cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pj475
title: Data from: Portable device for the detection of colorimetric assays

description: In this work, a low-cost, portable device is developed to detect
 colorimetric assays for in-field and point-of-care (POC) analysis. The
 device can rapidly detect both pH values and nitrite concentrations of 5
 different samples, simultaneously. After mixing samples with specific
 reagents, a Hi-resolution digital camera collects a picture of the sample,
 and a single-board computer processes the image in real time to identify
 the hue-saturation-value (HSV) coordinates of the image. An internal light
 source reduces the effect of any ambient light so the device can
 accurately determine the corresponding pH values or nitrite
 concentrations. The device was purposefully designed to be low-cost, yet
 versatile and the accuracy of the results have been compared to those from
 a conventional method. The results obtained for pH values have a mean
 standard deviation of 0.03 and a correlation coefficient (R) of 0.998. The
 detection of nitrites is between concentrations of 0.4 to 1.6mg/L with a
 low detection limit of 0.2mg/L and has a mean standard deviation of 0.073
 and an R-value of 0.999. The results represent the great potential of the
 proposed portable device as an excellent analytical tool for POC
 colorimetric analysis and offer broad accessibility in resource-limited
 settings.
description: Results presented in
 figure 7.The hue values as a
 function of pH values (ranging from 4 to 8) and the fitted polynomial
 curve.Results presented in
 figure 8 (a) and (b).(a) The sensor response
 to different nitrite concentrations in the sample, (b) nitrite
 concentration calibration curve (Line fitted to the experimental S values
 obtained for different nitrite concentrations using Griess
 reagents).Results presented in
 figure 9.A Linear relationship
 between the pH values obtained using the pH meter and those obtained using
 the portable device.Results presented in
 figure 10.A Linear relationship
 between the concentrations of the prepared nitrite solutions and those
 obtained using the portable device.Results presented in
 figure .11 (Top) and (Botoom)UV-vis measurements for
 nitrite concentrations (top) UV-vis spectrum for the determination of
 different nitrite concentration, (bottom) nitrite concentration
 calibration curve (Line fitted to the experimental absorbance values at
 540 nm obtained for different nitrite concentrations using Griess
 reagents)Photocolorimeter
 algorithm
DOI: 10.5061/dryad.8608
title: Data from: Ecological and phylogenetic influence on mandible shape variation of South American caviomorph rodents (Rodentia: Hystricomorpha)

description: We analyzed mandible shape variation of 17 genera belonging to three
 superfamilies (Cavioidea, Chinchilloidea and Octodontoidea) of South
 American caviomorph rodents using geometric morphometrics. The relative
 influence of phylogeny and ecology on this variation was assessed through
 phylogenetic comparative methods. Most morphological variation was
 concentrated in condylar, coronoid and angular processes, and the
 diastema. Features potentially advantageous for digging (i.e. high
 coronoid and condylar processes, relatively short angular process and
 diastema) were present only in octodontoids; cavioids showed opposite
 trends, which could represent a structural constraint for fossorial
 habits. Chinchilloids showed intermediate features. Genera distributed in
 the morphospace according to their classification into superfamilial
 clades. Phylogenetic signal for shape components was significant along
 phylogeny, while the relationship between mandibular shape and ecology was
 non significant when phylogenetic structure was taken into account. An
 early evolutionary divergence in the mandible shape among major caviomorph
 clades would explain the observed strong phylogenetic influence on the
 variation of this structure.
description: LandmarkDatabaseTwo dimensional coordinates (consensus for each caviomorph genera) for landmarks dataset (L). Data file was generated using tpsDig 2.12 (Rohlf, 2008. Available at: http://life.bio.sunysb.edu/morph/).LandmarkSemilandmarkDatabasetwo-dimensional coordinates (consensus for each caviomorph genera) for landmarks plus semilandmarks dataset (SL). Data file was generated using tpsDig 2.12 (Rohlf, 2008. Available at: http://life.bio.sunysb.edu/morph/)RWLandmarkRW scores (for each caviomorph genera) obtained through a Generalized Procrustes Analysis of the landmark dataset (L). Archive format: .nts. Data generated using tpsRelW 1.46 (Rohlf, 2008. Available at: http://life.bio.sunysb.edu/morph/)RWLandmarkSemilandmarkRW scores (for each caviomorph genera) obtained through a Generalized Procrustes Analysis of the landmarks plus semilandmarks dataset (SL). Archive format: .nts. Semilandmarks were slid using a minimum bending energy criterion with 5 iterations. Data generated using tpsRelW 1.46 (Rohlf, 2008. Available at: http://life.bio.sunysb.edu/morph/)
DOI: 10.5061/dryad.7tm53
title: Data from: Corticosterone: effects on feather quality and deposition into feathers

description: 1. The concentration of the glucocorticoid hormone corticosterone (CORT)
 is increasingly used in ecology and conservation biology as an integrated
 measure of the historical record of an individual's
 hypothalamo-pituitary-adrenal (HPA) activity during feather growth.
 However, where and how CORT is incorporated in feathers is incompletely
 known. 2. We therefore examined whether CORT is reliably measured with an
 enzyme immunoassay, where CORT is incorporated in the feather and where it
 affects feather quality, and whether CORT incorporation is related to
 plasma CORT levels, feather growth rate and melanin pigmentation. 3.
 During regrowth of plucked tail feathers, we injected pigeons with
 tritium-labelled CORT, and implanted a CORT-releasing pellet to increase
 plasma CORT concentration for about three days. In feather segments we
 measured labelled CORT (DPM3H) and we quantified CORT with an enzyme
 immunoassay EIA (CORTEIA) and double-checked the results with ultra-high
 performance liquid chromatography-tandem mass spectrometry (LCMS)
 (CORTMS). 4. Administered CORT affected feather structure and colour at
 the very base of the feather (epidermal collar, ramogenic zone) and
 reduced growth rate. In contrast, incorporation of CORT into the feather
 happened mainly in the blood quill, as shown with all three methods
 (DPM3H, CORTEIA, and CORTMS). 5. Incorporation of CORT into feathers was
 only roughly proportional to plasma concentration, proportional to
 feather-growth rate and increased with melanin pigmentation. 6. Measuring
 CORT in feather is a way to reveal past events of increased stress during
 feather growth in birds.
description: FeatherCort for
 Dryad
DOI: 10.5061/dryad.177q4
title: Data from: Species-habitat relationships and ecological correlates of butterfly abundance in a transformed tropical landscape

description: Tropical butterfly conservation strategies often focus on total and/or
 common species richness to assess the conservation value of a patch or
 habitat. However, such a strategy overlooks the unique dynamics of rare
 species. We evaluated the species-habitat relationships of 209 common,
 intermediate, and rare butterfly species (including morphospecies) across
 four habitat types (mature, degraded, or fragmented forest, and urban
 parks) and two patch sizes (&lt;400 ha, ≥400 ha) in Singapore. Common
 species richness was consistent across habitat types. Intermediate species
 richness declined by more than 50 percent in urban parks (relative to all
 forest habitats), and rare species richness was reduced by 50 percent in
 degraded and fragmented forest and by 90 percent in urban parks (relative
 to mature forest). Large patches had comparable overall richness to small
 patches, but they supported more rare species and three times as many
 habitat-restricted species over a similar area. Importantly, a number of
 rare species were confined to single small patches. Mixed-effects
 regression models were constructed to identify habitat and ecological/life
 history variables associated with butterfly abundance. These models
 revealed that species with greater habitat specialization, rare larval
 host plants, few larval host plant genera, and narrow global geographic
 ranges were more likely to be rare species. Overall, these results
 demonstrate that the richness of habitat-restricted and rare species do
 not follow the same spatial distribution patterns as common species.
 Therefore, while conserving mature forests is key, effective butterfly
 conservation in a transformed landscape should take into account rare and
 habitat-restricted species.
description: Butterfly abundance
 across sitesThis file lists the
 butterfly abundance across 22 sites used in this study. Transect data at
 each site has been lumped together in the attached file and the total
 butterfly species abundance at each site has been presented. See further
 instructions in the excel file.Jain_etal_2016_Butterfly
 abundance across sites_22Dec2016.xlsx
DOI: 10.5061/dryad.478f5
title: Data from: The time of origin and genetic diversity of three isolated Kokanee populations in southwest Alaska

description: We examined the time of origin and genetic diversity of native kokanee,
 the nonanadromous ecotype of Sockeye Salmon Oncorhynchus nerka, from three
 isolated lakes in the Katmai National Park and Preserve in southwest
 Alaska. These kokanee evolved independently from Sockeye Salmon when
 migration barriers arose, blocking ocean access. We used information about
 the relative age of each barrier to hypothesize the relative time of
 origin for kokanee in each lake. In addition, we used data from 13
 microsatellite loci to test our time of origin hypotheses and assess
 genetic diversity of kokanee from these three lakes and proximate Sockeye
 Salmon populations. Coalescent-based estimates of the time of origin for
 kokanee in Jo-Jo Lake (170 years before present [ybp]) and Devil’s Cove
 Lake (6,583 ybp) were consistent with the relative age of barriers
 isolating each lake. However, data from Dakavak Lake (1,379 ybp) suggested
 that the barrier was older than hypothesized. Indices of intrapopulation
 diversity were lower for kokanee than for Sockeye Salmon. Estimates for
 kokanee population divergence (RST; the FST analog for microsatellites)
 among the three lakes were consistent with time of origin estimates.
 Furthermore, the most recently isolated kokanee (Jo-Jo Lake population)
 were most closely related to neighboring Sockeye Salmon. Only the kokanee
 from Jo-Jo Lake exhibited a relatively low historical effective population
 size (Ne ≈ 107) and evidence of a genetic bottleneck. Taken together, the
 results of this study show that although rare, kokanee in Alaska are not
 ephemeral and can persist in isolation for hundreds of generations despite
 the colder temperatures and shorter growing season, that are thought to
 limit their sustainability in Alaska.
description: KATM Kokanee and Sockeye
 Salmon genotypesGenotype data from 13
 microsatellite loci for Kokanee and Sockeye Salmon from the Katmai
 National Park and Preserve in southwest AlaskaKATM.DAT
DOI: 10.5061/dryad.v0cf2
title: Data from: Seasonality and locality affect the diversity of Anopheles gambiae and Anopheles coluzzii midgut microbiota from Ghana.

description: Symbiotic bacteria can have important implications in the development and
 competence of disease vectors. In Anopheles mosquitoes, the composition of
 the midgut microbiota is largely influenced by the larval breeding site,
 but the exact factors shaping this composition are currently unknown.
 Here, we examined whether the proximity to urban areas and seasons have an
 impact on the midgut microbial community of the two major malaria vectors
 in Africa, An. coluzzii and An. gambiae. Larvae and pupae were collected
 from selected habitats in two districts of Ghana during the dry and rainy
 season periods. The midgut microbiota of adults that emerged from these
 collections was determined by 454-pyrosequencing of the 16S ribosomal DNA.
 We show that in both mosquito species, Shewanellaceae constituted on
 average of 54% and 73% of the midgut microbiota from each site in the dry
 and rainy season, respectively. Enterobacteriaceae was found in
 comparatively low abundance below 1% in 22/30 samples in the dry season,
 and in 25/38 samples in the rainy season. Our data indicate that
 seasonality and locality significantly affect both the diversity of
 microbiota and the relative abundance of bacterial families with a
 positive impact of dry season and peri-urban settings.
description: Multiple aligned OTU
 sequences associated with midgut microbiota of Anopheles mosquitoes
 sampled from GhanaData file included the
 following information: Operational Taxonomic Unit (OTU) name;Bacterial
 taxon assigned to OTU;Mosquito species associated with the OTU;Status of
 collection site from with the mosquito samples were collected;Season
 during which mosquito samples were collected.Akorli,J_2016_OTUs.txt
DOI: 10.5061/dryad.m3752
title: Data from: Wolbachia increases susceptibility to Plasmodium infection in a natural system

description: Current views about the impact of Wolbachia on Plasmodium infections are
 almost entirely based on data regarding artificially transfected
 mosquitoes. This work has shown that Wolbachia reduces the intensity of
 Plasmodium infections in mosquitoes, raising the exciting possibility of
 using Wolbachia to control or limit the spread of malaria. Whether natural
 Wolbachia infections have the same parasite-inhibiting properties is not
 yet clear. Wolbachia–mosquito combinations with a long evolutionary
 history are, however, key for understanding what may happen with
 Wolbachia-transfected mosquitoes after several generations of coevolution.
 We investigate this issue using an entirely natural
 mosquito–Wolbachia–Plasmodium combination. In contrast to most previous
 studies, which have been centred on the quantification of the midgut
 stages of Plasmodium, we obtain a measurement of parasitaemia that relates
 directly to transmission by following infections to the salivary gland
 stages. We show that Wolbachia increases the susceptibility of Culex
 pipiens mosquitoes to Plasmodium relictum, significantly increasing the
 prevalence of salivary gland stage infections. This effect is independent
 of the density of Wolbachia in the mosquito. These results suggest that
 naturally Wolbachia-infected mosquitoes may, in fact, be better vectors of
 malaria than Wolbachia-free ones.
description: Zélé et al. Full dataset
 Proc. R. Soc. B 2014Zele et al - complete
 dataset.pdf
DOI: 10.5061/dryad.512
title: Data from: Networks, trees, and treeshrews: assessing support and identifying conflict with multiple loci and a problematic root

description: Multiple unlinked genetic loci often provide a more comprehensive picture
 of evolutionary history than any single gene can, but analyzing multigene
 data presents particular challenges. Differing rates and patterns of
 nucleotide substitution, combined with the limited information available
 in any data set, can make it difficult to specify a model of evolution. In
 addition, conflict among loci can be the result of real differences in
 evolutionary process or of stochastic variance and errors in
 reconstruction. We used 6 presumably unlinked nuclear loci to investigate
 relationships within the mammalian family Tupaiidae (Scandentia),
 containing all but one of the extant tupaiid genera. We used a
 phylogenetic mixture model to analyze the concatenated data and compared
 this with results using partitioned models. We found that more complex
 models were not necessarily preferred under tests using Bayes factors and
 that model complexity affected both tree length and parameter variance. We
 also compared the results of single-gene and multigene analyses and used
 splits networks to analyze the source and degree of conflict among genes.
 Networks can show specific relationships that are inconsistent with each
 other; these conflicting and minority relationships, which are implicitly
 ignored or collapsed by traditional consensus methods, can be useful in
 identifying the underlying causes of topological uncertainty. In our data,
 conflict is concentrated around particular relationships, not widespread
 throughout the tree. This pattern is further clarified by considering
 conflict surrounding the root separately from conflict within the ingroup.
 Uncertainty in rooting may be because of the apparent evolutionary
 distance separating these genera and our outgroup, the tupaiid genus
 Dendrogale. Unlike a previous mitochondrial study, these nuclear data
 strongly suggest that the genus Tupaia is not monophyletic with respect to
 the monotypic Urogale, even when uncertainty about rooting is taken into
 account. These data concur with mitochondrial DNA on other relationships,
 including the close affinity of Tupaia tana with the enigmatic Tupaia
 splendidula and of Tupaia belangeri with Tupaia glis. We also discuss the
 taxonomic and biogeographic implications of these results.
description: Roberts et al Data Set
 1Combined Data
 SetRoberts_et_al_data.nexRoberts et al Data Set 2Figure 5A, SplitsTree network fileroberts_et_al_fig5a_splitstree.nexRoberts et al Data Set 3Figure 5B, SplitsTree network file, no outgrouproberts_et_al_fig5b_splitstree_no_outgroup.nexSpecimensspecimens.txt
DOI: 10.5061/dryad.5g76b10
title: Data from: Ecology can inform genetics: disassortative mating contributes to MHC polymorphism in Leach’s storm-petrels (Oceanodroma leucorhoa)

description: Studies of MHC-based mate choice in wild populations generally test
 hypotheses by assuming female choice and male-male competition, whether or
 not mate choice dynamics have been previously determined for the species
 under study. Here we examined mate choice patterns in a small
 burrow-nesting seabird, the Leach’s storm-petrel (Oceanodroma leucorhoa),
 using the Major Histocompatibility Complex (MHC). The life history and
 ecology of this species is extreme: both partners work together to fledge
 a single chick during the breeding season, a task that requires regularly
 traveling hundreds of kilometers to and from foraging grounds over a six
 to eight-week provisioning period. Using a five-year dataset unprecedented
 for this species (n=1027 adults and 925 chicks), we found a positive
 relationship between variation in female reproductive quality and
 heterozygosity at Ocle-DAB2, a MHC class IIB locus. Contrary to previous
 reports rejecting disassortative mating as a mechanism for maintaining
 genetic polymorphism in this species, here we show that males make
 significant disassortative mate choice decisions. Variability in female
 reproductive success suggests that the most common homozygous females
 (Ocle-DAB201 / Ocle-DAB201) may be physiologically disadvantaged and,
 therefore, less preferred as lifelong partners for choosy males. The
 results from this study support the role of mate choice in maintaining
 high levels of MHC variability in a wild seabird species, and highlights
 the need to incorporate a broader ecological framework and sufficient
 sample sizes into studies of MHC-based mating patterns in wild populations
 in general.
description: Confirmed_Breeding_Pairs_GenotypesFile contains genotypes for DAB1 and DAB2 MHC alleles, for all established breeding pairs identified between 2010-2015. Female allele IDs are listed in columns FDAB1.1 : FDAB2.2; males in MDAB1.1 : MDAB2.2.DAB1_Amino_Acid_MatrixNumber of amino acid substitutions between Ocle-DAB1 MHC allele pairings.DAB2_Amino_Acid_MatrixNumber of amino acid substitutions between Ocle-DAB2 allele pairings.Adult_morphometric_dataYear, mass, tarsus length, wing chord, for adults used in morphometrics*genotype analysesHatch datesVetted hatch dates for chicks 2011-2015, within +- 3 days.Hatch_dates.txtMHC genotypes and reproductive successOcle-DAB1 and Ocle-DAB2 MHC genotypes for all adults in sampled background population (breeders and non-breeders), with number of chicks each individual has produced.All_adults_MHC_genotypes.txt
DOI: 10.5061/dryad.30nj0tb
title: Data from: Short-term, low-level nitrogen deposition dampens a trophic cascade between bears and plants

description: Human activities have substantially increased atmospheric nitrogen (N)
 deposition in ecosystems worldwide, often leading to higher plant quality
 for herbivores and greater herbivory. Predators frequently suppress
 herbivores and indirectly benefit plants via ‘trophic cascades’, and the
 strength of these interactions can also depend on N availability. However,
 the evidence for N deposition effects on cascades primarily comes from
 studies of high-level N deposition. Most terrestrial ecosystems currently
 receive elevated, but low-level N deposition, and it is unclear whether
 this subtle N enrichment has any effect on cascades. Here, I asked whether
 low-level N deposition alters a trophic cascade from black bears to plants
 in Colorado. In this ecological network, bears indirectly benefit plants
 by consuming ants and suppressing positive effects of ants on herbivores.
 Using a three year N enrichment experiment, I assessed changes in this
 cascade by measuring plant and arthropod responses to simulated N
 deposition, bear damage to ant nests, and the presence of mutualist
 herbivores and ants. I found that low-level N enrichment and bears had
 interacting effects on plant reproduction. In ambient N conditions, bears
 indirectly increased plant reproduction by causing ant nests to become
 inactive and suppressing positive ant effects on herbivores that were
 detrimental for plants. Yet, bear-induced ant nest inactivity had no
 effect on plant reproduction in N-enriched conditions. When N was added,
 ants had greater positive effects on herbivores, but herbivores had weak
 effects on plants, potentially because plants were more resistant to
 herbivores. Ultimately, the results indicate that N enrichment
 strengthened resource control of the community and weakened
 plant-herbivore interactions and the cascade from bears to plants. This
 study suggests that common rates of low-level N deposition are changing
 the strength of trophic cascades and may have already altered resource vs.
 consumer control of ecological community structure in many ecosystems.
description: Plant&Insect_Data_Grinath_2018_E&E.csvData for plant-insect communities evaluated by Grinath (2018).