cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tx95x69zp
title: Context dependent variation in corticosterone and phenotypic divergence of Rana arvalis populations along an acidification gradient

description: Background Physiological processes, as immediate responses to the
 environment, are important mechanisms of phenotypic plasticity and can
 influence evolution at ecological time scales. In stressful environments,
 physiological stress responses of individuals are initiated and integrated
 via the release of hormones, such as corticosterone (CORT). In
 vertebrates, CORT influences energy metabolism and resource allocation to
 multiple fitness traits (e.g. growth and morphology) and can be an
 important mediator of rapid adaptation to environmental stress, such as
 acidification. The moor frog, Rana arvalis, shows
 adaptive divergence in larval life-histories and predator defense traits
 along an acidification gradient in Sweden. Here we take a first step to
 understanding the role of CORT in this adaptive divergence. We conducted a
 fully factorial laboratory experiment and reared tadpoles from three
 populations (one acidic, one neutral and one intermediate pH origin) in
 two pH treatments (Acid versus Neutral pH) from hatching to metamorphosis.
 We tested how the populations differ in tadpole CORT profiles and how CORT
 is associated with tadpole life-history and morphological traits. Results
 We found clear differences among the populations in CORT profiles across
 the developmental stages, but only weak effects of pH treatment on CORT.
 Tadpoles from the acid origin population had, on average, lower CORT
 levels than tadpoles from the neutral origin population, and the
 intermediate pH origin population had intermediate CORT levels. Overall,
 tadpoles with higher CORT levels developed faster and had shorter and
 shallower tails as well as shallower tail muscles. Conclusions Our common
 garden results indicate among population divergence in CORT levels, likely
 reflecting acidification mediated divergent selection on tadpole
 physiology, concomitant to selection on larval life-histories and
 morphology. However, CORT levels were highly environmental context
 dependent. Jointly these results indicate a potential role for CORT as a
 mediator of multi-trait divergence along environmental stress gradients in
 natural populations. At the same time, the population level differences
 and high context dependency in CORT levels suggest that snapshot
 assessment of CORT in nature may not be reliable bioindicators of stress.
description: The methods include laboratory rearing.
DOI: 10.5061/dryad.m37pvmd3d
title: RNA allows identifying the consumption of carrion prey

description: Facultative scavenging by predatory carnivores is a prevalent but
 frequently underestimated feeding strategy. DNA-based methods for diet
 analysis, however, do not allow to distinguish between scavenging and
 predation, thus, the significance of scavenging on population dynamics and
 resource partitioning is widely unknown. Here, we present a methodological
 innovation to differentiate between scavenging and fresh prey consumption
 using prey RNA as a target molecule. We hypothesized that the rapid
 post-mortem breakdown of RNA in prey tissue should lead to a significantly
 lower detection probability of prey RNA than DNA when carrion rather than
 fresh prey is consumed. To test this hypothesis, ground beetles
 (Pseudoophonus rufipes (De Geer)) were offered either fresh or one-day-old
 dead Drosophila melanogaster fruit flies (carrion). The detectability of
 prey RNA and DNA in the beetles’ regurgitates was assessed with diagnostic
 Drosophila-specific RT-PCR and PCR assays at 0, 6, 12, 24 and 48 hours
 post-feeding. After fresh fly consumption, prey RNA and DNA were
 detectable equally well at all times. When carrion prey was consumed, the
 detection strength of prey RNA immediately after feeding was significantly
 lower than that of prey DNA and reached zero in most samples within 6
 hours of digestion. Our findings provide evidence that prey RNA allows
 distinguishing between the consumption of fresh and scavenged prey,
 thereby overcoming a long-known weakness of molecular diet analysis. The
 assessment of prey RNA offers a generally applicable approach for
 examining the importance of scavenging in food webs to unravel its
 functional consequences for populations, communities, and ecosystems.
description: In feeding experiments, ground
 beetles (<em>Pseudoophonus rufipes </em>(De Geer)) were
 offered either fresh or one-day-old dead <em>Drosophila melanogaster
 </em>fruit flies (carrion). Batches of 10-14 regurgitates were collected
 per prey type (fresh or carrion prey) at 0, 6, 12, 24, and 48 h after
 feeding. The detectability
 of prey RNA and DNA in the beetles’ regurgitates was assessed with
 diagnostic <em>Drosophila</em>-specific RT-PCR and PCR assays.
 PCR products were separated and visualized with capillary electrophoresis
 and relative fluorescent units (RFU) were recorded for each sample as a
 relative measure of prey DNA or RNA. For more details, refer to our 2022
 manuscript.
description: A ReadMe file is provided, that gives information on the content
 of the different data columns.
DOI: 10.5061/dryad.dv41ns209
title: Schistosoma mansoni raw genotype calls from exome data

description: Schistosoma mansoni, a snail-vectored, blood fluke that infects humans,
 was introduced into the Americas from Africa during the Trans-Atlantic
 slave trade. As this parasite shows strong specificity to the snail
 intermediate host, we expected that adaptation to S. American Biomphalaria
 spp. snails would result in population bottlenecks and strong signatures
 of selection. We scored 475,081 single nucleotide variants (SNVs) in 143
 S. mansoni from the Americas (Brazil, Guadeloupe, and Puerto Rico) and
 Africa (Cameroon, Niger, Senegal, Tanzania, and Uganda), and used these
 data to ask: (i) Was there a population bottleneck during colonization?
 (ii) Can we identify signatures of selection associated with colonization?
 And (iii) what were the source populations for colonizing parasites? We
 found a 2.4-2.9-fold reduction in diversity and much slower decay in
 linkage disequilibrium (LD) in parasites from East to West Africa.
 However, we observed similar nuclear diversity and LD in West Africa and
 Brazil, suggesting no strong bottlenecks and limited barriers to
 colonization. We identified five genome regions showing selection in the
 Americas, compared with three in West Africa and none in East Africa,
 which we speculate may reflect adaptation during colonization. Finally, we
 infer that unsampled African populations from central African regions
 between Benin and Angola, with contributions from Niger, are likely the
 major source(s) for Brazilian S. mansoni. The absence of a bottleneck
 suggests that this is a rare case of a serendipitous invasion, where S.
 mansoni parasites were preadapted to the Americas and were able to
 establish with relative ease.
description: We examined published exomic
 and genomic data from 178 individual <em>Schistosoma
 </em>samples/isolates, from multiple geographical locations,
 available from three studies (Berriman et al., 2009; Chevalier et al.,
 2019; Crellen et al., 2016). All exome data is from Chevalier <em>et
 al</em>. (2016) and Chevalier <em>et al</em>. (2019).
 These data were generated from individual larval miracidia hatched from
 <em>S. mansoni</em> eggs and preserved on FTA cards. Exome
 libraries were generated via whole genome amplification followed by
 targeted capture of the exome (Le Clec'h et al., 2018). This method
 specifically targets 95% (14.81 Mb) of the exome with 2x tiled probes. The
 whole genome sequence data came from adult worms cultured through
 laboratory rodents and snails for two or more generations before whole
 genome library prep and sequencing (Berriman et al., 2009; Crellen et al.,
 2016; International Helminth Genomes Consortium, 2019).
DOI: 10.5061/dryad.tb2rbp022
title: Importance of melanin-based colouration and environment in shaping intracellular glutathione levels in nestling and adult tawny owls (Strix aluco)

description: Resources allocated in reproduction are traded off against those invested
 in self-maintenance such as antioxidant response. Glutathione (GSH) is an
 intracellular antioxidant defence that scavenges reactive oxygen species,
 the deleterious byproducts of oxygen consumption. Given the role of
 intracellular GSH in pheomelanogenesis, a trade-off in GSH allocation
 between resistance to oxidative stress and melanin production may take
 place. To investigate how intracellular GSH is regulated in differently
 coloured individuals at the time of reproduction (in adults) and of
 intense melanogenesis (in nestlings), we measured the total pool of GSH
 produced ( t GSH), consumed (oxGSH) and available (redGSH) in adult tawny
 owls and their offspring which were cross-fostered between randomly chosen
 nests. Our goal was to describe potential correlations between resistance
 in oxidative stress and colour morphs in natural conditions. Nestling GSH
 levels were correlated with GSH levels in their genetic and foster parents
 suggesting that producing GSH is genetically and environmentally
 determined (although the effect of the foster nest seemed stronger). This
 species shows continuous variation in phe - omelanin reddish colouration,
 which is associated with life-history strategies. Based on the hypothesis
 of GSH dependence of pheomelanism, we expected a greater amount of oxGSH
 in dark compared to light pheomelanic nestlings, which was not the case.
 In contrast, light melanic breeding adults had higher levels of t GSH and
 redGSH than dark breeders probably because of a higher investment in
 antioxidant capacity. The link between pheomelanism and GSH may therefore
 be due to the fact that differently colored individuals have different
 life-history strategies rather than because the production of pheomelanin
 pigments requires GSH.
description: See the description of the methods in the published paper.
description: Dataset is provided in one MS Excel dataset with 3
 tabs: 1. Data collected on chicks (GSH JUV)
 2. Data collected on adults (GSH AD) 3.
 Metadata providing a description of the different column headers of GSH
 JUV and GSH AD The nest-box ID and/or Ring ID can be
 used to merge the data on adults with the data on chicks to replicate the
 analyses presented in the article.
DOI: 10.5061/dryad.ksn02v758
title: Evaluating alternative study designs for optimal sampling of species’ climatic niches

description: Ecologists have traditionally studied intraspecific variation by sampling
 species across their geographic ranges. However, whether this classic
 approach produces samples that accurately represent species’ climatic
 niches is largely unknown. Alternative, niche-based study designs using
 species’ climatic niches to inform sampling locations should more
 efficiently and completely capture the breadth of the niche, but the
 magnitude of this difference and how it may vary is unclear. Here we use
 conifers as a model system to explore these issues and reach specific
 recommendations for future sampling designs. Using an independent dataset
 of high-quality species’ occurrences, we first show that recent
 publications examining variation across geographic space do a poor job of
 capturing the full breadth of species’ niches, such that on average, only
 22% of species’ niche space was sampled. This was also true of a large
 compiled database, the International Tree-Ring Data Bank (ITRDB), which
 yielded average niche coverage of only 45%. Finally, we simulated common
 sampling designs (i.e., random points, grids, and transects) in both
 geographic and niche-based sampling frameworks. Using two sampling
 metrics, niche coverage and niche undersampling, we measured how
 completely and evenly these simulated studies characterized the niches of
 64 North American conifers. Niche-based sampling better represented
 species’ niches than geographic sampling, with the magnitude of this
 difference depending on study design and sample size. Niche-based gridded
 study designs achieved the most complete sampling at all but the smallest
 sample sizes, covering ~15-25% more of a species’ niche than similar
 designs implemented geographically. With fewer than 10 samples, however,
 all study designs performed poorly, and niche-based transects achieved
 slightly higher niche coverage. Consequently, when more than a handful of
 samples are collected, we recommend that studies seeking to characterize
 variation across a species’ niche consider using a gridded study design
 implemented in a niche-based sampling framework.
description: All the data used in this paper were compiled from freely and
 publicly available sources.  Conifer occurrence data
 was downloaded from the Conifer
 Database: https://herbaria.plants.ox.ac.uk/bol/conifers ; contact Aljos
 Farjon ( a.farjon@kew.org ) for use. Climate data was
 downloaded from the CliMond database: https://www.climond.org/ , and is
 the same climate dataset as that used in Perret et al. 2019.
 Metadata for the International Tree-Ring Data Bank (ITRDB) is
 available from the public data
 repository: https://www1.ncdc.noaa.gov/pub/data/paleo/treering/
description: The R code for all novel functions developed as part of this
 paper's analyses are contained in the attached .R file.
DOI: 10.5061/dryad.4mw6m90bp
title: Predictability and parallelism in the contemporary evolution of hybrid genomes

description: Hybridization between species is widespread across the tree of life. As a
 result, many species, including our own, harbor regions of their genome
 derived from hybridization. Despite the recognition that this process is
 widespread, we understand little about how the genome stabilizes following
 hybridization, and whether the mechanisms driving this stabilization tend
 to be shared across species. Here, we dissect the drivers of variation in
 local ancestry across the genome in replicated hybridization events
 between two species pairs of swordtail fish: Xiphophorus birchmanni × X.
 cortezi and X. birchmanni × X. malinche . We find surprisingly high levels
 of repeatability in local ancestry across the two types of hybrid
 populations. This repeatability is attributable in part to the fact that
 the recombination landscape and locations of functionally important
 elements play a major role in driving variation in local ancestry in both
 types of hybrid populations. Beyond these broad scale patterns, we
 identify dozens of regions of the genome where minor parent ancestry is
 unusually low or high across species pairs. Analysis of these regions
 points to shared sites under selection across species pairs, and in some
 cases, shared mechanisms of selection. We show that one such region is a
 previously unknown hybrid incompatibility that is shared across X.
 birchmanni × X. cortezi and X. birchmanni × X. malinche hybrid
 populations.
DOI: 10.5061/dryad.mw6m905xp
title: Data from: A diversification relay race from Caribbean-Mesoamerica to the Andes: historical biogeography of Xylophanes hawkmoths

description: The regions of the Andes and Caribbean-Mesoamerica are both hypothesized
 to be the cradle for many Neotropical lineages, but few studies have fully
 investigated the dynamics and interactions between Neotropical bioregions.
 The NewWorld hawkmoth genus Xylophanes is the most taxonomically diverse
 genus in the Sphingidae, with the highest endemism and richness in the
 Andes and Caribbean-Mesoamerica. We integrated phylogenomic and DNA
 barcode data and generated the first time-calibrated tree for this genus,
 covering 93.8% of the species diversity. We used event-based likelihood
 ancestral area estimation and biogeographic stochastic mapping to examine
 the speciation and dispersal dynamics of Xylophanes across bioregions. We
 also used trait-dependent diversification models to compare speciation and
 extinction rates of lineages associated with different bioregions. Our
 results indicate that Xylophanes originated in Caribbean-Mesoamerica in
 the Late Miocene, and immediately diverged into five major clades. The
 current species diversity and distribution of Xylophanes can be explained
 by two consecutive phases. In the first phase, the highest Xylophanes
 speciation and emigration rates occurred in the Caribbean-Mesoamerica, and
 the highest immigration rates occurred in the Andes, whereas in the second
 phase the highest immigration rates were found in Amazonia, and the Andes
 had the highest speciation and emigration rates.
DOI: 10.5061/dryad.kprr4xh5t
title: Unprecedented heat mortality of Magellanic penguins

description: Extreme weather events are becoming more frequent and severe, leading to
 an increase in direct, adverse thermoregulatory impacts to wildlife. Here
 we document an unprecedented, single day, heat-related mortality event of
 Magellanic penguins (Spheniscus magellanicus) at Punta Tombo, Chubut
 Province, Argentina, one of the largest breeding colonies for this
 species. We found 264 dead adults and 90 dead chicks in the breeding
 colony and along the beaches after recording the highest temperature in
 the shade (44°C on 19 January 2019) since the study started in December
 1982. We found dead adults and chicks in postures used to release heat,
 i.e., lying prone with flippers and feet extended away from the body
 and/or bills open. We found no evidence for other causes of mortality
 other than heat (e.g., disease, toxic algae, starvation). Adults likely
 died of dehydration, because dead adults were in significantly worse body
 condition than adults that survived. Dead adults had either empty stomachs
 or &lt; 50g of food and 27% of the dead adults died traveling between
 the nesting area and the water. More males died than females (83% male,
 17% female, n=94). In one section of the colony, ~5% of 1153 adults died
 in the heat. Mortality rates of adults were unevenly distributed across
 the colony, suggesting that the presence of microclimates or easier beach
 access were important factors to penguin survival. The body condition
 indices of dead and live chicks were similar. Chicks that died from heat
 had food in their stomachs (mean = 405 ± 128g, n=14), suggesting digestion
 inhibited their ability to thermoregulate. Documenting the effects of
 extreme weather events on populations is crucial to predicting how they
 will respond to climate change because these events, although rare, are
 expected to become more frequent and could have severe impacts on
 populations.
description: All data were collected in accordance with the University of
 Washington IACUC (Protocol #2213-02). The Offices of Turismo and Flora and
 Fauna in the Province of Chubut, Argentina provided permits.
description: Author contributions: 1. Conceived the idea,
 design, experiment (supervised research, formulated question or
 hypothesis): KAH, PDB 2. Performed the experiments
 (collected data, conducted the research): KAH, PDB 3.
 Wrote the paper (or substantially edited the paper): KAH, PDB
 4. Developed or designed methods: KAH, PDB 5.
 Analyzed the data: KAH
DOI: 10.5061/dryad.70rxwdbzp
title: The stabilising impact of natural selection on the allometry of sexual ornaments: Fish that escape locomotor constraints exhibit extravagant ornamentation

description: 1. Positive allometry has been considered a hallmark of sexual selection
 whereby larger males of superior condition develop disproportionately
 larger ornaments for their body size compared to smaller males of poorer
 condition. 2. Yet many structures known to be sexually selected often
 exhibit other allometric patterns. This has led to controversy over the
 utility of allometry in adequately capturing the signature of sexual
 selection, particularly if static (within population) and evolutionary
 (across species) allometries are functionally constrained by stabilising
 natural selection. 3. To investigate this, we evaluated the allometries of
 ornamental head crests and dorsal fins across multiple species of blenny
 fish. In particular, we compared species that occupied an aquatic
 environment—where swimming performance was expected to have constrained
 ornament size—with species that have transitioned onto land where such
 biomechanical constraints on ornament size have been removed. 4. Static
 allometries of both head crest and dorsal fin ornaments were found to be
 positive in males, but less so in females, across all species examined.
 This was consistent with the allometric theory of sexual selection that
 predicts positive allometry specifically in male ornamentation.
 Nevertheless, male allometric slopes were constrained in aquatic species
 whereas males of terrestrial species were free to exaggerate the size of
 their ornaments. Natural selection therefore appears to suppress ornament
 size in aquatics because of the biomechanical constraints associated with
 swimming. These differences in within-population static allometry between
 aquatic and terrestrial species in turn manifested in a greater
 across-species evolutionary allometric intercept, but not slope, for
 terrestrial species relative to aquatic and species. 5. These findings
 indicate that the study of ornament allometries can provide useful
 insights into the role of sexual selection on ornament elaboration and
 also help reveal the presence of opposing natural selection that might
 result in alternative allometric patterns. The relationship between static
 and evolutionary allometries remains complex, and our results caution
 against the interpretation of evolutionary allometry in the absence of a
 clear understanding of the underlying static allometries associated with
 it.
DOI: 10.5061/dryad.9p8cz8whh
title: Dates of hospitalization patients in the pediatric department of FJMUUH from 2019-2021

description: Data of electronic medical records of patients hospitalised in the
 paediatric department of  Fujian Medical University Union
 Hospital(FJMUUH) from 21 January 2019 to 20 January 2021 were analysed
 before and during the COVID-19 pandemic. During the COVID-19 outbreak
 period, paediatric hospitalisation was reduced by 29.6%, from 1255 to 884.
 The proportions of infection-related diseases (36.3% (455 cases) vs 20.8%
 (184 cases)), respiratory system-related diseases (22.5% (283 cases) vs
 9.4% (83 cases)); and endocrine, nutritional and metabolic diseases (17.1%
 (214 cases) vs 9.2% (81 cases)) decreased significantly, whereas that of
 musculoskeletal and connective tissue diseases increased from 11.0% (138
 cases) to 20.1% (178 cases), thereby becoming the most common reason for
 hospitalisation. The proportions of diseases of the nervous system (12.4%
 (156 cases) to 18.8% (166 cases)) and mental and behavioural disorders
 (0.2% (3 cases) to 2.1% (19 cases)) increased significantly. The average
 length of hospital stay increased after the outbreak (7.57±6.53 vs
 8.36±6.87).