cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z612jm6bm
title: Phylogeny of African long-fingered frogs (Arthroleptidae: Cardioglossa) reveals recent allopatric divergences in coloration

description: The African anuran genus Cardioglossa contains 19 described species, most
 of which are distinguished from one another by striking patterns and
 colors. We present a well- resolved phylogeny based on analyses of
 mitochondrial and nuclear loci for 18 species of Cardioglossa. This
 provides the basis for species-delimitation analyses and interpreting
 historical biogeography in the genus. Whereas much of the diversification
 within the genus occurred among Central African lineages during the
 Miocene following the origin of Cardioglossa in the latest Oligocene or
 earliest Miocene, most species-pairs in the genus diverged more recently
 during the Plio-Pleistocene. The two most geographically peripheral
 species— C. cyaneospila in the Albertine Rift Mountains and C.
 occidentalis in the Upper Guinean Forests of West Africa—both diverged
 from other lineages during the mid-late Miocene. Because our analyses do
 not support C. manengouba and C. oreas as distinct species, we recognize
 these geographically separate and phenotypically distinct populations as
 subspecies of C. oreas that diverged subsequent to the origin of Mount
 Manengouba during the past 1.5 million years. In contrast, we find that C.
 leucomystax likely represents two species found in the Lower Guinean and
 Congolian forests, respectively. We find recent divergences between
 several allopatric lineages (either species or populations) that differ in
 coloration and pattern, including in C. nigromaculata which varies in
 color across its range in Central Africa and Bioko Island. These recent
 divergences among allopatric lineages with distinctive coloration and
 pattern raise new questions about the significance of these traits in this
 genus for which little is known of its natural history and biology.
description: The data files here are part of a multi-locaus molecular
 phylogenetic study of the African frog
 genus <em>Cardioglossa</em>. The data files include (1) a PHY
 file containing concatenated aligned DNA sequences that was analyzed in
 RAxML, (2) a file containing the partitions used in RAxML, (3) a NEX file
 containing concatenated aligned DNA sequences that was analyzed in MrBayes
 and containing the partition block for that analysis, (4) the resulting
 maximum likelihood phylogeny from RAxML, (5) the maximum clade credibility
 tree from analysis in MrBayes, (6) the maximum clade credibility tree from
 analysis in BEAST, and (7) the results of analysis in PartitionFinder to
 find the best partitioning scheme for these data. Last, Supplementary
 Table 1 from this study is also included to provide information on the
 samples and GenBank accession numbers from this study.
description: If you are using these files, please know that the
 genus <em>Cardioglossa</em> might just be the best anuran
 taxon in sub-Saharan Africa.
DOI: 10.5061/dryad.gmsbcc2mn
title: Genomic and fitness consequences of inbreeding in an endangered carnivore

description: Reduced fitness through genetic drift and inbreeding is a major threat to
 small and isolated populations. Although previous studies have generally
 used genetically verified pedigrees to document effects of inbreeding and
 gene flow, these often fail to capture the whole inbreeding history of the
 species. By assembling a draft arctic fox (Vulpes lagopus) genome and
 re-sequencing complete genomes of 23 additional foxes born before and
 after a well-documented immigration event in Scandinavia, we here look
 into the genomic consequences of inbreeding and genetic rescue. We found a
 difference in genome-wide diversity, with 18% higher heterozygosity and
 81% lower FROH in immigrant F1 compared to native individuals. However,
 more distant descendants of immigrants (F2, F3) did not show the same
 pattern. We also found that foxes with lower inbreeding had higher
 probability to survive their first year of life. Our results demonstrate
 the important link between genetic variation and fitness as well as the
 transient nature of genetic rescue. Moreover, our results have
 implications in conservation biology as they demonstrate that inbreeding
 depression can effectively be detected in the wild by a genomic approach.
DOI: 10.5061/dryad.j6q573nd4
title: Asymmetrical effects of temperature on stage-structured predator-prey interactions

description: Warming can impact consumer-resource interactions through multiple
 mechanisms. For example, warming can both alter the rate at which
 predators consume prey and the rate prey develop through vulnerable life
 stages. Thus, the overall effect of warming on consumer-resource
 interactions will depend upon the strength and asymmetry of warming
 effects on predator and prey performance. Here, we quantified the
 temperature dependence of both 1) density-dependent predation rates for
 two dragonfly nymph predators on a shared mosquito larval prey, via the
 functional response, and 2) the development rate of mosquito larval prey
 to a predator-invulnerable adult stage. We united the results of these two
 empirical studies using a temperature- and density-dependent
 stage-structured predation model. Warming accelerated both larval mosquito
 development and increased dragonfly consumption. Model simulations suggest
 that differences in the magnitude and rate of predator and prey responses
 to warming determined the change in magnitude of the overall effect of
 predation on prey survival to adulthood. Specifically, we found that
 depending on which predator species prey were exposed to in the model, the
 net effect of warming was either an overall reduction or no change in
 predation strength across a temperature gradient. Our results highlight a
 need for better mechanistic understanding of the differential effects of
 temperature on consumer-resource pairs to accurately predict how warming
 affects food web dynamics.
DOI: 10.5061/dryad.5mkkwh754
title: A simple expression for the strength of selection on recombination generated by interference among mutations

description: One of the most widely cited hypotheses to explain the evolutionary
 maintenance of genetic recombination states that the reshuffling of
 genotypes at meiosis increases the efficiency of natural selection by
 reducing interference among selected loci. However, and despite several
 decades of theoretical work, a quantitative estimation of the possible
 selective advantage of a mutant allele increasing chromosomal map length
 (the average number of crossovers at meiosis) remains difficult. This
 article derives a simple and accurate expression for the strength of
 selection acting on a modifier gene affecting the genetic map length of a
 whole chromosome or genome undergoing recurrent mutation. In particular,
 it shows that indirect selection for recombination caused by interference
 among mutations is proportional to (NeU)2 / (NeR)3, where Ne is the
 effective population size, U the deleterious mutation rate per chromosome
 and R the chromosome map length. Indirect selection is relatively
 insensitive to the fitness effects of deleterious alleles, epistasis, or
 the genetic architecture of recombination rate variation, andevolution of
 recombination, genetic architecture, genetic interference, meiosis,
 multilocus population genetics may compensate for substantial costs
 associated with recombination when linkage is tight. However, its effect
 generally stays weak in large, highly recombining populations.
DOI: 10.5061/dryad.qv9s4mwdc
title: Variable effects of mycorrhizal fungi on predator-prey dynamics under field conditions

description: 1. Interactions between herbivores and their predators are shaped, in
 part, by plant phenotype. Consequently, ubiquitous symbionts of plants
 belowground, such as arbuscular mycorrhizal fungi (AMF), may influence
 interactions aboveground between predators and their prey by altering
 plant phenotype. However, the ecological relevance of belowground
 organisms on predator-prey interactions under field conditions remains
 unclear. 2. We assessed how AMF influence herbivore-predator interactions
 through a field experiment. 3. We planted two milkweed species (Asclepias
 curassavica, A. incarnata) provided with different amounts of AMF inoculum
 (zero, medium, high) in a randomized block design. We added aphids to
 plants and reduced predator pressure weekly for five weeks to evaluate
 effects of AMF on predator recruitment. We then allowed herbivore-predator
 interactions to reestablish naturally for the remainder of the season to
 examine whether AMF-mediated variation in predator recruitment influenced
 the suppression of aphid populations. 4. AMF availability in soils
 mediated interactions between predaceous aphid midge flies (Aphidoletes
 aphidimyza) and their aphid prey (Aphis nerii), but effects were plant
 species-specific. On A. curassavica, by mid-season, midges were recruited
 most strongly on plants under medium AMF availability and least on plants
 under high AMF availability. In contrast, each midge killed fewer aphids
 with increasing aphid density on medium AMF plants, but killed more aphids
 with increasing aphid density on high AMF plants. In combination, aphid
 mortality rates imposed by midges were greatest on medium AMF plants,
 followed by high and zero AMF plants. By comparison, on A. incarnata, the
 recruitment of midges was strongest on high AMF plants and weakest on
 medium AMF plants. AMF had no effect on the number of aphids killed per
 midge, relative to aphid density, so mortality rates of aphids imposed by
 midges mirrored recruitment. Rates of decline in aphid populations
 following predator recolonization were associated with midge densities, as
 well as lacewing and syrphid densities, which were unaffected by AMF
 availability. Therefore, effects of AMF on aphid population decline were
 not a simple function of AMF-midge interactions. 5. Our findings
 demonstrate that the availability of AMF in soils has pervasive, but
 complex, effects on predator-herbivore dynamics in the field.
DOI: 10.5061/dryad.j6q573nd5
title: Season, anthocyanin supplementation, and flight training have mixed effects on the antioxidant system of migratory European starlings (Sturnus vulgaris)

description: Migratory birds engage in two periods of endurance flight annually as they
 travel between summer breeding and overwintering grounds, and such
 endurance flights likely incur oxidative costs. These costs may differ
 between fall and spring migration, especially for females who must prepare
 for breeding and egg laying in spring. The objective of this study of a
 migratory bird was to test proposed hypotheses about how key components of
 the female’s antioxidant system differ in response to flight training in
 the fall and spring and to dietary antioxidant supplementation. We
 hand-raised female European starlings (Sturnus vulgaris) and then fed them
 either a diet supplemented with dietary anthocyanins or a diet without
 added anthocyanins. We then flew females in a windtunnel for 15 days
 during fall and spring migration seasons and measured over time oxidative
 damage (d-ROMs) and three components of the antioxidant
 system—non-enzymatic antioxidant capacity (OXY), uric acid, and
 glutathione peroxidase (GPx) activity. Prior to flight training,
 non-enzymatic antioxidant capacity and oxidative damage were lower in
 females during spring compared to fall, and females fed a low-antioxidant
 diet had consistently higher circulating uric acid. GPx activity decreased
 more in spring immediately after a long-duration flight. Females fed a
 high-antioxidant diet had a greater decrease in non-enzymatic antioxidant
 capacity after the 15-day flight training. Flight-trained females had
 higher circulating uric acid than untrained females immediately after the
 longest-duration flight, and decreased GPx activity after the 15-day
 flight training. In sum, females upregulated enzymatic and non-enzymatic
 endogenous antioxidants in spring, and females fed a diet with less
 antioxidants appear to compensate by increasing circulating uric acid. Our
 findings emphasize the important role of dietary antioxidants for birds
 during migration, and that similar flights in fall and spring likely
 represent distinct oxidative challenges in the life history of female
 birds.
description: We fed female European
 Starlings diets with different quantities of anthocyanin, a dietary
 antioxidant, and then measured during both fall and spring migration
 periods how their antioxidant system responded to diet and two weeks of
 daily flight in a windtunnel. All analyses were conducted in R.
DOI: 10.5061/dryad.tx95x69x5
title: Decentralizing PrEP delivery: implementation and dissemination strategies to increase PrEP uptake among MSM in Toronto, Canada

description: Pre-exposure prophylaxis (PrEP) is traditionally prescribed by HIV
 specialist physicians. Given finite specialist resources, there is a need
 to scale up PrEP delivery by decentralizing services via other healthcare
 professionals. We aimed to assess the feasibility of delivering PrEP to
 men who have sex with men (MSM) through primary care physicians and sexual
 health clinic nurses. We piloted a multi-component, implementation and
 dissemination research program to increase provision of PrEP through
 primary care physicians and sexual health clinic nurses in Toronto,
 Canada. Community-based organizations (CBOs) provided prospective
 participants with information cards that contained links to an online
 module on engaging providers in a conversation about PrEP. In our
 patient-initiated continuing medical education (PICME) strategy,
 participants saw their family doctors and gave them the card, which also
 contained a link to a Continuing Medical Education module. In the
 nurse-led strategy, participants visited one of two participating clinics
 to obtain PrEP. We administered an optional online questionnaire to
 patients and providers at baseline and six months. CBOs distributed 3043
 cards. At least 339 men accessed the online module and 196 completed
 baseline questionnaires. Most (55%) intended to visit nurses while 21%
 intended to consult their physicians. Among 45 men completing follow-up
 questionnaires at 6 months, 31% reported bringing cards to their
 physicians and obtaining PrEP through them; sexual health clinics
 delivered PrEP to 244 patients. Participants who went through the PICME
 approach reported no changes in relationships with their providers. Nurses
 showed fidelity to PrEP prescribing guidelines. Nurse-led PrEP and
 patient-initiated continuing medical education (PICME) for primary care
 physicians are feasible strategies to increase PrEP uptake. Nurse-led PrEP
 delivery was preferred by most patients.
description: The methods for data collection can be found in the following
 articles: Sharma M, Chris A, Chan A, et al. Decentralizing the delivery of
 HIV pre-exposure prophylaxis (PrEP) through family physicians and sexual
 health clinic nurses: a dissemination and implementation study protocol.
 BMC Health Serv Res;18:513. doi:10.1186/s12913-018-3324-2; Charest M,
 Sharma M, Chris A, et al. Decentralizing PrEP delivery: Implementation and
 dissemination strategies to increase PrEP uptake in Toronto, Canada. PLOS
 ONE; in press.  Data were collected via an online
 survey platform. Participants who did not consent to the study or did not
 complete the questionnaire were removed from the dataset. Missing data
 were left as is and assigned a value of -99, which was an impossible value
 in our dataset. Participants' answers were initially textual (e.g.,
 very satisfied) and were assigned numeric values which are described in
 the ReadMe file.
DOI: 10.5061/dryad.tqjq2bvz6
title: Grasshoppers, other arthropods, plant, and soil data from Konza Prairie bison grazing lawns

description: 1. We contrast the response of arthropod abundance and composition to
 bison grazing lawns during a drought and non-drought year, with an
 emphasis on acridid grasshoppers, an important grassland herbivore. 2.
 Grazing lawns are grassland areas where regular grazing by mammalian
 herbivores creates patches of short-statured, high nutrient vegetation.
 Grazing lawns are predictable microsites that modify microclimate, plant
 structure, community composition, and nutrient availability, with likely
 repercussions for arthropod communities. 3. One year of our study occurred
 during an extreme drought. Drought mimics some of the effects of mammalian
 grazers: decreasing above-ground plant biomass while increasing plant
 foliar % nitrogen. 4. We sampled arthropods and nutrient availability on
 and nearby (“off”) ten bison-grazed grazing lawns in a tallgrass prairie
 in NE Kansas. Total grasshopper abundance was higher on grazing lawns and
 the magnitude of this difference increased in the wetter year of 2019
 compared to 2018, when drought led to high grass foliar nitrogen
 concentrations on and off grazing lawns. Mixed-feeding grasshopper
 abundances were consistently higher on grazing lawns while grass-feeder
 and forb-feeder abundances were higher on lawns only in 2019, the wetter
 year. In contrast, the abundance of other arthropods (e.g., Hemiptera,
 Hymenoptera, and Araneae) did not differ on and off lawns, but increased
 overall in 2019, relative to the drought of 2018. 5. Understanding these
 local scale patterns of abundances and community composition improves
 predictability of arthropod responses to ongoing habitat change.
description: Please refer to the article: Tracking nutrients in space and time:
 Interactions between grazing lawns and drought drive abundances of
 tallgrass prairie grasshoppers Katerina A. Ozment, Ellen A. R. Welti,
 Monica Shaffer, Michael Kaspari Ecology & Evolution
 2021
description: Please see meta-data tab for details.
DOI: 10.5061/dryad.63xsj3v1r
title: A systematic assessment of medical diagnoses preceding the first diagnosis of multiple sclerosis: Supplementary materials

description: Objective: To explore the occurrence of diseases and symptoms in the five
 years prior to diagnosis in patients with multiple sclerosis (MS) in a
 case-control study. Methods: Using ambulatory claims data we
 systematically assessed differences in the occurrence of diseases and
 symptoms in the five years prior to first diagnosis in patients with MS
 (n=10,262) as compared to patients with two other autoimmune diseases –
 Crohn’s disease (n=15,502) and psoriasis (n=98,432) - and individuals
 without these diseases (n=73,430). Results: Forty-three ICD-10 codes were
 recorded more frequently for patients with MS before diagnosis as compared
 to controls without autoimmune disease. Many of these findings were
 confirmed in a comparison to the other control groups. A high proportion
 of these ICD-10 codes represent symptoms suggestive of demyelinating
 events or other neurological diagnoses. In a sensitivity analysis
 excluding patients with such recordings prior to first diagnosis, no
 association remained significant. Seven ICD-10 codes were associated with
 lower odds ratios of MS, four of which represented upper respiratory tract
 infections. Here, the relations with MS were even more pronounced in the
 sensitivity analysis. Conclusions: Our analyses suggest that patients with
 MS are frequently not diagnosed at their first demyelinating event but
 often years later. Symptoms and physician encounters before MS diagnosis
 seem to be related to already ongoing disease rather than a prodrome. The
 observed association of upper respiratory tract infections with lower ORs
 of MS diagnosis suggests a link between protection from infection and MS
 that however needs to be validated and further investigated.
DOI: 10.5061/dryad.jq2bvq886
title: Fish and environmental variable data in mountain streams of the Ren River

description: The spatial-temporal patterns of fish assemblages in lotic systems can
 provide useful information in developing effective conservation measures.
 This study aimed to explore the spatial and seasonal changes in fish
 assemblages and their association with environmental factors in mountain
 streams of the Ren River, south-west China. Field investigations were
 conducted at 18 sites during the rainy and dry seasons in 2017. A total of
 1330 individuals, belonging to three orders, eight families, 19 genera and
 21 species, were collected. Analysis of similarities (ANOSIM) showed that
 the structure of fish assemblages varied significantly at the spatial
 scale, but not at the seasonal scale. In low order sites, fish assemblages
 were mainly dominated by cold water and rheophilic species (e.g.
 Rhynchocypris oxycephalus, Scaphesthes macrolepis, Metahomaloptera
 omeiensis and Gnathopogon herzensteini), while those in high order sites
 were predominated by warm water and eurytopic or stagnophilic species
 (e.g. Squalidus argentatus, Hemiculter leucisculus and Zacco platypus).
 Canonical correspondence analysis (CCA) showed that the fish assemblages
 were structured by a combination of large-scale landscape factors (e.g.
 altitude and C-link) and small-scale habitat features (e.g. channel width,
 water temperature and depth). Among these factors, landscape had the
 greatest influence on fish assemblages, while local habitat variables were
 less important or were only significant in certain seasons. 
description: The dataset was collected at 18 sites during the rainy and dry
 seasons in 2017 in mountain streams of the Ren River, south-west China,
 and has been processed by a series of Analysis of similarities (ANOSIM)
 and Canonical correspondence analysis (CCA) to produce a MS accepted for
 publicated in Ecology and Evolution.
description: The fish
 data refers to the relative abundance of different fish species. The
 enviromental data refers to the  mean values measured at each site.
 Information on how the measurements were done can be found in the
 associated manuscript referenced above.
DOI: 10.82294/dvncuibhi
title: Datos consolidados de COPUS. Territorio: Cundinamarca. Sector: Cultura, Educación, Total. Año: 2025

description: En este apartado se presentan los datos consolidados del territorio de Cundinamarca a partir de las observaciones semiestructuradas realizadas en 2025, esta vez analizadas bajo los criterios del protocolo de observación estructurada COPUS. Este dataset contiene la sumatoria de todas las observaciones COPUS por territorio, por sector, cultura y educación, una sumatoria de estos dos para definir la tendencia en el territorio y una sumatoria de todos los territorios.
DOI: 10.5061/dryad.547d7wm7q
title: Data and code from: Amphibian speciation rates support a general role of mountains as biodiversity pumps

description: Continental mountain areas cover less than 15% of global land surface,
 yet, these regions concentrate over 80% of global terrestrial diversity.
 One prominent hypothesis to explain this pattern proposes that high
 mountain diversities could be explained by higher diversification rates in
 regions of high topographic complexity. While high speciation in mountains
 has been detected for particular clades and regions, the global extent to
 which lineages experience faster speciation in mountains remains unknown.
 Here we address this issue using amphibians as model system (&gt;7,000
 species) and found that families showing high diversification rates
 contain a high proportion of species distributed in mountains. Moreover,
 we found that lineages inhabiting areas of high topographic complexity
 speciate faster than lineages occupying areas topographically less
 complex. When comparing across regions, we identified the same pattern in
 five biogeographical realms where higher speciation rates are associated
 with higher levels of complex topography. Low magnitude differences in
 speciation rates between some low and high complex topographies suggest
 that high mountain diversity is also affected by low extinction and/or
 high colonization rates. Nevertheless, our results bolster the importance
 of mountains as engines of speciation at different geographical scales and
 highlight their importance for the conservation of global biodiversity.