cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3tx95x6c0
title: Detecting selected haplotype blocks in evolve and resequence experiments

description: Shifting from the analysis of single nucleotide polymorphisms to the
 reconstruction of selected haplotypes greatly facilitates the
 interpretation of Evolve and Resequence (E&R) experiments. Merging
 highly correlated hitchhiker SNPs into haplotype blocks reduces thousands
 of candidates to few selected regions. Current methods of haplotype
 reconstruction from Pool-Seq data need a variety of data-specific
 parameters that are typically defined ad hoc and require haplotype
 sequences for validation. Here, we introduce haplovalidate, a tool which
 detects selected haplotypes in Pool-seq time series data without the need
 for sequenced haplotypes. Haplovalidate makes data-driven choices of two
 key parameters for the clustering procedure, the minimum correlation
 between SNPs constituting a cluster and the window size. Applying
 haplovalidate to simulated and experimental E&R data reliably
 detects selected haplotype blocks with low false discovery rates.
 Importantly, our analyses identified a restriction of the haplotype
 block-based approach to describe the genomic architecture of adaptation.
 We detected a substantial fraction of haplotypes containing multiple
 selection targets. These blocks were considered as one region of selection
 and therefore led to under-estimation of the number of selection targets.
 We demonstrate that the separate analysis of earlier time points can
 significantly increase the separation of selection targets into individual
 haplotype blocks. We conclude that the analysis of selected haplotype
 blocks has great potential for the characterisation of the adaptive
 architecture with E&R experiments.
DOI: 10.5061/dryad.hdr7sqvdp
title: Dispersive liquid-liquid microextraction with extractant removal by magnetic nanoparticles for chloramphenicol preconcentration in water samples

description: This work describes the development of a new methodology based on
 dispersive liquid-liquid microextraction with extractant removal by
 magnetic nanoparticles (DLLME-MNPs) for preconcentration and extraction of
 chloramphenicol (CAP) antibiotic residues in water. The approach is based
 on the use of decanoic acid as the extraction solvent followed by the
 application of MNPs to magnetically retrieve the extraction solvent
 containing the extracted CAP. The coated MNPs were then desorbed with
 methanol, and the clean extract was analysed using UV-Vis
 spectrophotometry. Several important parameters, such as the amount of
 decanoic acid, extraction time, stirring rate, amount of MNPs, type of
 desorption solvent, salt addition, and sample pH, were evaluated and
 optimized. Optimum parameters were as follows: amount of decanoic acid:
 200 mg; extraction time: 10 min; stirring rate: 800 rpm; amount of MNPs:
 60 mg; desorption solvent: methanol; salt: 10%; and sample pH, 8. Under
 the optimum conditions, the method demonstrated acceptable linearity (R2 =
 0.9933) over a concentration range of 50 to 1000 µg L–1. Limit of
 detection and limit of quantification were 16.5 and 50.0 µg L–1,
 respectively. Good analyte recovery (91–92.7%) and acceptable precision
 with good RSDs (0.45–6.29%, n = 3) were obtained. The method was
 successfully applied to tap water and lake water samples. The proposed
 method is rapid, simple, reliable, and environmentally friendly for the
 detection of CAP.
DOI: 10.5061/dryad.xd2547dd5
title: A new species of Hiptage (Malpighiaceae) from Nujiang Gorge of Southwest China

description: Hiptage lushuiensis, a new species from the Hengduan Mountains,
 northwestern Yunnan Province, China, is here described and illustrated.
 This species was found growing at the margin of an open forest in the
 Nujiang Gorge of Lushui City. H. lushuiensis is distinctive for its pink
 petals, 2 or more calyx glands, large and red pink samara with white
 hairs. This species is isolated in the deep gorge (25°51′N, 98° 51′E,
 altitude 917 m), located at the northern edge of the genus’s distribution
 range. These distinctive differences in morphological traits and
 geographical location suggest a history of long-distance dispersal and
 allopatric speciation for this new species
description: Photos taken by Camera
DOI: 10.5061/dryad.x95x69pdz
title: Data from: Oxidative damage to lipids is rapidly reduced during migratory stopovers

description: Most migrating birds need to stopover in between flights in order to
 refuel. Lately, additional purposes of stopover have been suggested,
 including physiological recovery from metabolically demanding migratory
 flight. One apparently unavoidable, but harmful physiological effect of
 migratory flight is increased oxidative damage to lipids and proteins. We
 here, for the first time, tested whether migrating birds are able to
 reduce their oxidative damage during stopover. To be able to collect
 longitudinal data on a large number of individual birds, we temporarily
 caged wild northern wheatears, a long-distance migrant which does not
 suffer stress when caged during migration. Around noon on the first and
 third day at stopover, the birds were blood-sampled to determine
 malondialdehyde concentration, a commonly used marker of oxidative damage
 to lipids. We found that malondialdehyde concentrations significantly
 decreased during stopover, a result unchanged when correcting for the
 peroxidizability of the substrate. The extent of the decrease was
 unrelated to the amounts of food consumed or of fuel accumulated. Our
 findings support the hypothesis that stopovers serve reduction of
 oxidative damage, warranting re-thinking of how birds accomplish their
 migrations. They also highlight the need to include physiological recovery
 as a driver of the (temporal) organization of migration.
description: The data presented are parameters of the oxidative balance, food
 intake and changes in fuel stores in temporarily caged migrating northern
 wheatears (<em>Oenanthe oenanthe</em>). The oxidative balance
 parameters were taken on both the first and third full day in captivity.
 Food intake was total food intake during days 1-3. Changes in fuel stores
 were calculated from the first to third morning in captivity.
description: The sample size for antioxidant capacity is much lower because of
 limited plasma volumes.
DOI: 10.5061/dryad.80gb5mknh
title: A genetic mechanism for sexual dichromatism in birds

description: Sexual dichromatism — a difference in coloration between males and females
 — is central to the study of ornamentation, mate choice, and sexual
 selection. Here, we show that carotenoid-based dichromatism in mosaic
 canaries, a hybrid product between the sexually dichromatic red siskin and
 monochromatic canaries, is controlled by the carotenoid-cleaving enzyme
 Beta-Carotene Oxygenase 2 (BCO2). Dichromatism in mosaic canaries is
 explained by differential carotenoid degradation in the integument of each
 sex, rather than sex-specific variation in physiological functions such as
 pigment uptake or transport. Transcriptome analyses suggest that
 carotenoid degradation in the integument might be a common mechanism
 contributing to sexual dichromatism in other finches. Our findings
 demonstrate how differences in ornamental coloration between sexes can
 evolve through simple molecular mechanisms controlled by genes of major
 effect.
description: File
 “snp_call_freebayes.vcf.gz” – includes all the variants identified using
 whole-genome sequencing of DNA pools of six canary breeds, one wild
 population, and red siskin. The breeds or populations are listed in the
 vcf file in the following order: mosaic red, mosaic yellow, red
 lipochrome, black red intense, gibber italicus, white recessive, wild, and
 red siskin. File
 “genotyping.xlxs” – includes individual genotypes for 52 SNPs and 78
 canaries and red siskins (mosaic individuals = 56; common canaries = 14;
 red siskins = 8). The SNPs were selected from the whole-genome sequencing
 data among those characterized by diagnostic alleles between wild canaries
 and red siskin. Positions homozygous for the siskin allele are represented
 in red, positions homozygous for the canary allele in yellow, and
 positions heterozygous in orange. The location of the SNPs in scaffold
 NW_007931177 of the canary reference genome is indicated. Missing data is
 indicated by the number 1 and a white box. Files
 “*_transcriptome_assembly.fa” – De novo transcriptome assemblies for three
 species: Atlantic canary, European serin, and house finch. File
 "DE_genes_sex_dichromatism.xlsx" – lists of differentially
 expressed genes in pairwise comparisons
DOI: 10.5061/dryad.bvq83bk5d
title: Variations in immune parameters with age in a wild rodent population and links with survival

description: Recent findings suggest that immune functions do not unidirectionally
 deteriorate with age but that a potentially adaptive remodelling, where
 functions of the immune system get down regulated while others get
 upregulated with age could also occur. Scarce in wild populations,
 longitudinal studies are yet necessary to properly understand the patterns
 and consequences of age variations of the immune system in the wild.
 Meanwhile, it is challenging to understand if the observed variations in
 immune parameters with age are due to changes at the within-individual
 level or to selective (dis)appearance of individuals with peculiar immune
 phenotypes. Thanks to a long-term and longitudinal monitoring of a wild
 Alpine marmot population, we aimed to understand within- and
 between-individual variation in the immune phenotype with age, in order to
 improve our knowledge about the occurrence and the evolutionary
 consequences of such age-variations in the wild. To do so, we recorded the
 age-specific leukocyte concentration and leukocyte profile in repeatedly
 sampled dominant individuals. We then tested whether the potential changes
 with age were attributable to within-individual variations and/or
 selective (dis)appearance. Finally, we investigated if the leukocyte
 concentration and profiles were correlated to the probability of death at
 a given age. The leukocyte concentration was stable with age, but the
 relative number of lymphocytes decreased, while the relative number of
 neutrophils increased, over the course of an individual’s life. Moreover,
 between individuals of the same age, individuals with fewer lymphocytes
 but more neutrophils were more likely to die. Therefore, selective
 disappearance seems to play a role in the age variations of the immune
 parameters in this population. Further investigations linking age
 variations in immune phenotype to individual fitness are needed to
 understand whether remodelling of the immune system with age could or
 could not be adaptive.
DOI: 10.7272/q6jq0z6j
title: Dynamic post-translational modification profiling of M. tuberculosis-infected primary macrophages

description: Macrophages are highly plastic cells with critical roles in immunity,
 cancer, and tissue homeostasis, but how these distinct cellular fates are
 triggered by environmental cues is poorly understood. To uncover how
 primary murine macrophages respond to bacterial pathogens, we globally
 assessed changes in post-translational modifications of proteins during
 infection with Mycobacterium tuberculosis, a notorious intracellular
 pathogen. We identified hundreds of dynamically regulated phosphorylation
 and ubiquitylation sites, indicating that dramatic remodeling of multiple
 host pathways, both expected and unexpected, occurred during infection.
 Most of these cellular changes were not captured by mRNA profiling, and
 included activation of ubiquitin-mediated autophagy, an evolutionarily
 ancient cellular antimicrobial system. This analysis also revealed that a
 particular autophagy receptor, TAX1BP1, mediates clearance of
 ubiquitylated Mtb and targets bacteria to LC3-positive phagophores. These
 studies provide a new resource for understanding how macrophages shape
 their proteome to meet the challenge of infection.
description: Immunofluorescence microscopy images were obtained with the Opera
 Phenix (Perkin Elmer) at 63X magnification. Immunoblot
 images were obtained with a Li-Cor Odyssey instrument.
description: Please see the manuscript file for details about staining
 protocols.
DOI: 10.25338/b8402g
title: Utilizing Highway Rest Areas for Electric Vehicle Charging: Economics and Impacts of Renewable Energy Penetration in California

description: California policy is incentivizing rapid adoption of zero emission
 electric vehicles for light duty and freight applications. In this
 project, we explored how locating charging facilities at California’s
 highway rest stops, might impact electricity demand, grid operation, and
 integration of renewables like solar and wind into California’s energy
 mix.   Assuming a growing population of electric
 vehicles to meet state goals, we estimated state-wide growth of
 electricity demand, and identified the most attractive rest stop locations
 for siting chargers. Using a California-specific electricity dispatch
 model developed at ITS, we estimated how charging vehicles at these
 stations would impact renewable energy curtailment in California. We
 estimated the impacts of charging infrastructures on California’s
 electricity system and how they can be utilized to decrease the duck curve
 effect resulting from a large amount of solar energy penetration by 2050.
DOI: 10.5281/zenodo.18376328
title: CMI_Brand7_150F_1_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 150F SC sample 1 CMI   - EDLC single- Brand7

Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.18376327
title: CMI_Brand7_150F_1_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 150F SC sample 1 CMI   - EDLC single- Brand7

Part of the Constant Temperature DataBase
DOI: 10.6086/d1vh4h
title: Data from: Mark-recapture experiments reveal foraging behavior and plant fidelity of native bees in plant nurseries

description: Understanding the spatial and temporal foraging patterns of pollinators is
 essential to conserving these organisms in human‐modified landscapes, such
 as agroecosystems (Cranmer et al. 2011). Particularly, understanding
 foraging fidelity (i.e., returns to a particular plant species or area) is
 crucial for providing supportive habitats. Numerous approaches have been
 used to discern the movement and foraging of individual bees (reviewed by
 Mola and Williams 2019), ranging from highly technological to more
 traditional methods like mark–release–recapture experiments. Although
 mark–recapture experiments are often hampered by low recapture rates,
 density dependence, and logistical constraints (Mola and Williams 2019),
 they can help us understand short‐term local movement patterns (Dorchin et
 al. 2013) and fidelity (Ogilvie and Thomson 2016) of highly mobile
 organisms like bees.
description: We conducted eight mark–release–recapture experiments (Appendix
 S1) at five large-scale commercial plant nurseries in southern California,
 USA, surrounded by both suburban and natural landscapes. Experiments were
 conducted in summer and autumn 2018, between 11:00 and 14:00 on
 consecutive clear, sunny days. Three nurseries were sampled in both
 seasons, one was sampled in summer only, and one in autumn only. A single
 observer hand-netted male and female <em>Halictus ligatus</em>
 on patches of blooming plants over areas up to 2 ha. If <em>H.
 ligatus</em> was not sufficiently abundant, we then focused on the
 few most abundant species of non-<em>Apis</em> bees, including
 solitary species. Captured bees were iden- tified, marked on the thorax
 (Fig. 1) using nontoxic paint, then released. Paint color was used to
 indicate the plant species on which the bee was captured. The following
 day, we returned and netted marked and unmarked bees in the same and
 nearby patches where we marked bees the previous day. All individuals were
 retained in vials to ensure no individual was recaptured twice.
description: Both data files have a "metadata" tab describing the
 variables. "recapture.xlsx" contains data for
 each individual bee that was captured on the first day of an
 experiment, e.g. the bee's genus, the nursery, the season, the plant
 on which it was captured, whether it was recaptured on the second day of
 the experiment, whether it switched plants, etc.
 "electivity.xlsx" contains data used to calculate an
 electivity index for each species of plant in the experiment. For each
 species of plant at each nursery in each season, provided are data on the
 patch area as well as how many bees were captured on that plant species.
 For reference, see Jenkins, S. H. (1979). Seasonal and year-to-year
 differences in food selection by beavers. <i>Oecologia</i>,
 <i>44</i>(1), 112-116.
DOI: 10.5061/dryad.7sqv9s4pk
title: Contrasting the suitability of shade coffee agriculture and native forest as overwinter habitat for Canada Warbler (Cardellina canadensis) in the Colombian Andes.

description: In the Neotropics, coffee production occurs on a large scale in some of
 the planet’s most biodiverse regions: tropical mountains. Coffee
 production systems involving shade trees are considered to have a lower
 impact on biodiversity than alternative sun coffee. To date, the majority
 of evidence for the value of shade coffee plantations has not taken into
 account the relative quality of this habitat compared to the native
 forests they replaced. We determined the suitability of shade coffee and
 forest as winter habitat for Canada Warbler (Cardellina canadensis) by
 comparing variation in the likelihood of capturing individuals, seasonal
 changes in body condition, and estimates of annual survival between the
 two habitats. We also determined the effect of the strong 2015-2016 El
 Niño event on survival. Males were relatively more likely to be captured
 in forest than females and this likelihood increased during drier years.
 Body condition change over the winter and apparent annual survival were
 very similar for individuals that used forest and coffee. However,
 condition and survival decreased in both habitats during the El Niño year.
 Apparent survival was also lower for individuals carrying a radiotag or
 geolocator. Our findings suggest that shade coffee with high canopy cover
 and height offers similar benefits to forest in terms of body condition
 and survival. Landscape conservation approaches, promoting diverse
 matrices of structurally complex shade coffee and forest might best ensure
 long-term survival in Neotropical migrants like Canada Warbler.
description: Data were collected from December to March over five field
 seasons  (2013-2014, 2014-2015, 2015-2016, 2016-2017, and 2017-2018) in
 three study sites located on the western slope of the Eastern Andes in
 Colombia: “Hacienda La Fragua” (shade coffee 1400 m asl, forest 1500 m
 asl), “Los Vientos” (shade coffee and forest 1350 m asl); and “La Vuelta”
 (shade coffee 1400, forest 1700 m asl).  We carried out
 constant-effort mist netting at fixed banding stations from 1 December to
 30 March during eight days a month in each habitat. Weather permitting,
 12-15 mist nets (30 mm mesh) were operated from 06:00 to 11:00 h and from
 15:00 to 17:30 h. All captured birds were fitted with a U.S. Fish and
 Wildlife Service numbered aluminium band and processed and released at the
 capture site. We determined age and sex, and recorded body mass (±0.1 g,
 using an electronic balance) for each bird at first capture and for all
 birds recaptured.
DOI: 10.5061/dryad.2jm63xskd
title: Local adaptation of a parasite to solar radiation impacts disease transmission potential, spore yield, and host fecundity

description: Environmentally transmitted parasites spend time in the abiotic
 environment, where they are subjected to a variety of stressors.
 Understanding how they face this challenge is essential if we are to
 understand how host-parasite interactions may vary across environmental
 gradients. We used a zooplankton-bacteria host-parasite system where
 availability of sunlight (solar radiation) influences disease dynamics to
 look for evidence of parasite local adaptation to sunlight exposure. We
 also examined how variation in sunlight tolerance among parasite strains
 impacted host reproduction. Parasite strains collected from clearer lakes
 (with greater sunlight penetration) were most tolerant of the negative
 impacts of sunlight exposure, suggesting local adaptation to sunlight
 conditions. This adaptation came with both a cost and a benefit for
 parasites: parasite strains from clearer lakes produced relatively fewer
 transmission stages (spores) but these strains were more infective. After
 experimental sunlight exposure, the most sunlight-tolerant parasite
 strains reduced host fecundity just as much as spores that were never
 exposed to sunlight. Sunlight availability varies greatly among lakes
 around the world. Our results suggest that the selective pressure sunlight
 exposure exerts on parasites may impact both parasite and host fitness,
 potentially driving variation in disease epidemics and host population
 dynamics across sunlight availability gradients. 
description: See manuscript methods for complete methodological
 information.  Three data files include:
 1) spore counts and numbers of offspring produced throughout the
 experiment for each Daphnia host individual 2) mean
 host offspring production and calculation of parasite transmission
 potential, based on data set 1 See metadata and
 manuscript methods for details on these calculations.
 3) data corresponding with the online supplement showing
 infection (yes/no) and spore yields in clear or darkened containers in the
 laboratory portion of the experiment. See supplemental methods and
 metadata for more details.   
description: See metadata in Excel files (second tab)
DOI: 10.5061/dryad.kkwh70s25
title: Supplemental material for: The dynamics of bird diversity in the new world

description: Three prominent explanations have been proposed to explain the dramatic
 differences in species richness across regions and elevations, (1) time
 for speciation, (2) diversification rates, and (3) ecological limits. But
 the relative importance of these explanations and, especially, their
 interplay and possible synthesis remain largely elusive. Integrating
 diversification analyses, null models, and GIS, I study avian richness
 across regions and elevations of the New World. My results reveal that
 even though the three explanations are differentially important (with
 ecological limits playing the dominant role), each contributes uniquely to
 the formation of richness gradients. Further, my results reveal the likely
 interplay between the explanations. They indicate that ecological limits
 hinder the diversification process, such that the accumulation of species
 within a region gradually slows down over time. Yet, it does not seem to
 converge toward a hard ceiling on regional richness. Instead, species-rich
 regions show suppressed, but continued, diversification, coupled with
 signatures of possible competition (esp. Neotropical lowlands).
 Conversely, species-poor, newly-colonized regions show fast
 diversification and weak to no signs of competition (esp. Nearctic
 highlands). These results held across five families of birds, across grid
 cells, biomes, and elevations. Together, my findings begin to illuminate
 the rich, yet highly consistent, interplay of the mechanisms that together
 shape richness gradients in the New World, including the most species-rich
 biodiversity hotspots on the planet, the Andes and the Amazon.
description: The Supplementary Material includes 80 pages (Supplementary
 Methods and Results, 10 tables and 54 figures)