cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gtht76hh7
title: Oceanographic features and limited dispersal shape the population genetic structure of the vase sponge Ircinia campana in the Greater Caribbean

description: Understanding population genetic structure can help us to infer dispersal
 patterns, predict population resilience and design effective management
 strategies. For sessile species with limited dispersal, this is especially
 pertinent because genetic diversity and connectivity are key aspects of
 their resilience to environmental stressors. Here, we describe the
 population structure of Ircinia campana, a common Caribbean
 sponge subject to mass mortalities and disease. Microsatellites were used
 to genotype 440 individuals from 19 sites throughout the Greater
 Caribbean. We found strong genetic structure across the region, and
 significant isolation by distance across the Lesser Antilles, highlighting
 the influence of limited larval dispersal. We also observed spatial
 genetic structure patterns congruent with oceanography. This includes
 evidence of connectivity between sponges in the Florida Keys and the
 southeast coast of the United States (&gt;700 km away) where the
 oceanographic environment is dominated by the strong Florida Current.
 Conversely, the population in southern Belize was strongly differentiated
 from all other sites, consistent with the presence of dispersal-limiting
 oceanographic features, including the Gulf of Honduras gyre. At smaller
 spatial scales (&lt;100 km), sites showed heterogeneous patterns of
 low-level but significant genetic differentiation (chaotic genetic
 patchiness), indicative of temporal variability in recruitment or local
 selective pressures. Genetic diversity was similar across sites, but there
 was evidence of a genetic bottleneck at one site in Florida where past
 mass mortalities have occurred. These findings underscore the relationship
 between regional oceanography and weak larval dispersal in explaining
 population genetic patterns, and could inform conservation management of
 the species.
description: <em>Ircinia campana</em> genotyped at 10
 microsatellite loci described by Griffiths et al. (2019)
 Griffiths SM, Antwis RE, Lenzi L, Lucaci A, Behringer DC, Butler
 MJ, Preziosi RF (2019) Host genetics and geography influence microbiome
 composition in the sponge<em> Ircinia campana. Journal of Animal
 Ecology </em>(88) 1684 - 1695.
description: File is in Genepop 3-digit format, missing data coded by
 000000
DOI: 10.25349/d93888
title: Data from: Mating system and historical climate conditions affect population mean seed mass: evidence for adaptation and a new component of the selfing syndrome in Clarkia

description: 1. The evolution of seed size may be influenced by intrinsic attributes of
 populations, such as mating system, and extrinsic factors, such as
 climate. Several hypotheses propose that the evolution of
 self-fertilization from an outcrossing progenitor will be accompanied by a
 reduction in seed size, but this prediction has not been rigorously
 tested. Many studies report that the mean seed size of populations or taxa
 is associated with long-term climate conditions. Here, we examined the
 effects on seed size of both mating system and climate within a single
 genus. 2. In the California wildflower genus, Clarkia (Onagraceae), we
 sampled seeds from 58 populations representing three pairs of sister taxa;
 each pair included a predominantly outcrossing and a facultatively selfing
 taxon. We then examined the independent effects on population mean seed
 size of mating system, elevation, long-term (30-year) climate conditions,
 and climate anomalies (the deviation between conditions in the year of
 collection and the long-term mean), focusing on maximum monthly
 temperature (Tmax), cumulative moisture deficit, and cumulative
 precipitation (PPT) during Clarkia’s growing season (fall, winter, and
 spring). 3. In each taxon pair, the selfing taxon had smaller seeds than
 the outcrosser. Local, long-term (1921-1980 and 1981-2000) mean Tmax, PPT,
 and elevation were independently and negatively associated with seed size.
 Long-term means for Tmax and PPT explain geographic variation in seed size
 better than climate anomalies in the year of collection. 4. Synthesis: We
 corroborated two key hypotheses concerning the drivers of geographic
 variation in mean seed size. Small seeds in Clarkia co-evolve with selfing
 (although the mechanism remains elusive) and in response to chronically
 warm and wet conditions. The effect of long-term mean precipitation on
 seed size differs qualitatively from the effect of precipitation
 anomalies; relatively large seeds are produced in populations experiencing
 wetter-than-normal years. Ongoing climate change may therefore generate
 conflicting selection on seed size in Clarkia: intensifying drought is
 likely to lead to an evolutionary increase in seed size due to its effects
 on seedling survivorship, while climate-driven declines in pollinators or
 selection favoring more rapid reproduction may promote the evolution of
 self-pollination, facilitating the evolution of smaller seeds. 
description: Metadata in second tab of Excel spreadsheet.
DOI: 10.15468/dl.vuu4kj
title: Occurrence Download

description: A dataset containing 1756 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cambarus striatus"
 ]
}

 The dataset includes 1756 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002088-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.zs7h44j4v
title: Large-scale RNAi screening uncovers new therapeutic targets in the human parasite Schistosoma mansoni

description: Schistosomes kill 250,000 people every year. Treatment of schistosomiasis
 relies on a single drug (praziquantel). Unfortunately, a scarcity of
 molecular tools has hindered the discovery of new drug targets. Here, we
 describe a large-scale RNA interference screen in adult Schistosoma
 mansoni examining the function of 2,216 genes. We discovered 250 genes
 with phenotypes affecting neuromuscular function, tissue integrity, stem
 cell maintenance, and parasite survival. Leveraging these data, we
 prioritize compounds with activity against the parasites and uncover a
 pair of protein kinases (TAO and STK25) that cooperate to maintain
 muscle-specific mRNA transcription. Loss of either of these kinases
 results in paralysis and worm death in a mammalian host. These studies
 will expedite therapeutic development and invigorate studies of these
 neglected parasites. Large-scale RNAi screening uncovers new therapeutic
 targets in the human parasite Schistosoma mansoni.  
description: RNAi was performed on worms and videos were collected when a
 visable phenotype was observed.
DOI: 10.5061/dryad.djh9w0vw5
title: Multiple factors affect discrimination learning performance, but not between-individual variation, in wild mixed-species flocks of birds

description: Cognition arguably drives most behaviours in animals, but whether and why
 individuals in the wild vary consistently in their cognitive performance
 is scarcely known, especially under mixed-species scenarios. One reason
 for this is that quantifying the relative importance of individual,
 contextual, ecological and social factors remains a major challenge. We
 examined how many of these factors, and sources of bias, affected
 participation, and performance, in an initial discrimination learning
 experiment and two reversal learning experiments during self-administered
 trials in a population of great tits and blue tits. Individuals were
 randomly allocated to different rewarding feeders within an array.
 Participation was high and only weakly affected by age and species. In the
 initial learning experiment, great tits learned faster than blue tits.
 Great tits also showed greater consistency in performance across two
 reversal learning experiments. Individuals assigned to the feeders on the
 edge of the array learned faster. More errors were made on feeders
 neighbouring the rewarded feeder and on feeders that had been rewarded in
 the previous experiment. Our estimates of learning consistency were
 unaffected by multiple factors, suggesting that, even though there was
 some influence of these factors on performance, we obtained a robust
 measure of discrimination learning in the wild.
DOI: 10.5061/dryad.7d7wm37r9
title: Substantial genetic divergence and lack of recent gene flow support cryptic speciation in a colour polymorphic bumble bee (Bombus bifarius) species complex

description: Phenotypic polymorphism can constitute an inherent challenge for species
 delimitation. This issue is exemplified in bumble bees (Bombus),
 where species can exhibit high colour variation across their
 range, but otherwise exhibit little morphological variation to
 distinguish them from close relatives. We examine the species
 status of one of the most abundant North
 American bumble bees, Bombus bifarius Cresson,
 which historically was comprised of two major
 taxa, bifarius s.s. (sensu stricto)
 and nearcticus. These sublineages are
 recognized primarily by red and black variation in their mid-abdominal
 coloration, however, a continuum from black (nearcticus) to red
 (bifarius s.s.) variation has led to their
 historic synonymisation. Integrating mitochondrial and nuclear data and whole-genome sequencing, we reveal a high level of both mitochondrial and nuclear divergence delimiting two morphologically cryptic species – the red bifarius s.s. and the color variable (black to red) nearcticus. Population genomic analysis supports an absence of recent genomic admixture and a strong population structure between the two clades even in sympatry. Species distribution models predict partially differentiated niches between the genetically-inferred clades with annual precipitation being a leading differentiating variable. The bifarius s.s. lineage also occupies significantly higher elevations, with regions of sympatry being among the highest elevations in nearcticus. Our data also support a subspecies-level divergence between the broadly distributed nearcticus and the island population vancouverensis. In this paper, we formally recognize the two species, Bombus bifarius Cresson and Bombus vancouverensis Cresson, the latter including the subspecies B. vancouverensis vancouverensis comb. n. and B. vancouverensis nearcticus comb. n., with vancouverensis the name bearer due to year priority.
DOI: 10.5061/dryad.k0p2ngf4h
title: Genetic variation in GC and CYP2R1 affects 25-hydroxyvitamin D concentration and skeletal parameters: a genome-wide association study in 24-month-old Finnish children

description: Vitamin D is important for normal skeletal homeostasis, especially in
 growing children. There are no previous genome-wide association (GWA)
 studies exploring genetic factors that influence vitamin D metabolism in
 early childhood. We performed a GWA study on serum 25-hydroxyvitamin D
 (25(OH)D) and response to supplementation in 761 healthy term-born Finnish
 24-month-old children, who participated in a randomized clinical trial
 comparing effects of 10 µg and 30 µg of daily vitamin D supplementation
 from age 2 weeks to 24 months. Using
 the Illumina Infinium Global Screening Array, which has
 been optimized for imputation, a total of 686085 markers were genotyped
 across the genome. Serum 25(OH)D was measured at the end of the
 intervention at 24 months of age. Skeletal parameters reflecting bone
 strength were determined at the distal tibia at 24 months using peripheral
 quantitative computed tomography (pQCT) (data available for 648 children).
 For 25(OH)D, two strong GWA signals were identified, localizing
 to GC(Vitamin D binding protein) and CYP2R1(Vitamin D
 25-hydroxylase) genes. The GWA locus comprising the GCgene also
 associated with response to supplementation. Further evidence for the
 importance of these two genes was obtained by comparing association
 signals to gene expression data from the Genotype-Tissue Expression
 project and performing colocalization analyses. Through the identification
 of haplotypes associated with low or high 25(OH)D concentrations we used a
 Mendelian randomization approach to show that haplotypes associating with
 low 25(OH)D were also associated with low pQCT parameters in the
 24-month-old children. In this first GWA study on 25(OH)D in this age
 group we show that already at the age of 24 months genetic variation
 influences 25(OH)D concentrations and determines response to
 supplementation, with genome-wide significant associations
 with GCand CYP2R1. Also, the dual association between
 haplotypes, 25(OH)D and pQCT parameters gives support for vertical
 pleiotropy mediated by 25(OH)D.
DOI: 10.82294/dvn23irc2
title: Entrevistas semiestructuradas. Territorio: Norte de Santander. Sector: Cultura. Año: 2025

description: A partir de un proceso de acompañamiento situado, se recopilaron testimonios por medio de entrevistas semiestructuradas durante el año 2025, las cuales indagaron sobre 4 categorías que describían la práctica en educación artística de docentes, cultores, sabedores de la enseñanza del arte, que hacían parte de los programas de formación en educación artística y cultural del sector Cultura (educación informal) en el departamento de Norte de Santander.
DOI: 10.5061/dryad.s4mw6m93f
title: Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer

description: It is now clear that hybridization between species is much more common
 than previously recognized. As a result, we now know that the genomes of
 many modern species, including our own, are a patchwork of regions derived
 from past hybridization events. Increasingly researchers are interested in
 disentangling which regions of the genome originated from each parental
 species using local ancestry inference methods. Due to the diverse effects
 of admixture, this interest is shared across disparate fields, from human
 genetics to research in ecology and evolutionary biology. However, local
 ancestry inference methods are sensitive to a range of biological and
 technical parameters which can impact accuracy. Here we present paired
 simulation and ancestry inference pipelines, mixnmatch and ancestryinfer,
 to help researchers plan and execute local ancestry inference studies.
 mixnmatch can simulate arbitrarily complex demographic histories in the
 parental and hybrid populations, selection on hybrids, and technical
 variables such as coverage and contamination. ancestryinfer takes as input
 sequencing reads from simulated or real individuals, and implements an
 efficient local ancestry inference pipeline. We perform a series of
 simulations with mixnmatch to pinpoint factors that influence accuracy in
 local ancestry inference and highlight useful features of the two
 pipelines. Together, mixnmatch and ancestryinfer are powerful tools for
 predicting the performance of local ancestry inference methods on real
 data.
DOI: 10.5061/dryad.dfn2z34wr
title: The impact of local population genetic background on the spread of the selfish element Medea-1 in red flour beetles

description: Selfish genetic elements have been found in the genomes of many species,
 yet our understanding of their evolutionary dynamics is only partially
 understood. A number of distinct selfish Medea elements are naturally
 present in many populations of the red flour beetle (Tribolium castaneum).
 Although these Medea elements are predicted by models to increase in
 frequency within populations because any offspring of a Medea-bearing
 mother that do not inherit at least one Medea allele will die, experiments
 demonstrating an increase in a naturally occuring Medea element are
 lacking. Our survey of the specific Medea element, M1, in the United
 States showed that it had a patchy geographic distribution. From the
 survey it could not be determined if this distribution was caused by a
 slow process of M1 colonization of discrete populations or if some
 populations lacked M1 because they had genetic factors conferring
 resistance to the Medea mechanism. We show that populations with naturally
 low to intermediate M1 frequencies likely represent transient states
 during the process of Medea spread. Furthermore, we find no evidence that
 genetic factors are excluding M1 from US populations where the element is
 not presently found. We also show how a known suppressor of Medea can
 impair the increase of M1 in populations and discuss the implications of
 our findings for pest-management applications of Medea elements.
DOI: 10.5061/dryad.5mkkwh71w
title: Interspecific differences and ecological correlations of energy metabolism traits in freshwater fishes

description: 1. Metabolic energy fuels all biological processes, and thus, energy
 metabolism is vitally important for organisms. It has been suggested that
 interspecific variation in physiological functions is associated with the
 energetic metabolism of organisms, which varies considerably due to
 selection, adaptation and evolution. 2. Thus, the present study aimed to
 clarify the relationship between the interspecific diversification of
 maintenance energy expenditure and two forms of anaerobic capacity (in
 terms of exercise and hypoxia tolerance) in freshwater fishes. Moreover,
 in the context of environmental adaptation, we hypothesized that selection
 for increased locomotor performance in species with a fast-flow lifestyle
 favours a high aerobic and anaerobic capacity and, consequently, a high
 maintenance metabolism, whereas selection for strong hypoxia tolerance in
 species with a slow-flow lifestyle favours a reduced maintenance
 metabolism and a reduced aerobic capacity. 3. We examined these topics
 among 30 species of freshwater fish with different lifestyles based on the
 flow regimes of their habitats (fast, intermediate and slow flow). The
 resting metabolic rate of each species was measured, and then, the fish
 were subjected to two treatments: (i) exercise to exhaustion, after which
 we measured the maximum metabolic rate (MMR), excess post-exercise oxygen
 consumption (EPOCe) and metabolic recovery rate (MRR); and (ii) hypoxia to
 the point of loss of equilibrium (LOE), after which we measured the
 metabolic response to recovery from hypoxia, including the peak metabolic
 rate (PMRh) and the excess post-hypoxia oxygen consumption (EPOCh). 4. We
 found that the resting metabolic rate was positively correlated with both
 the aerobic and anaerobic capacity of the fishes and that species from
 fast-flow habitats have higher aerobic and anaerobic capacity with
 concomitantly increased resting metabolism. However, neither EPOCh nor LOE
 was correlated with resting metabolic rate. 5. In summary, we suggest that
 selection for increased aerobic and anaerobic capacity to facilitate the
 demands of exercise has occurred in fast-flow species, that selection for
 hypoxia tolerance may have favoured a reduction in this capacity in
 intermediate and slow-flow species, and that specialized adaptations (such
 as flexibility in gill morphology and altered metabolic pathways) play
 important roles in hypoxia tolerance in some species.
DOI: 10.15468/dl.7bubrq
title: Occurrence Download

description: A dataset containing 9648 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Kathetostoma giganteum",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 9648 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002089-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d7wm37pxf
title: Data from: Superposed epoch analysis of the energetic electron flux variations during CIRs measured by BD-IES

description: The flux variations of energetic electrons is one of the most important
 topics to understand dynamic processes in the space environment and the
 forecast for high-energy electron burst. BD-IES, an imaging energetic
 electron spectrometer onboard a Chinese navigation satellite at an
 inclined geosynchronous orbit (IGSO), can provide 50-600keV electron flux
 data, which is used to investigate electron flux variations at GEO orbit
 during Co-rotating Interactive Region events (CIRs). The superposed epoch
 analysis is applied to study the electron flux variations in different
 energy channels of BD-IES during CIRs and the results support previous
 works. It reveals that electron fluxes in different channels all have a
 dropout before or at CIR interface and then the recovery of electrons with
 low energy reaches maximum earlier than that of electrons with high
 energy, with longer time difference for larger energy gap, which is
 consistent of two major mechanisms for energizing particles: inward radial
 diffusion and local acceleration. In addition, we investigate the
 relationship between electron flux enhancement in each energy channel and
 magnetic local time (MLT) and the extent of enhancement for electron flux
 peak value compared with average value before interface. These results can
 contribute to our understanding of electron flux variations at GEO during
 CIRs, and thus lay foundations for forecast research on high-energy
 electron burst during CIRs.
description: Please read "README_for_BD-IES_data_CIR.txt"  for  data
 folder description.
DOI: 10.6078/d10q3n
title: Data from: Fragmented and isolated: limited gene flow coupled with weak isolation by environment in the paleoendemic giant sequoia (Sequoiadendron giganteum)

description: PREMISE: Patterns of genetic structure across a species’ range
 reflect the long-term interplay between genetic drift, gene flow, and
 selection. Given the importance of gene flow in preventing the loss of
 diversity through genetic drift among spatially isolated populations,
 understanding the dynamics of gene flow and the factors that influence
 connectivity across a species’ range is a major goal for conservation of
 genetic diversity. Here we present a detailed look at gene flow
 dynamics of Sequoiadendron giganteum, a paleoendemic tree species
 that will likely face numerous threats due to climate change.
 METHODS: We used microsatellite markers to examine nineteen
 populations of S. giganteum for patterns of genetic
 structure and to estimate admixture and rates of gene flow between eight
 population pairs. Also, we used Generalized Dissimilarity Models to
 elucidate landscape factors that shape genetic differentiation among
 populations.  RESULTS: We found minimal gene flow
 between adjacent groves in the northern disjunct range. In most of the
 southern portion of the range, groves showed a signal of connectivity
 which degrades to isolation in the extreme south. Geographic distance was
 the most important predictor of genetic dissimilarity across the range,
 with environmental conditions related to precipitation and temperature
 explaining a small, but significant, portion of the genetic variance.
 CONCLUSIONS: Due to their isolation and unique genetic
 composition, northern populations
 of S. giganteum should be considered a high
 conservation priority. In this region, we suggest germplasm
 conservation as well as restoration planting to enhance genetic
 diversity.    
description: Full SSR data set for 658 individuals sampled from
 19-populations. The first column is an individual ID, Second column is a
 population code, and remaining columns represent the 11 SSR loci. Each row
 represents a sampled individual.