cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jwstqjq4n
title: Melanism protects alpine zooplankton from DNA damage caused by ultraviolet radiation

description: Melanism is widely observed among animals, and is adaptive in various
 contexts for its thermoregulatory, camouflaging, mate-attraction, or
 photoprotective properties. Many organisms exposed to ultraviolet
 radiation show increased fitness resulting from melanin pigmentation; this
 has been assumed to result in part from reduced UV-induced damage to DNA.
 However, to effectively test the hypothesis that melanin pigmentation
 reduces UV-induced DNA damage requires quantification of UV-specific DNA
 damage lesions following UV exposure under controlled conditions using
 individuals that vary in pigmentation intensity. We accomplished this
 using alpine genotypes of the freshwater microcrustacean Daphnia melanica
 for which we quantified cyclobutane pyrimide dimers in DNA, a damage
 structure that can only be generated by UV exposure. For genotypes with
 carapace melanin pigmentation, we found that individuals with greater
 melanin content sustained lower levels of UV-induced DNA damage.
 Individuals with more melanin were also more likely to survive exposure to
 ecologically relevant levels of UV-B radiation. Parallel experiments with
 conspecific genotypes that lack carapace melanin pigmentation provide
 additional support for our conclusion that melanism protects individuals
 from UV-induced DNA damage. Finally, within-genotype comparisons with
 asexually-produced clonal siblings demonstrate that melanin content
 influences DNA damage even among genetically identical individuals raised
 in the same environment.
DOI: 10.5061/dryad.zgmsbcc68
title: Data from: Genetic connectivity of Lionfish (Pterois volitans) in marine protected areas of the Gulf of Mexico and Caribbean Sea

description: Lionfish (Pterois volitans) have rapidly invaded the tropical Atlantic and
 spread across the wider Caribbean in a relatively short period of time.
 Because of its high invasion capacity, we used it as a model to identify
 the connectivity among nine marine protected areas (MPAs) situated in four
 countries in the Gulf of Mexico and the Caribbean Sea.This study provides
 evidence of local genetic differentiation of P. volitansin the
 Gulf of Mexico and the Caribbean Sea.A total of 475 lionfish samples were
 characterized with 12 microsatellites, with 6 to 20 alleles per locus.
 Departures from Hardy-Weinberg equilibrium (HWE) were found in 10 of the
 12 loci, all caused by heterozygous excess. Moderate genetic
 differentiation was observed between Chiriviche, Venezuela and Xcalak ,
 México localities (FST= 0.012), and between the Los Roques and Veracruz
 (FST= 0.074) sites. STRUCTURE analysis found that four genetic entities
 best fit our data. A unique genetic group in the Gulf of Mexico may imply
 that the lionfish invasion unfolded both in a counter-clockwise manner in
 the Gulf of Mexico.In spite of thenotable dispersion of P.
 volitans, our results show some genetic structure, as do other noninvasive
 Caribbean fish species, suggesting that the connectivity in some MPAs
 analyzed in the Caribbean is limited and caused by only a few source
 individuals with subsequent genetic drift leading to local genetic
 differentiation. This indicates that P. volitansdispersion could
 be caused by mesoscale phenomena, which produce stochastic connectivity
 pulses. Due to the isolation of some MPAs from others, these findings may
 hold a promise for local short-term control of by means of intensive
 fishing, even in MPAs, and may have regional long-term effects.
DOI: 10.5061/dryad.m37pvmcxs
title: Complex ecological phenotypes on phylogenetic trees: a Markov process model for comparative analysis of multivariate count data

description: The evolutionary dynamics of complex ecological traits – including
 multistate representations of diet, habitat, and behavior – remain poorly
 understood. Reconstructing the tempo, mode, and historical sequence of
 transitions involving such traits poses many challenges for comparative
 biologists, owing to their multidimensional nature. Continuous-time Markov
 chains (CTMC) are commonly used to model ecological niche evolution on
 phylogenetic trees but are limited by the assumption that taxa are
 monomorphic and that states are univariate categorical variables. A
 necessary first step in the analysis of many complex traits is therefore
 to categorize species into a pre-determined number of univariate
 ecological states, but this procedure can lead to distortion and loss of
 information. This approach also confounds interpretation of state
 assignments with effects of sampling variation because it does not
 directly incorporate empirical observations for individual species into
 the statistical inference model. In this study, we develop a
 Dirichlet-multinomial framework to model resource use evolution on
 phylogenetic trees. Our approach is expressly designed to model ecological
 traits that are multidimensional and to account for uncertainty in state
 assignments of terminal taxa arising from effects of sampling variation.
 The method uses multivariate count data for individual species to
 simultaneously infer the number of ecological states, the proportional
 utilization of different resources by different states, and the
 phylogenetic distribution of ecological states among living species and
 their ancestors. The method is general and may be applied to any data
 expressible as a set of observational counts from different categories.
DOI: 10.5061/dryad.280gb5mm4
title: Identifying and classifying shared selective sweeps from multilocus data

description: Positive selection causes beneficial alleles to rise to high frequency,
 resulting in a selective sweep of the diversity surrounding the selected
 sites. Accordingly, the signature of a selective sweep in an ancestral
 population may still remain in its descendants. Identifying signatures of
 selection in the ancestor that are shared among its descendants is
 important to contextualize the timing of a sweep, but few methods exist
 for this purpose. We introduce the statistic SS-H12, which can identify
 genomic regions under shared positive selection across populations and is
 based on the theory of the expected haplotype homozygosity statistic H12,
 which detects recent hard and soft sweeps from the presence of
 high-frequency haplotypes. SS-H12 is distinct from comparable statistics
 because it requires a minimum of only two populations, and properly
 identifies and differentiates between independent convergent sweeps and
 true ancestral sweeps, with high power and robustness to a variety of
 demographic models. Furthermore, we can apply SS-H12 in conjunction with
 the ratio of statistics we term H2Tot and H1Tot to further classify
 identified shared sweeps as hard or soft. Finally, we identified both
 previously-reported and novel shared sweep candidates from human
 whole-genome sequences. Previously-reported candidates include the
 well-characterized ancestral sweeps at LCT and SLC24A5 in Indo-Europeans,
 as well as GPHN worldwide. Novel candidates include an ancestral sweep at
 RGS18 in sub-Saharan Africans involved in regulating the platelet response
 and implicated in sudden cardiac death, and a convergent sweep at C2CD5
 between European and East Asian populations that may explain their
 different insulin responses.
description: Contained are the scripts, simulations, and summary data
 necessary for confirming the results of our <em>GENETICS</em>
 manuscript, entitled "Identifying and classifying shared selective
 sweeps from multilocus data." For each research direction we have
 undertaken, we provide resources for interested parties to confirm our
 results. These include simulated replicates, summary statistics, and the
 raw script files used for internal data analysis. Please note that data
 are divided into four .tar.gz archives, titled *_p1*, *_p2*, *_p3*, and
 *_p4*. P-value results in *_p4* within the
 directory whole_genome_scans_singles supersede those in *_p1*, while data
 within larger_simulated_sequences_1Mb in *_p4* were simulated following
 the same protocol as those within ceugihyri_sims_95 in *_p1*, simply with
 a larger simulated chromosome.
DOI: 10.5061/dryad.pvmcvdngd
title: Data from: A rat liver transcriptomic point of departure predicts a prospective liver or non-liver apical point of departure

description: Identifying a toxicity point of departure (POD) is a required step in
 human health risk characterization of crop protection molecules, and this
 POD has historically been derived from apical endpoints across a battery
 of animal-based toxicology studies. Using rat transcriptome and apical
 data for 79 molecules obtained from Open TG-GATES (Toxicogenomics
 Project-Genomics Assisted Toxicity Evaluation System) (632 datasets), the
 hypothesis was tested that a short-term exposure, transcriptome-based
 liver biological effect POD (BEPOD) could estimate a longer-term exposure
 “systemic” apical endpoint POD. Apical endpoints considered were body
 weight, clinical observation, kidney weight and histopathology and liver
 weight and histopathology. A BMDExpress algorithm using Gene Ontology
 Biological Process gene sets was optimized to derive a liver BEPOD most
 predictive of a systemic apical POD. Liver BEPODs were stable from 3 hours
 to 29 days of exposure; the median fold difference of the 29 day BEPOD to
 BEPODs from earlier time points was approximately 1 (range of 0.7-1.1).
 Strong positive correlation (Pearson R = 0.86) and predictive accuracy
 (root mean square difference = 0.41) were observed between a concurrent
 (29 day) liver BEPOD and the systemic apical POD. Similar Pearson R and
 root mean square difference values were observed for comparisons between a
 29 day systemic apical POD and liver BEPODs derived from 3 hours to 15
 days of exposure. These data across 79 molecules suggest that a
 longer-term exposure study apical POD from liver and non-liver
 compartments can be estimated using a liver BEPOD derived from an acute or
 subacute exposure study.
DOI: 10.21223/p3/cinpso
title: Dataset for: Participatory Varietal Selection of 21 late blight resistant clones (B1C5) in the locality of Chaquicocha in La Libertad, Peru

description: The Mother and Baby (M&B) trial methodology was adapted by CIP for Participatory Variety Selection (PVS) through decentralized evaluation networks and multi-year evaluations in potato growing areas in the Andean region. The M&B trial design encourages active participation of farmers through the application of treatments through systematic evaluations and selections of treatments in their own plots called "Baby trials" (i.e. farmer managed trials) and in fields with an experimental design called "Mother trials" (i.e. researcher managed trials). Objective: Analyze characteristics, attributes and preferences that men and women have when selecting a new potato variety at the phase of flowering and harvesting. A M&B trial was performed to evaluate 21 clones of the population B1C5 with late blight resistance at the locality of Chaquicocha, in Pataz province, in La Libertad department, Peru. The trial design was a Randomized Complete Block Design (RCBD) with 3 replicates during 2009-2010. In this experiment, characteristics of plant (size, type of foliage) and resistance to diseases during flowering and harvesting were evaluated.
DOI: 10.5061/dryad.m63xsj3xd
title: An experimental test of community-based strategies for mitigating human-wildlife conflict around protected areas

description: Natural habitats are rapidly being converted to cultivated croplands, and
 crop-raiding by wildlife threatens both wildlife conservation and human
 livelihoods worldwide. We combined movement data from GPS-collared
 elephants with camera-trap data and local reporting systems in a
 before-after-control-impact design to evaluate community-based strategies
 for reducing crop raiding outside Mozambique’s Gorongosa National Park.
 All types of experimental fences tested (beehive, chili, beehive and chili
 combined, and procedural controls) significantly reduced the number of
 times elephants left the Park to raid crops. However, placing beehive
 fences at a subset of key crossing locations reduced the probability that
 elephants would leave the Park by up to 95% relative to unfenced
 crossings, and was the most effective strategy. Beehive fences also
 created opportunities for income generation via honey production. Our
 results provide experimental evidence that working with local communities
 to modify both animal behavior and human attitudes can mitigate conflict
 at the human-wildlife interface.
DOI: 10.5061/dryad.h44j0zpf9
title: Temporal isolation between sympatric host plants cascades across multiple trophic levels of host-associated insects

description: Phenological differences between host plants can promote temporal
 isolation among host-associated populations of insects with life cycles
 tightly coupled to plant phenology. Divergence in the timing of spring
 budbreak between two sympatric sister oak species has been shown to
 promote temporal isolation between host plants and their host-associated
 populations of a cynipid gall wasp. Here we examined the generality of
 this mechanism by testing the hypothesis of cascading temporal isolation
 for five additional gall-formers and three natural enemy species
 associated with these same oak species. The timing of adult emergence from
 galls differed significantly between host-associated populations for all
 nine species and parallels the direction of the phenological differences
 between host plants. Differences in emergence timing can reduce gene flow
 between host-associated populations by diminishing mating opportunities
 and/or reducing fitness of immigrants due to differences in the
 availability of ephemeral resources. Our study suggests that cascading
 temporal isolation could be a powerful “biodiversity generator” across
 multiple trophic levels in tightly coupled plant-insect systems.
DOI: 10.15468/dl.qzsf9h
title: Occurrence Download

description: A dataset containing 110 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Hancockia"
 ]
}

 The dataset includes 110 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001975-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sbcc2fr28
title: Host identity and symbiotic association affects the genetic and taxonomic diversity of the clownfish-hosting sea anemone microbiome

description: All eukaryotic life engages in symbioses with a diverse community of
 bacteria that are essential for performing basic life functions. In many
 cases, eukaryotic organisms form additional symbioses with other
 macroscopic eukaryotes. The tightly-linked physical interactions that
 characterize many macroscopic symbioses creates opportunities for
 microbial transfer, which likely affects the diversity and function of
 individual microbiomes, and may ultimately lead to microbiome convergence
 between distantly related taxa. Here, we sequence the microbiomes of five
 species of clownfish-hosting sea anemones that co-occur on coral reefs in
 the Maldives. We test the importance of evolutionary history, clownfish
 symbiont association, and habitat on the genetic and predicted functional
 diversity of the microbiome, and explore signals of microbiome convergence
 in anemone taxa that have evolved symbioses with clownfishes
 independently. Our data indicate that host identity shapes the majority of
 the genetic diversity of the clownfish-hosting sea anemone microbiome, but
 predicted functional microbial diversity analyses demonstrate a
 convergence among host anemone microbiomes, which reflect increased
 functional diversity over individuals that do not host clownfishes.
 Further, we identify up-regulated microbial functions in host anemones
 that are likely affected by clownfish presence. Taken together our study
 reveals an even deeper metabolic coupling between clownfishes and their
 host anemones, and what could be a previously unknown mutualistic benefit
 to anemones that are symbiotic with clownfishes
DOI: 10.5061/dryad.rv15dv44k
title: Data from: Where are all the moms? external fertilization predicts the rise of male parental care in bony fishes

description: Parental care shows remarkable variation across the animal kingdom, but
 while maternal and biparental care are common in terrestrial organisms,
 male-only care dominates in aquatic species that provide care. Using the
 most complete phylogenetic tree of bony fishes to date, we test whether
 the opportunity for external fertilization in aquatic environments can
 explain the more frequent evolution of male care in this group. We show
 that paternal care has evolved at least 30 times independently in fish and
 is found only in externally fertilizing species. Male care is positively
 associated with pair spawning, suggesting that confidence in parentage is
 an important determinant of the evolution of care. Crucially, while female
 care is constrained by other forms of reproductive investment, male care
 occurs more frequently when females invest heavily in gamete production.
 Our results suggest that moving control of fertilization outside of the
 female reproductive tract raises male confidence in parentage and
 increases the potential for paternal care, highlighting that in an aquatic
 environment in which fertilization is external, paternal care is an
 effective reproductive strategy.
description: Literature review (Fishbase, Primary literature)
 Scripts and analysis datafiles provided for analyses included in
 manuscript. Source datafiles available from the authors
 upon request, due to CC-BY-NC licensing through Fishbase.
DOI: 10.5061/dryad.wpzgmsbgt
title: Data from: Artificial light at night increases growth and reproductive output in Anolis lizards

description: Since the invention of electric lighting, artificial light at night (ALAN)
 has become a defining, and evolutionarily novel, feature of human-altered
 environments especially in cities. ALAN imposes negative impacts on many
 organisms, including disrupting endocrine function, metabolism, and
 reproduction. However, we do not know how generalized these impacts are
 across taxa that exploit urban environments. We exposed brown anole
 lizards, an abundant and invasive urban exploiter, to relevant levels of
 ALAN in the lab and assessed effects on growth and reproduction at the
 start of the breeding season. Male and female anoles exposed to ALAN
 increased growth and did not suffer increased levels of corticosterone.
 ALAN exposure induced earlier egg-laying, likely by mimicking a longer
 photoperiod, and increased reproductive output without reducing offspring
 quality. These increases in growth and reproduction should increase
 fitness. Anoles, and potentially other taxa, may be resistant to some
 negative effects of ALAN and able to take advantage of the novel niche
 space ALAN creates. ALAN and both its negative and positive impacts may
 play a crucial role in determining which species invade and exploit urban
 environments.
DOI: 10.60905/ygz5qm
title: Convocatoria Aula Abierta. Comunidad Arte y Resistencia

description: &lt;p&gt;Convocatorias a las jornadas de reflexi��n en el marco del Paro Nacional que demuestran las intenciones del Movimiento Barrial Zona 2 de ampliar el alcance de las marchas y otros repertorios de acci��n colectiva. Las Aulas Abiertas fue una estrategia en la que se vincularon adem��s profesores/as de la UdeA, movidos por la iniciativa de la movilizaci��n en la Zona Noroccidental de Medell��n. &lt;/p&gt; &lt;p&gt;Movimiento Barrial Zona 2&lt;/p&gt;
description: <br>Desescalamiento de la movilizaci��n. 7 de agosto a 28 de diciembre de 2021
DOI: 10.5061/dryad.573n5tb3m
title: SNP analyses reveal a diverse pool of potential colonists to earthquake‐uplifted coastlines

description: In species that form dense populations, major disturbance events are
 expected to increase the chance of establishment for immigrant lineages.
 Real-time tests of the impact of disturbance on patterns of genetic
 structure are, however, scarce. Central to testing these concepts is
 determining the pool of potential immigrants dispersing into a disturbed
 area. In 2016, a 7.8 magnitude earthquake occurred on the South Island of
 New Zealand. Affecting approximately 100 km of coastline, this quake
 caused extensive uplift (several metres high), extirpating many intertidal
 populations, including keystone intertidal kelp species. Following the
 uplift, we set out to determine the geographic origins of detached kelp
 specimens which rafted into the disturbed zone. Specifically, we used
 genotyping-by-sequencing (GBS) approaches to compare beach-cast southern
 bull-kelp (Durvillea antarctica and D. poha) samples to established
 populations throughout the species’ ranges, and thus infer the geographic
 origins of potential colonists reaching the disturbed coast. Our findings
 reveal an ongoing supply of diverse lineages dispersing to the newly
 uplifted coastline, suggesting potential for establishment of ‘exotic’
 lineages following disturbance. Furthermore, we found that some drifting
 individuals of each species came from far-distant regions, some
 &gt;1200 km away. These results show that diverse lineages – in many
 cases from very distant sources – have potential to compete for new space
 in the wake of an exceptional disturbance event, illustrating the
 potential of long-distance dispersal as a key mechanism for re-assembly of
 coastal ecosystems. Furthermore, our findings demonstrate that
 high-resolution genomic baselines can be used to robustly assign the
 provenance of dispersing individuals.
DOI: 10.60521/332599
title: Processed Acoustic Backscatter, Sidescan and Swath Bathymetry Data (EM302) acquired during E/V Nautilus expedition NA163 (2024)

description: This data set was acquired with a Kongsberg EM302 Multibeam Sonar during E/V Nautilus expedition NA163 conducted in 2024. These data files are of MBSystem-compatible format and include Acoustic Backscatter, Sidescan and Swath Bathymetry data that were processed after acquisition. This data was processed by Ocean Exploration Trust and was included in the Global Multi-Resolution Topography (GMRT) Synthesis (version 4.4.1). Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.