cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.738c1
title: Data from: First wave of the 2016-17 cholera outbreak in Hodeidah city, Yemen - ACF experience and lessons learned

description: Introduction: Although cases were reported only in 2010 and 2011, cholera
 is probably endemic in Yemen. In the context of a civil war, a cholera
 outbreak was declared in different parts of the country October 6th, 2016.
 This paper describes the ACF outbreak response in Hodeidah city from
 October 28th, 2016 to February 28th, 2017 in order to add knowledge to
 this large outbreak. Methods: The ACF outbreak response in Hodeidah city
 included a case management component and prevention measures in the
 community. In partnership with the Ministry of Public Health and
 Population of Yemen (MoPHP), the case management component included a
 Cholera Treatment Center (CTC) implemented in the Al Thoraw hospital, 11
 Oral Rehydration Therapy Corners (ORTCs) and an active case finding
 system. In partnership with other stakeholders, prevention measures in the
 community, including access to safe water and hygiene promotion, were
 implemented in the most affected communities of the city. Results: From
 October 28th, 2016 until February 28th, 2017, ACF provided care to 8,270
 Acute Watery Diarrhea (AWD) cases, of which 5,210 (63%) were suspected
 cholera cases, in the CTC and the 11 ORTCs implemented in Hodeidah city.
 The attack rate was higher among people living in Al Hali district, with a
 peak in November 2016. At the CTC, 8% of children under 5 years-old also
 presented with Severe Acute Malnutrition (SAM). The Case-Fatality Rate
 (CFR) was low (0.07%) but 15% of admitted cases defaulted for cultural and
 security reasons. Environmental management lacked the information to
 appropriately target affected areas. Financial resources did not allow
 complete coverage of the city. Conclusion: Response to the first wave of a
 large cholera outbreak in Hodeidah city was successful in maintaining a
 CFR &lt;1% in the CTC. However, considering the actual context of
 Yemen and its water infrastructure, much more efforts are needed to
 control the current outbreak resurgence.
description: Yemen_cholera_DatabaseThis file includes data of all admissions for acute watery diarrhea from October 28th, 2016 to February 28th, 2017 in the Cholera Treatment Center in Hodeida city, Yemen.
DOI: 10.5061/dryad.mc034
title: Data from: Dynamics of coral reef benthic assemblages of the Abrolhos Bank, eastern Brazil: inferences on natural and anthropogenic drivers

description: The Abrolhos Bank (eastern Brazil) encompasses the largest and richest
 coral reefs of the South Atlantic. Coral reef benthic assemblages of the
 region were monitored from 2003 to 2008. Two habitats (pinnacles’ tops and
 walls) were sampled per site with 3-10 sites sampled within different reef
 areas. Different methodologies were applied in two distinct sampling
 periods: 2003-2005 and 2006-2008. Spatial coverage and taxonomic
 resolution were lower in the former than in the latter period. Benthic
 assemblages differed markedly in the smallest spatial scale, with greater
 differences recorded between habitats. Management regimes and biomass of
 fish functional groups (roving and territorial herbivores) had minor
 influences on benthic assemblages. These results suggest that local
 environmental factors such as light, depth and substrate inclination exert
 a stronger influence on the structure of benthic assemblages than
 protection from fishing. Reef walls of unprotected coastal reefs showed
 highest coral cover values, with a major contribution of Montastraea
 cavernosa (a sediment resistant species that may benefit from low light
 levels). An overall negative relationship between fleshy macroalgae and
 slow-growing reef-building organisms (i.e. scleractinians and crustose
 calcareous algae) was recorded, suggesting competition between these
 organisms. The opposite trend (i.e. positive relationships) was recorded
 for turf algae and the two reef-building organisms, suggesting beneficial
 interactions and/or co-occurrence mediated by unexplored factors. Turf
 algae cover increased across the region between 2006 and 2008, while
 scleractinian cover showed no change. The need of a continued and
 standardized monitoring program, aimed at understanding drivers of change
 in community patterns, as well as to subsidize sound adaptive conservation
 and management measures, is highlighted.
description: BENTHOS
 2003-2005Benthic cover data for
 the study sites between 2003-2005BENTHOS
 2006-2008Benthic cover data for
 the study sites between 2006-2008
DOI: 10.5061/dryad.632p3
title: Data from: Beyond shading: litter production by neighbours contributes to overyielding in tropical trees

description: The influence of biodiversity on ecosystem functioning is now well
 established. However, our ability to predict the ecological consequences
 of biodiversity changes remains limited by our poor understanding of the
 mechanisms underlying biodiversity effects. We disentangled the
 contributions of light competition and residual neighbourhood interactions
 in a ten-year-old biodiversity experiment with tropical trees that display
 overyielding, i.e., higher community-level yields in mixtures compared
 with monocultures. We developed models of individual tree growth that
 partition the effects of neighbouring trees into shading and residual
 effects assumed to reflect primarily belowground interactions. These
 models reject the hypothesis that reduced light competition in mixtures is
 the only mechanism driving overyielding. After factoring out the effects
 of shading, litter production by neighbours was a far better predictor of
 tree growth than traditional crowding indices and contributed to
 overyielding by producing pairwise interactions that ranged from
 competitive to facilitative, but which on average concentrated competition
 within species. Consistent with litter-mediated biodiversity effects, the
 magnitude of overyielding increased over time. Our results provide
 evidence for diversity effects extending beyond that of light and reveal
 the neglected role of litter-mediated interactions among trees.
description: Tree census
 dataThese data are yearly
 measurements of status, height and diameter on individual trees from the
 experimental plantation of the Sardinilla project. The Sardinilla project
 is a biodiversity experiment with tropical trees, that is a replacement
 series experiment with plots containing either 1, 3 or 6 species. The
 Sardinilla Project is part of Treedivnet (http://www.treedivnet.ugent.be)
 a global network of nine similar biodiversity tree plantations including
 boreal, temperate and tropical forest experiments. See:
 http://biology.mcgill.ca/faculty/potvin/sardinilla_obj.html. Data from
 years 2002 to 2006 are provided. Seedlings were planted in July 2001.
 Measurements were made late December (of the previous year indicated in
 the columns), in January or in February (of the year indicated in the
 columns). Metadata are included in a readme file and in a separate sheet
 in the xls file.data_2002_2006.xlsx
DOI: 10.5061/dryad.m4g2n
title: Data from: Declining rates of species described per taxonomist: slowdown of progress or a side-effect of improved quality in taxonomy?

description: [No abstract entered]
description: Fig.
 S1FIGURE S1. Relationship
 between quality of original descriptions of species (1935–1999) and
 subsequent revision in five periods of 13 years. Significance levels (*P
 &lt; 0.05, **P &lt; 0.01) are based on Mann-Whitney U test (A, pages,
 specimens, characters, taxa compared) and Fisher’s Exact Test (B,
 illustrations, maps, sonagrams). N.s., not significant.Data
 fileNew species of birds
 described in 1935-2009, including details on authorship, number of pages,
 specimens, characters, and taxa, and presence/absence of illustrations of
 the new species, maps and sonagrams.Datafile.xlsx
DOI: 10.5061/dryad.f2d0df0
title: Data from: Geographic variation and environmental correlates of apparent survival rates in adult tree swallows Tachycineta bicolor

description: Determining demographic rates in wild animal populations and understanding
 why rates vary are important challenges in population ecology and
 conservation. Whereas reproductive success is reported frequently for many
 songbird species, there are relatively few corresponding estimates of
 annual survival for widespread populations of the same migratory species.
 We incorporated mark-recapture data into Cormack-Jolly-Seber models to
 estimate annual apparent survival and recapture rates of adult male and
 female tree swallows Tachycineta bicolor in eight local breeding
 populations across North America for periods of 7-33 years. We found
 strong site-specific and annual variation in apparent survival rates of
 adult swallows, and evidence of higher survival or site fidelity among
 males than females. There were no strong associations between putative
 overwintering region and survival. Strength and patterns of winter
 climate-apparent survival relationships varied across four sites monitored
 for &gt;15 years; at one site, spring pond conditions, local spring
 precipitation and, to a lesser extent, winter North Atlantic Oscillation
 Index were credible predictors of annual apparent survival. Further work
 is needed to evaluate how survival is related to environmental conditions
 throughout the annual cycle and how these factors affect population
 dynamics of swallows and related species of conservation concern.
description: Clark, RG combined data
 for DryadDescriptions have been
 added within the data file.
DOI: 10.5061/dryad.1b90t69
title: Data from: Gene flow improves fitness at a range edge under climate change

description: Populations at the margins of a species' geographic range are often
 thought to be poorly adapted to their environment. According to
 theoretical predictions, gene flow can inhibit these range edge
 populations if it disrupts adaptation to local conditions. Alternatively,
 if range edge populations are small or isolated, gene flow can provide
 beneficial genetic variation, and may facilitate adaptation to
 environmental change. We tested these competing predictions in the annual
 wildflower Clarkia pulchella using greenhouse crosses to simulate gene
 flow from sources across the geographic range into two populations at the
 northern range margin. We planted these between-population hybrids in
 common gardens at the range edge, and evaluated how genetic
 differentiation and climatic differences between edge populations and gene
 flow sources affected lifetime fitness. During an anomalously warm study
 year, gene flow from populations occupying historically warm sites
 improved fitness at the range edge, and plants with one or both parents
 from warm populations performed best. The effects of the temperature
 provenance of gene flow sources were most apparent at early life history
 stages, but precipitation provenance also affected reproduction. We also
 found benefits of gene flow that were independent of climate: after
 climate was controlled for, plants with parents from different populations
 performed better at later lifestages than those with parents from the same
 population, indicating that gene flow may improve fitness via relieving
 homozygosity. Further supporting this result, we found that increasing
 genetic differentiation of parental populations had positive effects on
 fitness of hybrid seeds. Gene flow from warmer populations, when it
 occurs, is likely to contribute adaptive genetic variation to populations
 at the northern range edge as the climate warms. On heterogeneous
 landscapes, climate of origin may be a better predictor of gene flow
 effects than geographic proximity.
description: Bontrager and Angert -
 Clarkia pulchella transplant data and codeBontrager_transplant_dryad.zip
DOI: 10.5061/dryad.8108d
title: Data from: Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes

description: Genome size varies significantly across eukaryotic taxa and the largest
 changes are typically driven by macro-mutations such as whole genome
 duplications (WGDs) and proliferation of repetitive elements. These two
 processes may affect the evolutionary potential of lineages by increasing
 genetic variation and changing gene expression. Here we elucidate the
 evolutionary history and mechanisms underpinning genome size variation in
 a species rich group of Neotropical catfishes (Corydoradinae) with extreme
 variation in genome size - 0.6pg to 4.4 pg per haploid cell. Firstly,
 genome size was quantified in 65 species and mapped onto a novel
 fossil-calibrated phylogeny. Two evolutionary shifts in genome size were
 identified across the tree - the first between 43-49 Mya (95% highest
 posterior density (HPD) 36.2-68.1 Mya) and the second at ~19 Mya (95% HPD
 15.3-30.14 Mya). Secondly, RAD sequencing was used to identify potential
 WGD events and quantify transposable element abundance in different
 lineages. Evidence of two lineage scale WGDs were identified across the
 phylogeny, the first event occurring between 54-66 Mya (95% HPD 42.56-99.5
 Mya) and the second at 20-30 Mya (95% HPD 15.3-45 Mya) based on haplotype
 numbers per contig and between 35-44 Mya (95% HPD 30.29-64.51 Mya) and
 20-30 Mya (95% HPD 15.3-45 Mya) based on SNP read ratios. Transposable
 element abundance increased considerably in parallel with genome size,
 with a single TE-family (TC1-IS630-Pogo) showing several increases across
 the Corydoradinae, with the most recent at 20-30 Mya (95% HPD 15.3-45 Mya)
 and an older event at 35-44 Mya (95% HPD 30.29-64.51 Mya). We identified
 signals congruent with two WGD duplication events, as well as an increase
 in TE abundance across different lineages, making the Corydoradinae an
 excellent model system to study the effects of WGD and TEs on genome and
 organismal evolution.
description: Beast xml file for
 Corydoradinae chronogramBeast xml file for
 Corydoradinae chronogramcory_final_bmodel.xml
DOI: 10.5061/dryad.n14ph
title: Data from: Statolith morphometrics can discriminate among taxa of cubozoan jellyfishes

description: Identification of potentially harmful cubomedusae is difficult due to
 their gelatinous nature. The only hard structure of medusae, the
 statolith, has the potential to provide robust measurements for
 morphometric analysis. Traditional morphometric length to width ratios (L:
 W) and modern morphometric Elliptical Fourier Analysis (EFA) were applied
 to proximal, oral and lateral statolith faces of 12 cubozoan species. EFA
 outperformed L: W as L: W did not account for the curvature of the
 statolith. Best discrimination was achieved with Canonical Discriminant
 Analysis (CDA) when analysing proximal + oral + lateral statolith faces in
 combination. Normalised Elliptical Fourier (NEF) coefficients classified
 98% of samples to their correct species and 94% to family group. Statolith
 shape agreed with currently accepted cubozoan taxonomy. This has potential
 to assist in identifying levels of risk and stock structure of populations
 in areas where box jellyfish envenomations are a concern as the severity
 of envenomation is family dependent. We have only studied 12 (27%) of the
 45 currently accepted cubomedusae, but analyses demonstrated that
 statolith shape is an effective taxonomic discriminator within the Class.
description: Raw data for cubozoan
 statolith morphometricsThese are the raw data
 for Length: Width measurements and Normalised Elliptical Fourier
 coefficients resulting from analyses conducted for "Statolith
 morphometrics can discriminate among taxa of cubozoan jellyfishes".
 Morphometric analyses were conducted on statolith silhouettes in R using
 scripts detailed in the manuscript.
DOI: 10.5061/dryad.509k2
title: Data from: Cryptic female choice enhances fertilization success and embryo survival in chinook salmon

description: In this study we investigated two potentially important intersexual
 postcopulatory gametic interactions in a population of chinook salmon
 (Oncorhynchus tshawytscha): (i) the effect of female ovarian fluid (OF) on
 the behaviour of spermatozoa during fertilisation, and (ii) the effects of
 multilocus heterozygosity (as an index of male quality) and female-male
 genetic relatedness on sperm behaviour and male fertilisation success when
 there is sperm competition in the presence of that ovarian fluid. To do
 this, we conducted a series of in vitro competitive fertilisation
 experiments and found that,when ejaculates from two males are competing
 for access to a single female’s unfertilised eggs, fertilisation success
 was significantly biased toward the male whose sperm swam fastest in the
 female’s ovarian fluid. Embryo survival—a measure of fitness—was also
 positively correlated with both sperm swimming speed in ovarian fluid and
 male multilocus heterozygosity, providing novel evidence that cryptic
 female choice is adaptive for the female, enhancing the early survival of
 her offspring and potentially influencing her fitness.
description: READMEThis file explains all
 of the variables in each of the datasets that accompany: Rosengrave P,
 Montgomerie R 2015ms. Cryptic female choice enhances fertilization success
 and embryo survival in chinook salmonTrialsDataset for experimental
 competitive and non-competitive fertilization trialsReplicatesDataset for replicates of competitive fertilization trialsEsurvivalDataset for embryo survivalTRIOMLDataset for genetic relatedness estimates, using TrioML for degree of genetic relatedness between male and femaleReplicates2Same data as Replicates.csv but rearranged for loglinear analysisStatistical Supplement 2016This file includes all the R code and statistical analyses for - Rosengrave P, Montgomerie R, Gemmell, N. 2016. Cryptic female choice enhances fertilization success and embryo survival in chinook salmonStatistical Supplement.pdf
DOI: 10.5061/dryad.6ns97
title: Data from: Brain size, hunting and the risk of getting shot: a reply to Zink & Stuber (2017)

description: [No abstract entered]
description: Møller & Erritzøe
 Data
DOI: 10.5061/dryad.r9p70
title: Data from: Tropical tree growth is correlated with soil phosphorus, potassium, and calcium, though not for legumes

description: Tropical forest productivity is widely assumed to be limited by soil
 phosphorus (P), but biogeochemical processes that deplete P also could
 deplete base cations, suggesting multiple resource limitation. Limitation
 by several resources could arise from species and functional diversity,
 and variation among groups in resource requirements, including
 ecophysiological strategies that minimize P limitation. We hypothesized
 that tree growth is positively related to soil base cation and P
 availability and negatively related to local competition; Fabaceae growth
 is weakly correlated with soil resources if fixed N is used indirectly to
 acquire other resources; growth of species with low wood density is more
 strongly related to soil resource availability than species with high wood
 density. Diameter growth and soil resource availability were measured in
 five mapped stands situated across natural soil resource gradients in
 lowland wet tropical forest (La Selva Biological Station, Costa Rica).
 Soil resource availability, and associated uncertainty, was estimated for
 each tree using a Bayesian multivariate spatial regression model, with
 individual tree growth a function of diameter, local neighborhood, and
 soil resources. Separately, site-level mean tree growth and resource
 availability were modeled using linear regression. Individual diameter
 growth and site mean basal area increment correlated with soil base
 cations and P, but rarely with N; individual growth correlated negatively
 with neighborhood index for only three species. Growth of Fabaceae was
 unrelated to soil resources both at individual and site levels. When
 species were categorized by wood density, growth was related to soil P or
 base cation availability, with strongest correlation between
 lowest-density species and soil P. Several resources may limit tropical
 forest productivity because tree growth was similarly correlated with soil
 P and base cations, but functional groups responded differently.
 Negligible growth relationships with soil resources in Fabaceae suggest
 that N fixation may alleviate mineral nutrient limitations. Correlations
 of soil P with growth of low wood density species and base cations with
 species of higher density suggests variation in resource demands among
 functional groups. Thus, tropical tree growth may be limited by base
 cations and/or P, with degree and type of resource limitation dependent on
 functional or taxonomic group.
description: Dryad.Upload.11.1013.SoilsSoil resource data, La Selva plots, units ppmDryad.Upload.11.1013.TreesTree species, diameter, and census date data
DOI: 10.5061/dryad.vb766
title: Data from: Phylogenetic reconstruction of the myrrh genus, Commiphora (Burseraceae), reveals multiple radiations in Madagascar and clarifies infrageneric relationships

description: Commiphora (Burseraceae) is the most species-rich genus in the
 frankincense and myrrh family, whose widespread and often remote
 distribution in seasonally dry tropical forests globally has impeded
 efforts to resolve its taxonomy and investigate its systematic biology.
 Here we focus on establishing the origin and evolution of Commiphora
 species native to Madagascar, all of which are endemic. Recent work has
 uncovered 16 new Malagasy species, bringing the total number of island
 endemic species to 44 and comprising nearly 25% of the genus. Previous
 phylogenetic studies of Commiphora have indicated that Malagasy lineages
 immigrated to and radiated within the island twice. We test this
 biogeographic hypothesis more thoroughly using a nearly comprehensive
 sampling of species from Madagascar, an expanded sampling of Commiphora
 species native to other regions, and a greater depth of DNA sequence data
 from the nuclear (nrETS, nrITS) and chloroplast (psbA-trnH, ndhF-rpl32,
 and trnD—trnT) genomes. Results from this expanded phylogenetic analysis
 include strong support for seven infrageneric clades within a monophyletic
 Commiphora, which we refer to as the ‘Lasiodisca,’ ‘Granulifera,’
 ‘Saxicola,’ ‘Gariepensis,’ ‘Spinescens,’ ‘Arafy,’ and ‘Rhynchocarpa’
 clades. Malagasy species comprise four distantly related lineages,
 including one species sister to all other Commiphora species (C.
 lasiodisca), the species-rich ‘Arafy,’ and ‘Rhynchocarpa’ clades, and one
 species embedded within the predominantly East African ‘Spinescens’ clade
 (C. simplicifolia). We describe the morphological and geographic
 affinities of each infrageneric and Malagasy lineage and identify
 priorities for future systematic study of the genus.
description: Com_psbA__NexusAlignmentThis nexus file contains our alignment for sequences from the psbA-trnH chloroplast spacer.Com_psbA_Oct14.nexCom_ETS_NexusAlignmentThis nexus file is an alignment containing all sequences for the nrETS marker using in this study.Com_ETS_Oct14.nexITS_ARAFYThis nexus file is an alignment containing all sequences for the nrITS marker for the Arafy clade, used in this study.Com_ITS_Rhyncho_NexusAlignmentThis nexus file is an alignment containing all sequences for the nrITS marker for the Rhynchocarpa clade, used in this study.Com_ITS_Rhyncho_July2014.nexCom_trnDT_NexusAlignmentThis nexus file is an alignment containing all sequences for the trnD-trnT chloroplast spacer used in this study.trnDTFinal.nexCom_ndhFrpl32_NexusAlignmentThis nexus file is an alignment containing all sequences for the ndfH-rpl32 chloroplast spacer used in this study.ComndhFApr14.nex