cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28395155.v1
title: <b>Biomarkers of glycolysis and tricarboxylic acid (TCA) cycle in youth with and without obesity</b>

description: Given the rising prevalence of childhood obesity, it is critical to understand the metabolic consequences of excess adiposity in youth. In particular, investigating alterations in glycolysis and the tricarboxylic acid (TCA) cycle in youth with obesity is essential for elucidating the underlying mechanisms contributing to metabolic dysregulation in this population.Forty-eight adolescents and young adults aged 15-24 years had plasma obtained after a 12-hour fasting to measure levels of glucose, insulin, and TCA cycle intermediates: pyruvate, lactate, fumarate, malate, α-ketoglutarate, cis/trans aconitate, and isocitrate. Additionally, participants underwent an assessment of liver proton-density fat fraction (PDFF) and a 3-hour oral glucose tolerance test (OGTT).Nineteen youth without obesity (BMI 21.5 ± 0.5 kg/m<sup>2</sup>) and twenty-nine youth with obesity (BMI 37.3 ± 1.7 kg/m<sup>2</sup>) were enrolled in the study. Youth with obesity showed higher plasma concentrations of lactate (P=0.015) and pyruvate (P=0.096) and lower plasma concentrations of fumarate (P=0.022), malate (P=0.009), cis/trans aconitate (P=0.03), and citrate/isocitrate (P=0.012). PDFF was directly correlated with lactate (r=0.46, P=0.027). Adipose tissue insulin resistance was not associated with biomarkers of glycolysis. The metabolomic analysis revealed distinct characteristics between adolescents with and without obesity, thus demonstrating lower rates of aerobic glucose utilization in youth with obesity, which may contribute to the development of insulin resistance, type 2 diabetes, and cardiovascular disease.
DOI: 10.15493/obsdb.0000.0318
title: Salinity - Subsurface, Actual, Practical Salinity Unit for Estuaries, Multiparameter Meters, Kariega Estuary, Kariega Salinity 11 between 2.89m and 0.00m below sea level from 2021-02-05 to 2026-01-13

description: Salinity - Subsurface, Actual, Practical Salinity Unit for Estuaries, Multiparameter Meters, Kariega Estuary, Kariega Salinity 11 between 2.89m and 0.00m below sea level from 2021-02-05T11:48:23+02:00 to 2026-01-13T11:17:53+02:00 at -33.632800,26.643410 (+N-S,-W+E)
DOI: 10.15493/obsdb.0000.0350
title: Oxygen - Dissolved Oxygen Saturation, Actual, Percent for Estuaries, Multiparameter Meters, Kariega Estuary, Kariega Salinity 19 between 2.34m and 0.00m below sea level from 2021-02-05 to 2026-01-13

description: Oxygen - Dissolved Oxygen Saturation, Actual, Percent for Estuaries, Multiparameter Meters, Kariega Estuary, Kariega Salinity 19 between 2.34m and 0.00m below sea level from 2021-02-05T10:53:39+02:00 to 2026-01-13T10:56:21+02:00 at -33.616510,26.650560 (+N-S,-W+E)
DOI: 10.15493/obsdb.0000.02de
title: Oxygen - Dissolved Oxygen, Actual, Milligrams per liter for Estuaries, Multiparameter Meters, Kariega Estuary, Kariega Salinity 03 between 7.03m and 0.00m below sea level from 2021-02-05 to 2026-01-13

description: Oxygen - Dissolved Oxygen, Actual, Milligrams per liter for Estuaries, Multiparameter Meters, Kariega Estuary, Kariega Salinity 03 between 7.03m and 0.00m below sea level from 2021-02-05T12:28:59+02:00 to 2026-01-13T11:41:41+02:00 at -33.669080,26.672500 (+N-S,-W+E)
DOI: 10.15493/obsdb.0000.02fd
title: Inorganic Carbon - pH, Actual, Potential of Hydrogen for Estuaries, Multiparameter Meters, Kariega Estuary, Kariega Salinity 08 between 3.80m and 0.00m below sea level from 2021-02-05 to 2026-01-13

description: Inorganic Carbon - pH, Actual, Potential of Hydrogen for Estuaries, Multiparameter Meters, Kariega Estuary, Kariega Salinity 08 between 3.80m and 0.00m below sea level from 2021-02-05T12:02:59+02:00 to 2026-01-13T11:26:07+02:00 at -33.648520,26.646100 (+N-S,-W+E)
DOI: 10.5061/dryad.0jh5p
title: Data from: Decision making for mitigating wildlife diseases: from theory to practice for an emerging fungal pathogen of amphibians

description: 1.Conservation science can be most effective in its decision-support role
 when seeking answers to clearly formulated questions of direct management
 relevance. Emerging wildlife diseases, a driver of global biodiversity
 loss, illustrate the challenges of performing this role: in spite of
 considerable research, successful disease mitigation is uncommon. Decision
 analysis is increasingly advocated to guide mitigation planning, but its
 application remains rare. 2.Using an integral projection model, we
 explored potential mitigation actions for avoiding population declines and
 the ongoing spatial spread of the fungus Batrachochytrium salamandrivorans
 (Bsal). This fungus has recently caused severe amphibian declines in
 north-western Europe and currently threatens Palearctic salamander
 diversity. 3.Available evidence suggests that a Bsal outbreak in a fire
 salamander (Salamandra salamandra) population will lead to its rapid
 extirpation. Treatments such as antifungals or probiotics would need to
 effectively interrupt transmission (reduce probability of infection by
 nearly 90%) in order to reduce the risk of host extirpation and
 successfully eradicate the pathogen. 4.Improving the survival of infected
 hosts is most likely to be detrimental as it increases the potential for
 pathogen transmission and spread. Active removal of a large proportion of
 the host population has some potential to locally eradicate Bsal and
 interrupt its spread, depending on the presence of Bsal reservoirs and on
 the host's spatial dynamics, which should therefore represent
 research priorities. 5.Synthesis and applications. Mitigation of
 Batrachochytrium salamandrivorans epidemics in susceptible host species is
 highly challenging, requiring effective interruption of transmission and
 radical removal of host individuals. More generally, our study illustrates
 the advantages of framing conservation science directly in the management
 decision context, rather than adapting to it a posteriori.
description: Canessa_JAPPL_2017_00978_SI2Full set of random values used for integral projection model simulations (parameter distributions).
DOI: 10.15493/obsdb.0000.02d9
title: Turbidity, Actual, Formazin Nephelometric Unit for Estuaries, Multiparameter Meters, Kariega Estuary, Kariega Salinity 02 between 6.90m and 0.01m below sea level from 2021-02-05 to 2026-01-13

description: Turbidity, Actual, Formazin Nephelometric Unit for Estuaries, Multiparameter Meters, Kariega Estuary, Kariega Salinity 02 between 6.90m and 0.01m below sea level from 2021-02-05T12:34:15+02:00 to 2026-01-13T11:44:38+02:00 in area -33.675040,26.675640 (N,W) -33.679780,26.680400 (S,E) (+N-S,-W+E)
DOI: 10.5061/dryad.fn07jg1
title: Data from: Sperm divergence in a passerine contact zone: indication of reinforcement at the gametic level

description: Postcopulatory sexual selection may promote evolutionary diversification
 in sperm form, but the contribution of between-species divergence in sperm
 morphology to the origin of reproductive isolation and speciation remains
 little understood. To assess the possible role of sperm diversification in
 reproductive isolation, we studied sperm morphology in two closely related
 species, the common nightingale (Luscinia megarhynchos) and the thrush
 nightingale (L. luscinia), that hybridize in a secondary contact zone
 spanning Central and Eastern Europe. We found: (1) striking divergence
 between the species in total sperm length, accompanied by a difference in
 the length of the mitochondrial sperm component; (2) greater divergence
 between species in sperm morphology in sympatry than in allopatry, with
 evidence for character displacement in sperm head length detected in L.
 megarhynchos; (3) interspecific hybrids showing sperm with a length
 intermediate between the parental species, but no evidence for decreased
 sperm quality (the proportion of abnormal spermatozoa in ejaculates). Our
 results demonstrate that divergence in sperm morphology between the two
 nightingale species does not result in intrinsic postzygotic isolation,
 but may contribute to postcopulatory prezygotic isolation. This isolation
 could be strengthened in sympatry by reinforcement.
description: data_Albrecht_et_alData file containing three sheets - raw sperm data, sperm abnormality data and data used to calculate measurement repeatability
DOI: 10.5061/dryad.787d9
title: Data from: Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika

description: We obtained 398 cytochrome c oxidase subunit I barcodes of 96
 morphospecies of Lake Tanganyika (LT) cichlids from the littoral zone. The
 potential of DNA barcoding in these fishes was tested using both species
 identification and species delineation methods. The best match (BM) and
 best close match (BCM) methods were used to evaluate the overall
 identification success. For this, three libraries were analysed in which
 the specimens were categorized into Operational Taxonomic Units (OTU) in
 three alternative ways: (A) morphologically distinct, including
 undescribed, species, (B) valid species and (C) complexes of
 morphologically similar or closely related species. For libraries A, B and
 C, 73, 73 and 96% (BM) and 72, 70 and 94% (BCM) of the specimens were
 correctly identified. Additionally, the potential of two species
 delineation methods was tested. The General Mixed Yule Coalescent (GMYC)
 analysis suggested 70 hypothetical species, while the Automatic Barcode
 Gap Discovery (ABGD) method revealed 115 putative species. Although the
 ABGD method had a tendency to oversplit, it outperformed the GMYC analysis
 in retrieving the species. In most cases where ABGD suggested
 oversplitting, this was due to intraspecific geographical variation. The
 failure of the GMYC method to retrieve many species could be attributed to
 discrepancies between mitochondrial gene trees and the evolutionary
 histories of LT cichlid species. Littoral LT cichlids have complex
 evolutionary histories that include instances of hybridization,
 introgression and rapid speciation. Nevertheless, although the utility of
 DNA barcoding in identification is restricted to the level of complexes,
 it has potential for species discovery in cichlid radiations.
description: DNA sequence
 assemblyDNA sequence assembly
 used for the analyses, unique haplotypes (H001-H228) as in the
 phylogenetic tree (LTC.con). The two outgroup sequences (H227, H228) where
 only used for phylogeny reconstruction but not for the different species
 delineation and identification methods.barcodes_LTC.fasPhylogenetic treeBaysian Inference (BI) phylogenetic tree used for the ABGD method.LTC.con
DOI: 10.5061/dryad.2j8jr
title: Data from: Analysis of the karyotype structure in Ricolla quadrispinosa (Linneus, 1767): inferences about the chromosomal evolution of the tribes of Harpactorinae (Heteroptera, Reduviidae)

description: The subfamily Harpactorinae is composed of six tribes. Phylogenetic
 studies bring together some of Harpactorinae tribes, but by and large the
 data on evolutionary relationships of the subfamily are scarce. Chromosome
 studies are of great importance for understanding the systematics of
 different groups of insects. For Harpactorinae, these studies are
 restricted to some subfamilies and involved only conventional chromosome
 analysis. This work analyzed cytogenetically Ricolla quadrispinosa
 (Linneus, 1767). The chromosome number was determined as 2n = 24 + X1X2Y
 in males. In metaphase II the autosomal chromosomes were organized in a
 ring with the pseudo-trivalent of sex chromosomes in its center. After
 C-banding followed by staining with DAPI, AT-rich blocks in autosomes were
 observed and the negatively heteropycnotic sex chromosomes. The data
 obtained, together with existing data for other species of the group,
 indicated that different chromosomal rearrangements are involved in the
 evolution of the species. In addition, a proposal of karyotype evolution
 for the subfamily, based on existing phylogenetic studies for the group is
 presented.
description: Chromsomal
 AnalysisFigures with results of
 chromosomal analysis
DOI: 10.5061/dryad.45gg6
title: Data from: Carry-over effects of conditions at the wintering grounds on breeding plumage signals in a migratory bird: roles of phenotypic plasticity and selection

description: To understand the consequences of ever-changing environment on the
 dynamics of phenotypic traits, distinguishing between selection processes
 and individual plasticity is crucial. We examined individual
 consistency/plasticity in several male secondary sexual traits expressed
 during the breeding season (white wing and forehead patch size, UV
 reflectance of white wing patch and dorsal melanin colouration) in a
 migratory pied flycatcher (Ficedula hypoleuca) population over an 11-year
 period. Furthermore, we studied carry-over effects of three environmental
 variables (NAO, a climatic index; NDVI, a vegetation index; and rainfall)
 at the wintering grounds (during pre-breeding moult) on the expression of
 these breeding plumage traits of pied flycatcher males at individual- and
 population-levels. While NAO correlates negatively with moisture in West
 Africa, NDVI correlates positively with primary production. Forehead patch
 size and melanin colouration were highly consistent within individuals
 among years, while the consistency of the other two traits was moderate.
 Wing patch size decreased with higher NAO and increased with higher
 rainfall and NDVI at the individual-level. Interestingly, small-patched
 males suffered lower survival during high NAO winters than large-patched
 males, and vice versa during low NAO winters. These counteracting
 processes meant that the individual-level change was masked at the
 population-level where no relationship was found. Our results provide a
 good example of how variation in the phenotypic composition of a natural
 population can be a result of both environment-dependent individual
 plasticity and short-term microevolution. Moreover, when plasticity and
 viability selection operate simultaneously, their impacts on population
 composition may not be evident.
description: Järvistö_et_al_Data_2016_5_5The data set is composed of one excel file with two data sheets. One sheet is for population level analyses and the other one is for individual level analysis. Data includes environmental variables (winter NAO, NDVI and rainfall) describing environmental conditions at the wintering areas of pied flycatchers in Sub-Saharan Africa (2004-2014) and phenotypic (dorsal blackness, UV reflection, wing patch, forehead patch, tail patch) information of male pied flycatcher individuals caught during the breeding seasons (2004-2014) in Turku, Finland.
DOI: 10.5061/dryad.q5p7g
title: Data from: Sharp acoustic boundaries across an altitudinal avian hybrid zone despite asymmetric introgression

description: Birdsong is a sexually selected trait that could play an important
 evolutionary role when related taxa come into secondary contact. Many
 songbird species however learn their songs through copying one or more
 tutors, which complicates the evolutionary outcome of such contact. Two
 subspecies of a presumed vocal learner, the grey-breasted wood-wren
 (Henicorhina leucophrys), replace each other altitudinally across the
 western slope of the Ecuadorian Andes. These subspecies are
 morphologically very similar, but show striking differences in their song.
 We examined variation in acoustic traits and genetic composition across
 the altitudinal range covered by both subspecies and between two
 allopatric populations. The acoustic boundary between the subspecies was
 found to be highly abrupt across a narrow elevational range with virtually
 no evidence of song convergence. Mixed singing and use of
 hetero-subspecific song occurred in the contact zone and was biased
 towards the use of leucophrys song types. Hetero-subspecific song copying
 by hilaris and not by leucophrys reflected a previously found asymmetric
 pattern of response to song playback. Using AFLP markers, we detected
 hybridization in the contact zone and asymmetric introgression in
 parapatric populations, with more leucophrys alleles present in hilaris
 populations than vice versa. This pattern may be a trail of introgression
 due to upslope displacement of leucophrys by hilaris. Our data suggest
 that song learning may impact speciation and hybridization in contrasting
 ways at different spatial scales: while learning may speed up population
 divergence in songs, thereby enhancing assortative mating and reducing
 gene flow, it may at a local level also lead to the copying of
 heterospecific songs, therefore allowing some level of hybridization and
 introgression.
description: Song-measurements_Dryadfile containing all song measurements. For each individual bird we recorded several song types. We obtained 22 acoustic measurements for each song type. We analysed three renditions of the same song type per bird and data presented here is averaged over these song types.
DOI: 10.5061/dryad.mf1qf
title: Data from: Similarities and differences in altitudinal versus latitudinal variation for morphological traits in Drosophila melanogaster

description: Understanding how natural environments shape phenotypic variation is a
 major aim in evolutionary biology. Here, we have examined clinal, likely
 genetically-based variation in morphology among 19 populations of the
 fruit fly (Drosophila melanogaster) from Africa and Europe, spanning a
 range from sea level to 3000 m altitude and including locations
 approximating the southern and northern range limit. We were interested in
 testing whether latitude and altitude have similar phenotypic effects, as
 has often been postulated. Both latitude and altitude were positively
 correlated with wing area, ovariole number and cell number. In contrast,
 latitude and altitude had opposite effects on the ratio between ovariole
 number and body size, which was negatively correlated with egg production
 rate per ovariole. We also used transgenic manipulation to examine how
 increased cell number affects morphology and found that larger transgenic
 flies, due to a higher number of cells, had more ovarioles, larger wings
 and, unlike flies from natural populations, increased wing loading. Clinal
 patterns in morphology are thus not a simple function of changes in body
 size; instead, each trait might be subject to different selection
 pressures. Together, our results provide compelling evidence for profound
 similarities as well as differences between phenotypic effects of latitude
 and altitude.
description: Raw
 dataData_Klepsatel et
 al.xls
DOI: 10.5061/dryad.h0f41
title: Data from: Additional information on the primitive contour and wing feathering of paravian dinosaurs

description: Identifying feather morphology in extinct dinosaurs is challenging due to
 dense overlapping of filaments within fossilized plumage and the fact that
 some extinct feather morphologies are unlike those of extant birds or
 those predicted from an ‘evo-devo’ model of feather evolution. Here, we
 compare a range of dinosaur taxa with preserved integumentary appendages
 using high-resolution photographs to better understand fossil feather
 morphology and gain insight into their function and evolution. A specimen
 of the basal paravian Anchiornis possesses contour feathers disarticulated
 from the plumage, revealing a novel feather type: a ‘shaggy’, open-vaned,
 bifurcated feather with long barbs attached to a short rachis, which is
 much simpler than the contour feathers of most extant birds. In contrast,
 it is likely that the contour feathers of Sinosauropteryx were simpler
 than those seen in Anchiornis; a ‘tuft’ morphology of multiple barbs
 connected at their bases (e.g. via a shared follicle), but lacking a
 rachis, is tentatively inferred. However, conclusive morphological
 descriptions await the discovery of isolated Sinosauropteryx contour
 feathers. Paravian wing feathers also show potentially plesiomorphic
 traits. Comparison with Confuciusornis suggests that Anchiornis wing
 feathers were at least partially open-vaned. Combined with the
 interpretation of Anchiornis contour feathers, this suggests that
 differentiated barbicels are relatively derived compared to pennaceous
 feathers and the appearance of wings. ‘Shaggy’ contour feathers probably
 influenced thermoregulatory and water repellence abilities, and, in
 combination with open-vaned wing feathers, would have decreased
 aerodynamic efficiency. Simplified, open-vaned wing feathers were also
 observed on the oviraptorosaur Caudipteryx, consistent with, but not
 necessarily diagnostic of, its suggested flightlessness. Taken together,
 these observations have broad implications for how we depict a wide
 variety of dinosaurs and how we view the function and evolution of
 feathers.
description: S1Diagram showing how
 simple, non-branching filaments could result in the observed overlapping
 patterns seen in Sinosauropteryx. A, simple, non-branching filaments
 arranged in multiple, parallel tracts in vivo with some tracks more
 latero-ventral on the tail than others. B, filaments in A copied but where
 the area representing the flesh of the tail in vivo is not preserved. Only
 filaments dorsal to the tail are visible, as is mostly the case in such
 fossil specimens. Selective preservation of filaments dorsal to the
 vertebra gives the illusion of branching structures.S2Table of observations on
 Sinosauropteryx contour feathers and how they are expected support various
 plausible morphologies. Does the observation support a particular
 morphology? Y, yes. “?”, maybe or uncertain. N, no. Scoring system is
 arbitrary with Y=1, “?”=0.5, and N=0. Highest score is the tentatively
 preferred morphology.
DOI: 10.5061/dryad.h2j0n
title: Data from: Correlated evolution between climate and suites of traits along a fast-slow continuum in the radiation of Protea

description: Evolutionary radiations are responsible for much of Earth’s diversity, yet
 the causes of these radiations are often elusive. Determining the relative
 roles of adaptation and geographic isolation in diversification is vital
 to understanding the causes of any radiation, and whether a radiation may
 be labeled as ‘adaptive’ or not. Across many groups of plants,
 trait-climate relationships suggest that traits are an important indicator
 of how plants adapt to different climates. In particular, analyses of
 plant functional traits in global databases suggest that there is an
 “economics spectrum” along which combinations of functional traits covary
 along a fast-slow continuum. We examine evolutionary associations among
 traits and between trait and climate variables on a strongly supported
 phylogeny in the iconic plant genus Protea to identify correlated
 evolution of functional traits and the climatic-niches that species
 occupy. Results indicate that trait diversification in Protea has climate
 associations along two axes of variation: correlated evolution of plant
 size with temperature and leaf investment with rainfall. Evidence suggests
 that traits and climatic-niches evolve in similar ways, although some of
 these associations are inconsistent with global patterns on a broader
 phylogenetic scale. When combined with previous experimental work
 suggesting that trait-climate associations are adaptive in Protea, the
 results presented here suggest that trait diversification in this
 radiation is adaptive.
description: Protea_Trait_DataTrait data for all individuals used in this study.ProteaPhylogeniesPhylogenetic trees used in this study, including species trees from ASTRAL-II, SVDquartets, and RAxML, as well as 100 bootstrap trees from ASTRAL-II. Trees may also be found in the repository Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.; Mitchell N, Lewis PO, Lemmon EM, Lemmon AR, Holsinger KE; Date Published: January 20, 2017; https://doi.org/10.5061/dryad.vj32s