cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t41s2
title: Data from: Disparities in availability of essential medicines to treat non-communicable diseases in Uganda: a Poisson analysis using the Service Availability and Readiness Assessment

description: Objective: Although the WHO-developed Service Availability and Readiness
 Assessment (SARA) tool is a comprehensive and widely applied survey of
 health facility preparedness, SARA data have not previously been used to
 model predictors of readiness. We sought to demonstrate that SARA data can
 be used to model availability of essential medicines for treating
 non-communicable diseases (EM-NCD). Methods: We fit a Poisson regression
 model using 2013 SARA data from 196 Ugandan health facilities. The outcome
 was total number of different EM-NCD available. Basic amenities,
 equipment, region, health facility type, managing authority, NCD
 diagnostic capacity, and range of HIV services were tested as predictor
 variables. Findings: In multivariate models, we found significant
 associations between EM-NCD availability and region, managing authority,
 facility type, and range of HIV services. For-profit facilities’ EM-NCD
 counts were 98% higher than public facilities (p &lt; .001). General
 hospitals and referral health centers had 98% (p = .004) and 105% (p =
 .002) higher counts compared to primary health centers. Facilities in the
 North and East had significantly lower counts than those in the capital
 region (p = 0.015; p = 0.003). Offering HIV care was associated with 35%
 lower EM-NCD counts (p = 0.006). Offering HIV counseling and testing was
 associated with 57% higher counts (p = 0.048). Conclusion: We identified
 multiple within-country disparities in availability of EM-NCD in Uganda.
 Our findings can be used to identify gaps and guide distribution of
 limited resources. While the primary purpose of SARA is to assess and
 monitor health services readiness, we show that it can also be an
 important resource for answering complex research and policy questions
 requiring multivariate analysis.
description: De-identified SARA
 Uganda 2013 database with variables definedSARA Uganda 2013
 database with variables used in analysis for this manuscript.
 De-identified. Original database is property of Uganda Ministry of
 Health.ANALYTIC.SARA-with-variable-list.xlsx
DOI: 10.5061/dryad.f6rr4
title: Data from: Mapping quantitative trait loci using selected breeding populations: a segregation distortion approach

description: Quantitative trait locus (QTL) mapping is often conducted in line crossing
 experiments where progeny are derived randomly from the original crosses.
 The detected QTL from such experiments are rarely relevant to breeding
 populations because they are not detected from the breeding populations.
 We developed generalized linear model methods to perform QTL mapping in
 directionally selected populations using a segregation distortion
 approach. A selected population is often small and thus has low power for
 QTL detection. The segregation distortion approach actually takes
 advantage of the small populations because small selected populations
 often reflected strong selection and thus possess a high degree of
 segregation distortion. We also developed methods to combine results of
 several populations and results from different types of data analyses from
 the same populations. Such a combined analysis can boost statistical
 powers. Simulation studies showed that the new methods of QTL mapping in
 selected populations are powerful. We illustrated the methods using two
 selected rice populations and detected several QTL responsible to yield
 selection. The new methods can be applied not only to rice breeding
 programs but also to breeding programs of all crops.
description: selected breeding
 population
DOI: 10.5061/dryad.g1qg040
title: Data from: Sexual conflict and ecology: species composition and male density interact to reduce male mating harassment and increase female survival

description: Sexual conflict is a pervasive evolutionary force that can reduce female
 fitness. Experimental evolution studies in the laboratory might
 overestimate the importance of sexual conflict since the ecological
 conditions in such settings typically include only a single species. Here,
 we experimentally manipulated conspecific male density (high or low) and
 species composition (sympatric or allopatric) to investigate how
 ecological conditions affect female survival in a sexually dimorphic
 insect, the banded demoiselle (Calopteryx splendens). Female survival was
 strongly influenced by an interaction between male density and species
 composition. Specifically, at low conspecific male density, female
 survival increased in the presence of heterospecific males (C. virgo).
 Behavioural mating experiments showed that interspecific interference
 competition reduced conspecific male mating success with large females.
 These findings suggest that reproductive interference competition between
 con- and heterospecific males might indirectly facilitate female survival
 by reducing mating harassment from conspecific males. Hence, interspecific
 competitors can show contrasting effects on the two sexes thereby
 influencing sexual conflict dynamics. Our results call for incorporation
 of more ecological realism in sexual conflict research, particularly how
 local community context and reproductive interference competition between
 heterospecific males can affect female fitness.
description: SurvivalSurvival data for mesocosm experimentsTrialsMating trials experimentgomez_llano_et_alCode used to analyse the data
DOI: 10.5061/dryad.j2h11
title: Data from: Bushmeat genetics: setting up a reference framework for the DNA-typing of African forest bushmeat

description: The bushmeat trade in tropical Africa represents illegal, unsustainable
 off-takes of millions of tons of wild game – mostly mammals – per year. We
 sequenced four mitochondrial gene fragments (cyt b, COI, 12S, 16S) in
 &gt;300 bushmeat items representing nine mammalian orders and 59
 morphological species from five western and central African countries
 (Guinea, Ghana, Nigeria, Cameroon and Equatorial Guinea). Our objectives
 were to assess the efficiency of cross-species PCR amplification and to
 evaluate the usefulness of our multilocus approach for reliable bushmeat
 species identification. We provide a straightforward amplification
 protocol using a single ‘universal’ primer pair per gene that generally
 yielded &gt;90% PCR success rates across orders and was robust to
 different types of meat preprocessing and DNA extraction protocols. For
 taxonomic identification, we set up a decision pipeline combining
 similarity- and tree-based approaches with an assessment of taxonomic
 expertise and coverage of the GENBANK database. Our multilocus approach
 permitted us to: (i) adjust for existing taxonomic gaps in GENBANK
 databases, (ii) assign to the species level 67% of the morphological
 species hypotheses and (iii) successfully identify samples with uncertain
 taxonomic attribution (preprocessed carcasses and cryptic lineages). High
 levels of genetic polymorphism across genes and taxa, together with the
 excellent resolution observed among species-level clusters
 (neighbour-joining trees and Klee diagrams) advocate the usefulness of our
 markers for bushmeat DNA typing. We formalize our DNA typing decision
 pipeline through an expert-curated query database – DNAbushmeat – that
 shall permit the automated identification of African forest bushmeat
 items.
description: Nucleotide sequence
 files used for tree-based analyses.Unaligned nucleotide
 sequence files used for tree-based analyses in the five mammalian orders
 (Artiodactyla, Carnivora, Pholidota, Primates, Rodentia) represented by
 more than one species.DRYAD_nucleotidesequences.zip
DOI: 10.5061/dryad.7002q
title: Data from: Aphid symbionts and endogenous resistance traits mediate competition between rival parasitoids

description: Insects use endogenous mechanisms and infection with protective symbionts
 to thwart attacks from natural enemies. Defenses that target specific
 enemies, however, potentially mediate competition between rivals and
 thereby impact community composition. Following its introduction to North
 America to control pea aphids (Acyrthosiphon pisum), the parasitoid
 Aphidius ervi competitively displaced other parasitoids, except for the
 native Praon pequodorum. The pea aphid exhibits tremendous clonal
 variation in resistance to A. ervi, primarily through infection with the
 heritable bacterial symbiont Hamiltonella defensa, although some
 symbiont-free aphid genotypes encode endogenous resistance. Interestingly,
 H. defensa strains and aphid genotypes that protect against A. ervi,
 provide no protection against the closely related, P. pequodorum. Given
 the specificity of aphid defenses, we hypothesized that aphid resistance
 traits may contribute to the continued persistence of P. pequodorum. We
 conducted multiparasitism assays to determine whether aphid resistance
 traits mediate internal competition between these two solitary parasitoid
 species, but found this was not the case; P. pequodorum was the successful
 internal competitor across lines varying in susceptibility to A. ervi.
 Next, to determine whether resistance traits influence competitive
 interactions resulting in the stable persistence of P. pequodorum, we
 established replicated cages varying in the proportion of resistant aphids
 and recorded successful parasitism for each wasp species over time. As
 expected, A. ervi outcompeted P. pequodorum in cages containing only
 susceptible aphids. However, P. pequodorum not only persisted, but was the
 superior competitor in populations containing any proportion (20–100%) of
 resistant aphids (20–100%). Smaller scale, better replicated competition
 cage studies corroborated this finding, and no-competition and behavioral
 assays provide insight into the processes mediating competition. Genetic
 variation, including that acquired via infection with protective
 symbionts, may provide a supply of hosts susceptible only to particular
 enemies, mediating competition with effects on community richness and
 stability.
description: Internal competition
 assayMultiparasitism assay
 investigating internal competition between two parasitoid when attacking
 aphid with different resistance traits.Kraft et al. Internal
 competition.xlsxSmall cage competition
 assaySmaller scale
 competition assays to complement our larger cage studies but with much
 greater replication,allowing us to determine if the presence of a
 competitor affected the pattern of parasitism of the parasitoids relative
 to our no competition experimentSmall cage
 competition.xlsxSmall cage no
 competitionParasitism assays
 performed in the absence of competition to determine patterns of
 parasitism of each wasp species in response to different proportions of
 resistant and susceptible aphids.
DOI: 10.5061/dryad.g84p3
title: Data from: Extreme dentition does not prevent diet and tooth diversification within combtooth blennies (Ovalentaria: Blenniidae)

description: The dentition of fishes can be quite striking and is often correlated with
 a specific diet. Combtooth blennies have long incisiform oral teeth,
 unlike most actinopterygians. It has been suggested that the long tooth
 morphology is an adaptation for detritivory, but given the diversity of
 diets (detritus, coral polyps, polychaetes, and pieces of other fishes),
 are blenny teeth indeed monomorphic? Or does tooth variation associated
 with diet still exist at this extreme? To explore tooth and diet
 diversification, we used a new phylogenetic hypothesis of Blenniidae,
 measured tooth shape, number, and mode of attachment, and quantified
 blenniid diet. The ancestral diet of blennies contained detritus and
 diversified into many different diets, including almost exclusively
 detritivory. Our results reveal a dental cline that may be constrained by
 tooth shape, but has not prevented diet diversification. Ancestral state
 reconstruction of tooth morphologies suggests that the ancestor of
 blennies had many unattached teeth and featured transitions to fewer
 attached teeth, with several transitions back to attached or unattached
 teeth. The dentition of blenniids is not monotypic; rather it is diverse
 and small changes in tooth shape are accompanied by changes in size,
 number, attachment, and often diet.
description: Tooth shape ratios
 (.xlsx spreadsheet)Tooth shape ratios from
 the dentary and premaxilla jawbones of blennies. Tooth_ratios tab has
 tooth shape ratios calculated from linear measurements of blenny teeth.
 Log_tooth_ratios has log transformed ratios.Tooth_shape_ratios.xlsx
DOI: 10.5061/dryad.531th0h5
title: Data from: Diversity partitioning confirms the importance of beta components in tropical rainforest Lepidoptera

description: Tropical beta diversity, and particularly that of herbivorous insects in
 rainforests, is often considered enormous, but this notion has recently
 been challenged. As tropical beta diversity is highly relevant to our view
 on biodiversity, it is important to gain more insights and resolve
 methodological problems that may lead to the contradictions in different
 studies. We used data on two ecologically distinct moth families from
 Southeast-Asia and analyzed separately the contribution of beta components
 to overall species richness at three spatial scales. Observed diversity
 partitions were compared under different types of null models. We found
 that alpha diversity was lower than expected from null models, whereas
 hierarchical beta components were larger than expected. Beta components
 played a significant role in shaping gamma diversity, and their
 contribution can be high (multiplicative beta &gt;5). We found a
 reduction of beta components when comparing primary forests and
 agricultural sites (cf. “biotic homogenization”), but even in these
 habitats beta components were still substantial. Our analyses show that
 beta components do play an important role in our data on tropical
 herbivorous insects, and that these results are not due to lumping
 different habitats when sampling environmental gradients.
description: Beck et
 al_dataSee
 ReadMe.txt
DOI: 10.5061/dryad.s57k2
title: Data from: Temperature and sex related effects of serine protease alleles on larval development in the Glanville fritillary butterfly

description: The body reserves of adult Lepidoptera are accumulated during larval
 development. In the Glanville fritillary butterfly, larger body size
 increases female fecundity, but in males fast larval development and early
 eclosion, rather than large body size, increase mating success and hence
 fitness. Larval growth rate is highly heritable, but genetic variation
 associated with larval development is largely unknown. By comparing the
 Glanville fritillary population living in the Åland Islands in northern
 Europe with a population in Nantaizi in China, within the source of the
 post-glacial range expansion, we identified candidate genes with reduced
 variation in Åland, potentially affected by selection under cooler
 climatic conditions than in Nantaizi. We conducted an association study of
 larval growth traits by genotyping the extremes of phenotypic trait
 distributions for 23 SNPs in 10 genes. Three genes in clip-domain serine
 protease family were associated with larval growth rate, development time
 and pupal weight. Additive effects of two SNPs in the
 prophenoloxidase-activating proteinase-3 (ProPO3) gene, related to
 melanization, showed elevated growth rate in high temperature but reduced
 growth rate in moderate temperature. The allelic effects of the
 vitellin-degrading protease precursor gene on development time were
 opposite in the two sexes, one genotype being associated with long
 development time and heavy larvae in females but short development time in
 males. Sexually antagonistic selection is here evident in spite of sexual
 size dimorphism.
description: Temperature and sex
 related larval development traits and SNP dataThis file contains
 network, sex and treatment information, phenotypic data for four life
 history traits, and genotypic data for 23 SNPs in 10 genes, for (n=335)
 Glanville fritillary butterflies collected from the Åland Islands,
 Finland.Melitaea_cinxia_larvalTraits_genotypes.txt
DOI: 10.5061/dryad.r54m2
title: Data from: Experimental evolution of female traits under different levels of intersexual conflict in Drosophila melanogaster

description: A number of studies have documented the evolution of female resistance to
 mate harm in response to the alteration of intersexual conflict in the
 populations. However, the life-history consequence of such evolution is
 still a subject of debate. In the present study, we subjected replicate
 populations of Drosophila melanogaster to different levels of sexual
 conflict (generated by altering the operational sex ratio) for over 45
 generations. Our results suggest that females from populations
 experiencing higher level of intersexual conflict evolved increased
 resistance to mate harm, in terms of both longevity and progeny
 production. Females from the populations with low conflict were
 significantly heavier at eclosion and were more susceptible to mate harm
 in terms of progeny production under continuous exposure to the males.
 However, these females produced more progeny upon single mating and had
 significantly higher longevity in absence of any male exposure – a
 potential evidence of trade-offs between resistance-related traits and
 other life-history traits, such as fecundity and longevity. We also report
 tentative evidence, suggesting an increased male cost of interacting with
 more resistant females.
description: Data on evolution of
 female traits under different levels of intersexual conflict in Drosophila
 melanogasterData generated in an
 Experimental evolution study. Assays done under laboratory
 conditions.Nandy et al.
 13-0268.R2_data.xlsx
DOI: 10.5061/dryad.fs21935
title: Data from: Direct and indirect effects of nitrogen enrichment on soil organisms and carbon and nitrogen mineralization in a semi‐arid grassland

description: 1. Semi-arid grasslands on the Mongolian Plateau are expected to
 experience high inputs of anthropogenic reactive nitrogen in this century.
 It remains unclear, however, how soil organisms and nutrient cycling are
 directly affected by N enrichment (i.e., without mediation by plant input
 to soil) vs. indirectly affected via changes in plant-related inputs to
 soils resulting from N enrichment. 2. To test the direct and indirect
 effects of N enrichment on soil organisms (bacteria, fungi, and nematodes)
 and their associated C and N mineralization, in 2010 we designated two
 subplots (with plants and without plants) in every plot of a six-level
 N-enrichment experiment established in 1999 in a semi-arid grassland. 3.
 In 2014, 4 years after subplots with and without plant were established, N
 enrichment had substantially altered the soil bacterial, fungal, and
 nematode community structures due to declines in biomass or abundance
 whether plants had been removed or not. N enrichment also reduced the
 diversity of these groups (except for fungi) and the soil C mineralization
 rate and induced a hump-shaped response of soil N mineralization. As
 expected, plant removal decreased the biomass or abundance of soil
 organisms and C and N mineralization rates due to declines in soil
 substrates or food resources. 4. Analyses of plant removal-induced changes
 (ratios of without- to with-plant subplots) showed that microorganisms and
 C and N mineralization rates were not enhanced as N enrichment increased
 but that nematodes were enhanced as N enrichment increased, indicating
 that the effects of plant removal on soil organisms and mineralization
 depended on trophic level and nutrient status.5. Surprisingly, there was
 no statistical interaction between N enrichment and plant removal for most
 variables, indicating that plant-related inputs did not qualitatively
 change the effects of N enrichment on soil organisms or mineralization.
 Structural equation modeling confirmed that changes in soil communities
 and mineralization rates were more affected by the direct effects of N
 enrichment (via soil acidification and increased N availability) than by
 plant-related indirect effects. Our results provide insight into how
 future changes in N-deposition and vegetation may modify below-ground
 communities and processes in grassland ecosystems.
description: Effects of nitrogen
 enrichment and plant removal on grasslandDirect and indirect
 effects of nitrogen enrichment on soil organisms and carbon and nitrogen
 mineralization in a semi-arid grasslandPlant_Nitrogen.xlsx
DOI: 10.5061/dryad.30cj7
title: Data from: Abyssal benthic foraminifera in the eastern equatorial Pacific (IODP Exp 320) during the middle Eocene

description: We report on the faunal transition of benthic foraminifera during the
 middle Eocene at Site U1333 (4862 m water depth, 3560-3720 m paleo-water
 depth) of Integrated Ocean Drilling Program Expedition 320 in the eastern
 equatorial Pacific Ocean. During the period ~41.5-40.7 Ma, which includes
 carbonate accumulation event 3 (CAE-3), the benthic foraminiferal
 accumulation rate (BFAR) increased gradually and then it declined rapidly.
 In contrast, BFAR was considerably lower during ~40.7-39.4 Ma,
 corresponding to the middle Eocene climatic optimum (MECO), and then it
 increased during ~39.3-38.4 Ma, including CAE-4. Diversity (E [S200]) was
 slightly lower in the upper part of the study interval than in the lower
 part. The most common benthic foraminifera were Nuttallides truempyi,
 Oridorsalis umbonatus and Gyroidinoides spp. in association with
 Globocassidulina globosa and Cibicidoides grimsdalei during the period
 studied. Quadrimorphina profunda occurred abundantly with N. truempyi, O.
 umbonatus and G. globosa during ~39.4-38.4 Ma, including CAE-4, although
 this species was also relatively common in the lower part of the study
 interval. Virgulinopsis navarroanus and Fursenkoina sp. A, morphologically
 infaunal taxa, were common during ~38.8-38.4 Ma, corresponding to the late
 stage of CAE-4. Based on Q-mode cluster analysis, four sample clusters
 were recognized and their stratigraphic distributions were generally
 discriminated in the lower and upper parts of the study interval.. Thus,
 there was only a small faunal transition in the abyssal eastern equatorial
 Pacific during the middle to late-middle Eocene. The faunal transition
 recognized in this study may be related to recovery processes following
 intense carbonate corrosiveness in the eastern equatorial Pacific during
 MECO.
description: Supplmental_Data_takataFaunal data of middle Eocene benthic foraminifera at IODP SIte U1333, Exp 320