics, whereby members of the same sex use
 different tactics to secure matings are often associated with conditional
 intrasexual dimorphisms. Given the different selective pressures on males
 adopting each mating tactic,, intrasexual dimorphism is more likely to
 arise if phenotypes are genetically uncoupled and free to evolve towards
 their phenotypic optima. However, in this context, genetic correlations
 between male morphs could result in intralocus tactical conflict. We
 investigated the genetic architecture of male dimorphism in bulb mites
 (Rhizoglyphus echinopus) and earwigs (Forficula auricularia). We used
 half-sibling breeding designs to assess the heritability and
 intra/intersexual genetic correlations of dimorphic and monomorphic traits
 in each species. We found two contrasting patterns; F. auricularia
 exhibited low intrasexual genetic correlations for the dimorphic trait,
 suggesting that the intralocus tactical conflict is moving towards a
 resolution. Meanwhile, R. echinopus exhibited high and significant
 intrasexual genetic correlations for most traits, suggesting that morphs
 in the bulb mite may be limited in evolving to their optima. This also
 shows that intrasexual dimorphisms can evolve despite strong genetic
 constraints, contrary to current predictions. We discuss the implications
 of this genetic constraint and emphasize the potential importance of
 intralocus tactical conflict for our understanding of intrasexual
 dimorphisms.
description: Data for Pike et al.
 2017All relevant information
 available in the article.Data for Pike et al
 2017.xlsx
DOI: 10.5061/dryad.3695391
title: Data from: Going to extremes for sodium acquisition: use of community land and high-altitude areas by mountain gorillas Gorilla beringei in Rwanda

description: Space use in mammals may be influenced not only by their primary foods,
 but also by localized sources of physiologically critical resources such
 as sodium-rich plants. We examined how sodium acquisition influences
 habitat use in mountain gorillas (Gorilla beringei) in Rwanda which have
 increased the amount of time they forage on community land outside of
 Volcanoes National Park (VNP), where eucalyptus (Eucalyptus spp.) tree
 bark is their most frequently eaten food. We measured sodium content in
 samples from 34 main dietary items and quantified sodium intake by 22
 gorillas in three social groups over one-year. On a dry weight basis,
 eucalyptus bark contains 3100 mg Na/kg. In contrast, the four herbs most
 frequently exploited for food inside the park are relatively sodium-poor
 (&lt;70mg/kg each). Further, sodium intake rates were highest when the
 gorillas were on community land. Of the two groups that fed outside of the
 park, one obtained 73% and the other one 45% of their sodium in that
 habitat despite only feeding for minimal amounts of time there. However,
 one group that did not feed on community land acquired 78% of its sodium
 in the subalpine and alpine zones through the consumption of pith of giant
 lobelias and groundsels. Obtaining sodium thus likely creates an incentive
 for the gorillas to leave the park and make forays into high-altitude
 habitat. Both strategies are not without risks: exiting their natural
 habitat and feeding on crops may increase human-wildlife conflict and
 visiting high-altitude areas may increase the risk of hypothermia.
description: Sodium_dataExcel file containing the R code and the data used in the model.
DOI: 10.5061/dryad.g3s10
title: Data from: Competition in slow motion: the unusual case of benthic marine communities in the wake of the end-Permian mass extinction

description: Changes of community structure in response to competition usually take
 place on timescales that are much too short to be visible in the
 geological record. Here we report the notable exception of a benthic
 marine community in the wake of the end-Permian mass extinction, which is
 associated with the microbial limestone facies of the earliest Triassic of
 South China. The newly reported fauna is well preserved and
 extraordinarily rich (30 benthic macroinvertebrate species, including the
 new species Astartella? stefaniae (Bivalvia) and Eucochlis obliquecostata
 (Gastropoda)) and stems from an environmentally stable setting providing
 favourable conditions for benthic organisms. Whereas changes in the
 taxonomic composition are negligible over the observed time interval of
 10–100 ka, three ecological stages are identified, in which relative
 abundances of initially rare species continuously increased at the cost of
 previously dominant species. Concomitant with the changes of dominant
 species is an increase in faunal evenness and heterogeneity. In the
 absence of both environmental and taxonomic changes, we attribute this
 pattern to the long-term effects of interspecific competition, which acted
 at an unusually slow pace because the number of competing species and
 potential immigrants was dramatically reduced by the end-Permian mass
 extinction. We suggest that these non-actualistic conditions led to
 decreased rates of niche differentiation and hence to the delayed
 rediversification of benthos that characterizes the aftermath of the
 greatest Phanerozoic mass extinction event. A hyperbolic diversification
 model is proposed, which accounts for the positive relationship between
 the intensity of interspecific competition and the rate of niche
 differentiation and resolves the conundrum of delayed rediversification at
 a time when niche space was largely vacated.
description: Hautmann-et-al_Appendix
 S1Appendix S1: Conodont
 biostratigraphy of the Wuzhuan section.Hautmann-et-al_AppendixS2Appendix S2. Individuals per species and sample and diversity indices.Hautmann-et-al_AppendixS3Appendix S3. Individuals per species and faunal interval, species’ ecology, evolutionary context and previous Griesbachian records of genera.Hautmann-et-al_AppendixS4Appendix S4. Diversity and ecological parameters of faunal intervals FI1 – FI3.
DOI: 10.5061/dryad.tt0tq
title: Data from: Review of Namibimydas Hesse, 1972 and Nothomydas Hesse, 1969 (Diptera: Mydidae: Syllegomydinae: Halterorchini) with the description of new species

description: The Mydidae genera Namibimydas Hesse, 1972 and Nothomydas Hesse, 1969 are
 reviewed. Both genera were known from two species each occurring in
 southern Namibia and western South Africa and are here redescribed. Four
 new species, all from Namibia, are described herein: Namibimydas psamminos
 sp. n., Namibimydas stuckenbergi sp. n., Nothomydas aquilonius sp. n., and
 Nothomydas picketti sp. n. A dichotomous key to all species is presented
 and illustrations and photographs are provided to support the descriptions
 and future identification. Distribution, occurrence in biodiversity
 hotspots sensu Conservation International, and seasonal incidence are
 discussed for all species. Information of all four genera of
 Syllegomydinae: Halterorchini is summarised and photographs of all genera
 provided. A novel structure of the male terminalia, termed
 supra-hypandrial sclerite, is described and illustrated.
description: Species descriptions of
 Namibimydas and Nothomydas in SDD formatNatural language species
 descriptions of Namibimydas and Nothomydas as exported from Lucid Builder
 3.5 in SDD format.namibimydas+nothomydas.sdd
DOI: 10.5061/dryad.4c2bj
title: Data from: The relationship between risk of bias criteria, research outcomes, and study sponsorship in a cohort of preclinical thiazolidinedione animal studies: a meta-analysis

description: Introduction: There is little evidence regarding the influence of
 conflicts of interest on preclinical research. This study examines whether
 industry sponsorship is associated with increased risks of bias and/or
 effect sizes of outcomes in published preclinical thiazolidinedione (TZD)
 studies. Methods: We identified preclinical TZD studies published between
 January 1, 1965, and November 14, 2012. Coders independently extracted
 information on study design criteria aimed at reducing bias, results for
 all relevant outcomes, sponsorship source and investigator financial ties
 from the 112 studies meeting the inclusion criteria. The average
 standardized mean difference (SMD) across studies was calculated for
 plasma glucose (efficacy outcome) and weight gain (harm outcome). In
 subgroup analyses, TZD outcomes were assessed by sponsorship source and
 risk of bias criteria. Results: Seven studies were funded by industry
 alone, 17 studies funded by both industry and non-industry, 49 studies
 funded by non-industry alone and 39 studies had no disclosures. None of
 the studies used sample size calculations, intention-to-treat analyses,
 blinding of investigators or concealment of allocation. Most studies
 reported favourable results (88 of 112) and conclusions (95 of 112)
 supporting TZD use. Efficacy estimates were significantly larger in six
 studies sponsored by industry alone (−3.41; 95% CI −5.21, −1.53; I2 = 93%)
 versus 42 studies sponsored by non-industry sources (−0.97; 95% CI −1.37,
 −0.56; I2 = 81%; p-value = 0.01). Harms estimates were significantly
 larger in four studies sponsored by industry alone (5.00; 95% CI 1.22,
 8.77; I2 = 93%) versus 38 studies sponsored by non-industry sources (0.30;
 95% CI −0.08, 0.68; I2 = 79%; p-value = 0.02). TZD efficacy and harms did
 not differ by disclosure of financial COIs or risks of bias. Conclusions:
 Industry-sponsored TZD animal studies have exaggerated efficacy and harms
 outcomes compared with studies funded by non-industry sources. There was
 poor reporting of COIs.
description: Risk of bias
 meta-analysis dataRisk of bias data
 extracted from publications identified through systematic review and
 included in a meta-analysis of preclinical thiazolidinedione animal
 studies. A user guide describing the data and abbreviations is included in
 the Excel file.Abdel-Sattar et
 al_EBPM_2014.xls
DOI: 10.15468/dl.z7cbex
title: Occurrence Download

description: A dataset containing 1407 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-180 -60,-70 -60,-70 70,-180 70,-180 -60))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (28eb1a3f-1c15-4a95-931a-4af90ecb574d, e9f60bdb-217d-4b4e-a22a-2781321220a1, c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f)",
 "TaxonKey is Balaenoptera physalus",
 "Year 2000-2026"
 ]
}

 The dataset includes 1407 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000579-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r1d6g
title: Data from: Natural selection for the Duffy-null allele in the recently admixed people of Madagascar

description: While gene flow between distantly related populations is increasingly
 recognized as a potentially important source of adaptive genetic variation
 for humans, fully characterized examples are rare. In addition, the role
 that natural selection for resistance to vivax malaria may have played in
 the extreme distribution of the protective Duffy-null allele, which is
 nearly completely fixed in mainland sub-Saharan Africa and absent
 elsewhere, is controversial. We address both these issues by investigating
 the evolution of the Duffy-null allele in the Malagasy, a recently admixed
 population with major ancestry components from both East Asia and mainland
 sub-Saharan Africa. We used genome-wide genetic data and extensive
 computer simulations to show that the high frequency of the Duffy-null
 allele in Madagascar can only be explained in the absence of positive
 natural selection under extreme demographic scenarios involving high
 genetic drift. However, the observed genomic single nucleotide
 polymorphism diversity in the Malagasy is incompatible with such extreme
 demographic scenarios, indicating that positive selection for the
 Duffy-null allele best explains the high frequency of the allele in
 Madagascar. We estimate the selection coefficient to be 0.066. Because
 vivax malaria is endemic to Madagascar, this result supports the
 hypothesis that malaria resistance drove fixation of the Duffy-null allele
 in mainland sub-Saharan Africa.
description: Hodgson et al Duffy
 program and datafastadsim.pl forward
 simulation computer program and 10k SNP genotype data