cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0zpc8670j
title: Speciation in coastal basins driven by staggered headwater captures: Dispersal of a species complex, Leporinus bahiensis, as revealed by genome-wide SNP data

description: Past sea level changes and geological instability along watershed
 boundaries have largely influenced fish distribution across coastal
 basins, either by dispersal via palaeodrainages now submerged or by
 headwater captures, respectively. Accordingly, the South American Atlantic
 coast encompasses several small and isolated drainages that share a
 similar species composition, representing a suitable model to infer
 historical processes. Leporinus bahiensis is a freshwater fish species
 widespread along adjacent coastal basins over narrow continental shelf
 with no evidence of palaeodrainage connections at low sea level periods.
 Therefore, this study aimed to reconstruct its evolutionary history to
 infer the role of headwater captures in the dispersal process. To
 accomplish this, we employed molecular-level phylogenetic and population
 structure analyses based on Sanger sequences (5 genes) and genome-wide SNP
 data. Phylogenetic trees based on Sanger data were inconclusive, but SNPs
 data did support the monophyletic status of L. bahiensis. Both COI and SNP
 data revealed structured populations according to each hydrographic basin.
 Species delimitation analyses revealed from 3 (COI) to 5 (multilocus
 approach) MOTUs, corresponding to the sampled basins. An intricate
 biogeographic scenario was inferred and supported by Approximate Bayesian
 Computation (ABC) analysis. Specifically, a staggered pattern was revealed
 and characterized by sequential headwater captures from basins adjacent to
 upland drainages into small coastal basins at different periods. These
 headwater captures resulted in dispersal throughout contiguous coastal
 basins, followed by deep genetic divergence among lineages. To decipher
 such recent divergences, as herein represented by L. bahiensis
 populations, we used genome-wide SNPs data. Indeed, the combined use of
 genome-wide SNPs data and ABC method allowed us to reconstruct the
 evolutionary history and speciation of L. bahiensis. This framework might
 be useful in disentangling the diversification process in other
 neotropical fishes subject to a reticulate geological history.
DOI: 10.5061/dryad.ffbg79cww
title: Data from: Rhytiphora: a phylogenetic and morphological study of Australia’s largest longhorn beetle genus

description: Rhytiphora Audinet-Serville is the most speciose longhorn beetle
 (Cerambycidae) genus in Australia, with about 200 species (from nearly 40
 former genera, now synonymised into one) distributed across the entire
 continent. We used mitochondrial genome data from whole genome shotgun
 sequencing and COI barcoding of museum specimens to reconstruct the
 phylogeny of 68 Rhytiphora species, and analyse their morphological
 diversity and biogeographic history. We recovered a monophyletic
 Rhytiphora containing two distinct clades, within which all of the former
 genera (except Achriotypa) are paraphyletic. Nine morphological traits
 (including body size and the male setose ‘sex patches’) show strong
 phylogenetic signal and can be used to differentiate between the two
 clades. One clade is mainly restricted to Australia’s tropical north,
 while the other, larger clade has many species along the mesic east coast.
 Both clades have experienced multiple biome shifts, displaying a
 remarkable flexibility in habitat occupancy.
description: <strong>Alignment files</strong>
 Rhyt_WGS_core_aa.nex (core dataset (31 taxa) concatenated
 alignment of amino acids) Rhyt_WGS_core_deg.nex (core
 dataset concatenated alignment of degeneracy-recoded
 nucleotides) Rhyt_WGS_core_nt.nex (core dataset
 concatenated alignment of nucleotides)
 Rhyt_WGS_exp_aa.nex (expanded dataset (96 taxa) concatenated
 alignment of amino acids) Rhyt_WGS_exp_deg.nex
 (expanded dataset concatenated alignment of degeneracy-recoded
 nucleotides) Rhyt_WGS_exp_nt.nex (expanded dataset
 concatenated alignment of nucleotides)
 Rhyt_WGS_exp_nt_pruned (pruned dataset (70 taxa) concatenated
 alignment of nucleotides)  
 <strong>Maximum likelihood phylogenies
 (IQ-TREE)</strong> Rhyt_WGS_core_aa.tree
 (Newick-format tree from core amino acid dataset)
 Rhyt_WGS_core_deg.tree (Newick-format tree from core
 degeneracy-recoded nucleotide dataset)
 Rhyt_WGS_core_nt.tree (Newick-format tree from core nucleotide
 dataset) Rhyt_WGS_exp_aa.tree (Nexus-format tree from
 expanded amino acid dataset) Rhyt_WGS_exp_deg.tree
 (Nexus-format tree from expanded degeneracy-recoded nucleotide
 dataset) Rhyt_WGS_exp_nt-149.tree (Nexus-format tree
 from expanded nucleotide dataset, tree search #149)
 Rhyt_WGS_exp_nt-201.tree (Nexus-format tree from expanded
 nucleotide dataset, tree search #201)
 Rhyt_WGS_exp_nt-476.tree (Nexus-format tree from expanded
 nucleotide dataset, tree search #476)  
 <strong>Bayesian phylogeny
 (BEAST2)</strong> Rhyt_WGS_exp_nt_BEAST.tree
 (Nexus-format tree from pruned nucleotide dataset)
   <strong>Other
 files</strong> Rhyt_WGS_BGB_biomes.txt (input
 file for BioGeoBEARS analyses) Rhyt_WGS_morph.csv
 (morphological data file for R statistical analyses)
   <strong>README
 file</strong>
 README_Rhytiphora_WGS_Dryad_metadata.txt (detailed information on
 the data package)
DOI: 10.5061/dryad.f4qrfj6xq
title: Data for fitness analyses used in: Environmentally-induced DNA methylation is inherited across generations in water fleas (Daphnia magna)

description: Data of fitness effects of environmental stressors on Daphnia magna over
 multiple generations. Ages of first and second reproduction, and sizes of
 first and second brood were measured and used to calculate replacement
 rate. This data is part of a study on whole-genome bisulphate sequencing
 on individual Daphnia magna to assess whether environmentally-induced DNA
 methylation can persist for up to four generations.
description: A stock of Daphnia magna was sourced from Lake Bysjön (surface
 area 10 ha, 55°40'32"N 13°32'42"E) in Southern Sweden.
 Single clonal lines were kept under laboratory conditions (Radersma et
 al., 2018) and allowed to reproduce asexually for 12 months before the
 onset of the experiment. All experiments in this study used a single clone
 to minimize any genetic effects. Individual <em>Daphnia
 </em>of the generation F0 were exposed to environmental stressors or
 a control treatment from birth to first reproduction. As stressors we used
 5-azacytidine, microcystin, high temperature and zinc (for more details
 such as concentrations see the main publication). Following the first
 brood, all individuals of the F0 generation were maintained under control
 conditions. We propagated these lines down to generation F4 by isolating
 five offspring from the second brood in each generation and keeping them
 under control conditions. Subsequent generations (F2, F3 and F4) did not
 encounter the stressors. This experiment was performed three times
 simultaneously (T1, T2 and T3), to account for potential incompleteness
 due to the extinction of maternal lines, and the most complete experiment
 for each stressor was subjected to further analyses. To assess how the
 stressor treatments affect the lifetime reproductive success of exposed
 individuals and their descendants, we collected the age of first and
 second reproduction (in days) and the sizes of the first and second brood
 for all individuals of the selected experiment. We estimated fitness by
 calculating, for each individual, the intrinsic rate of population
 increase r with a univariate root finding algorithm (uniroot in R) using
 the Euler equation.
DOI: 10.5281/zenodo.18382865
title: Data for "Caldera structure and hydrology of a peralkaline island volcano revealed by integrated gravity and airborne electromagnetics"

description: Gravity and electromagnetic data.  The files will be made public upon acceptance of the associated manuscript.
DOI: 10.5281/zenodo.18382866
title: Data for "Caldera structure and hydrology of a peralkaline island volcano revealed by integrated gravity and airborne electromagnetics"

description: Gravity and electromagnetic data.  The files will be made public upon acceptance of the associated manuscript.
DOI: 10.5281/zenodo.18399875
title: Dataset for paper "First-principles guidelines to select promising van der Waals materials for hybrid photovoltaic-triboelectric nanogenerators" (https://doi.org/10.1039/D4NR02217C)
DOI: 10.5281/zenodo.18399876
title: Dataset for paper "First-principles guidelines to select promising van der Waals materials for hybrid photovoltaic-triboelectric nanogenerators" (https://doi.org/10.1039/D4NR02217C)
DOI: 10.5061/dryad.vmcvdncvj
title: Data from: Opposite effects of nutrient enrichment and an invasive snail on the growth of invasive and native macrophytes

description: Many ecosystems are now co-invaded by alien plant and herbivore species.
 The evolutionary naivety of native plants to alien herbivores can make the
 plants more susceptible to detrimental effects of herbivory than
 co-occurring invasive plants, in accordance with the apparent competition
 hypothesis. Moreover, the invasional meltdown hypothesis predicts that in
 multiply invaded ecosystems, invasive species can facilitate each other’s
 impacts on native communities. Although there is growing empirical support
 for these hypotheses, facilitative interactions between invasive plants
 and herbivores remain underexplored in aquatic ecosystems. Many freshwater
 ecosystems are co-invaded by aquatic macrophytes and mollusks and
 simultaneously experience nutrient enrichment. However, the interactive
 effects of these ecological processes on native macrophyte communities
 remain an underexplored area. To test these effects, we performed a
 freshwater mesocosm experiment in which we grew a synthetic native
 community of three macrophyte species under two levels of invasion by an
 alien macrophyte Myriophyllum aquaticum (invasion vs. no-invasion) and
 fully crossed with two levels of nutrient enrichment (enrichment vs.
 no-enrichment) and herbivory by an invasive snail Pomacea canaliculata
 (herbivory vs. no-herbivory). In line with the invasional meltdown and
 apparent competition hypotheses, we found that the proportional
 above-ground biomass yield of the invasive macrophyte, relative to that of
 the native macrophyte community, was significantly greater in the presence
 of the invasive herbivore. Evidence of a reciprocal facilitative effect of
 the invasive macrophyte on the invasive herbivore is provided by the
 results showing that the herbivore produced greater egg biomass in the
 presence than in the absence of M. aquaticum. However, nutrient enrichment
 reduced the mean proportional above-ground biomass yield of the invasive
 macrophyte. Our results suggested that herbivory by invader P.
 canaliculata may enhance invasiveness of M. aquaticum. However, nutrient
 enrichment of habitats that already harbor M. aquaticum may slow down
 invasive spread of the macrophyte. Broadly, our study underscores the
 significance of considering several factors and their interactions when
 assessing the impact of invasive species, especially considering that many
 habitats experience co-invasion by plants and herbivores and
 simultaneously undergo various other disturbances, including nutrient
 enrichment.
description: We performed a freshwater mesocosm experiment, and collected all
 data from this experiment. More details please see the Methods Section in
 the paper.
description: Details please see the ReadMe file.
DOI: 10.5061/dryad.cnp5hqc6f
title: Attitudes of university hospital staff towards in-house assisted suicide

description: Objective: To investigate staff attitudes toward assisted suicide in the
 hospital and factors influencing its practices in Switzerland. Design:
 Cross-sectional study Setting: Two University Hospitals in French speaking
 regions of Switzerland. Participants: 13’834 health care professionals
 including all personal caring for patients were invited to participate.
 Main outcome measures and other variables: Attitudes towards the
 participation of hospital health care professionals in assisted suicide
 were investigated with an online questionnaire. Results: Among all invited
 professionals, 5’127 responded by filling in the survey at least partially
 (response rate 37.0%) and 3’683 completed the entire survey (26.6%). 72.6%
 of participants approved that this practice should be authorized in their
 hospital and saw more positive than negative effects. 57.6% would consider
 assisted suicide for themselves. Non-medical professionals were 1.23 to
 5.23 times more likely to approve assisted suicide than physicians
 (p&lt;0.001). 68.8% of respondents indicated that each professional
 should have the choice whether or not to assist in suicide. Conclusions:
 This multi-professional survey sheds light on hospital staff perceptions
 of assisted suicide happening within hospital walls, which may inform the
 development of rules considering their wishes but also their reluctance.
 Further research using a mixed-methods approach could help reaching an
 in-depth understanding of staff’s attitudes and considerations towards
 assisted suicide practices.
description: A cross-sectional study was
 conducted using a self-administered online questionnaire. The instrument
 was derived from a questionnaire employed in a nationwide survey of
 general practitioners by the Swiss Academy of Medical
 Sciences. It was adapted
 for use by all hospital health care professionals. It consisted of 15 main
 questions with a total of 80 sub-questions, addressing experiences and
 practices as well as personal attitudes concerning assisted suicide. Items
 on demographic characteristics were also included. The questionnaire was
 converted to an online form using the software REDCap (Vanderbilt
 University) and a link was sent to targeted population in a two-step
 procedures: at first participating center first (University hospitals of
 Geneva), then at second participating center (Centre Hospitalier
 Universitaire Vaudois). Finally both databases were exported in STATA
 format and combined in a single database.
description: For confidentiality matters, we deleted some variables that could
 help identifying some respondents potentially (service and department
 affiliations, religion). The dataset includes all observations to
 reproduce potentially our analyses. There are some missing data in almost
 every variables.
DOI: 10.5061/dryad.k98sf7m7j
title: A high-performance Ni-CeO2/Ni/Ni-Y2O3·ZrO2 three-layer anode for direct iso-octane feeding of solid oxide fuel cells

description: Solid oxide fuel cells (SOFCs) directly fed with iso-octane are expected
 to be power sources of mobile devices and automobiles. However, the
 conventional anode catalysts nickel (Ni) or cerium oxide (CeO2) used for
 direct feeding of iso-octane do not suppress carbon deposition or generate
 high-power. In this study, we investigated the
 Ni-CeO2/Ni/Ni-yttria-stabilized zirconia (YSZ) three-layer anode to
 establish the suppression of carbon deposition and high-power generation
 in the SOFC. The anode consists of a Ni-CeO2 catalyst layer as the top
 layer, a Ni catalyst layer as the second layer, and a Ni-YSZ catalyst
 layer as the third layer on top of the electrolyte. The concept of
 three-layer anode is follows: Fuel reforming occurs in the Ni-CeO2 layer,
 the reformed H2 or CO is electrochemically oxidized in the Ni-YSZ catalyst
 layer, and the Ni catalyst middle layer prevents the reaction between YSZ
 and CeO2. Scanning electron microscopy and electrochemical
 characterization confirmed carbon deposition suppression and improved
 power generation. The anode showed no carbon deposition and generated
 high-power, 600 mA cm−2 and 150 mW cm−2, at 950 °C and a steam/carbon
 ratio of 3.0. Additionally, we discuss the fuel reforming reactions on the
 three-layer electrode by the results of exhaust gas analysis.
DOI: 10.5061/dryad.ttdz08m19
title: A test of the role of associative learning in originating sexual preferences in the guppy

description: How do female sexual preferences for male ornamental traits arise? The
 developmental origins of female preferences are still an understudied
 area, with most explanations pointing to genetic mechanisms. One
 intriguing, little-explored, alternative focuses on the role of
 associative learning in driving this process. According to this
 hypothesis, a preference learned in an ecological context can be
 transferred into a sexual context, resulting in changes in mating
 preferences as a by-product. I tested this hypothesis by first training
 female guppies to associate either orange or black colour with food
 delivery; I then presented videos of males with computer-manipulated
 coloured spots and measured female preference towards them. I also allowed
 females from both treatments to mate with males differing in their ratio
 of orange-to-black spots and measured the males’ reproductive success.
 After training, female sexual preferences significantly diverged among
 treatments in the expected direction. In addition, orange males sired a
 greater proportion of offspring with females food-conditioned on orange
 compared to those conditioned on black. These results show that mating
 preferences can arise as a by-product of associative learning, which, via
 translation into variation in male fitness, can become associated with
 indirect genetic benefits, potentially leading to further evolution.
description: Eighty virgin, mature, guppy females from a laboratory population
 were trained to associate either orange or black colour with food
 delivery. They were then individually presented videos of males with
 computer-manipulated coloured spots (black vs. orange, or black-dominated
 vs. orange-dominated) and female preference towards them was measured,
 which was approximated by the time the female spent in a zone close to a
 male compartment. Thereafter, pairs of females from both treatments were
 allowed to mate pairs of males differing in their ratio of orange-to-black
 spots and male reproductive success with each female was
 measured. All methods and results are described in the
 article: "­­­Can female guppies
 learn to like male
 colours? A test of the
 role of associative learning in originating sexual
 preferences", which has been accepted for publication in
 Proceedings of the Royal Society B.
DOI: 10.5061/dryad.zs7h44jbz
title: Photoperiod controls wing polyphenism in a water strider independently of insulin receptor signaling

description: Insect wing polyphenism has evolved as an adaptation to changing
 environments and a growing body of research suggests that the nutrient
 sensing insulin receptor signaling pathway is a hot spot for the evolution
 of polyphenisms, as it provides a direct link between increased growth and
 the available nutrients in the environment. However, little is known about
 the role of insulin receptor signaling in polyphenisms which are
 controlled by seasonal variation in photoperiod. Here, we demonstrate that
 wing length polyphenism in the water strider Gerris buenoi is determined
 by photoperiod and nymphal density, but not by nutrient availability.
 Exposure to a long-day photoperiod is highly inducive of the short-winged
 morph whereas high nymphal densities moderately promote development of
 long wings. Using RNA interference we demonstrate that, unlike in several
 other species where wing polyphenism is controlled by nutrition, there is
 no detectable role of insulin receptor signaling in wing morph induction.
 Our results indicate that the multitude of possible cues that trigger wing
 polyphenism can be mediated through multiple genetic pathways in insects.
DOI: 10.5061/dryad.8sf7m0cqr
title: High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal

description: Host-specialist parasites of endangered large vertebrates are in many
 cases more endangered than their hosts. In particular, low host population
 densities and reduced among-host transmission rates are expected to lead
 to inbreeding within parasite infrapopulations living on single host
 individuals. Furthermore, spatial population structures of
 directly-transmitted parasites should be concordant with those of their
 hosts. Using population genomic approaches, we investigated inbreeding and
 population structure in a host-specialist seal louse (Echinophthirius
 horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis),
 which is endemic to Lake Saimaa in Finland and is one of the most
 endangered pinnipeds in the world. We conducted genome resequencing of
 pairs of lice collected from 18 individual Saimaa ringed seals throughout
 the Lake Saimaa complex. Our analyses showed high genetic similarity and
 inbreeding between lice inhabiting the same individual seal host,
 indicating low among-host transmission rates. Across the lake, genetic
 differentiation among individual lice was correlated with their geographic
 distance, and assignment analyses revealed a marked break in the genetic
 variation of the lice in the middle of the lake, indicating substantial
 population structure. These findings indicate that movements of Saimaa
 ringed seals across the main breeding areas of the fragmented Lake Saimaa
 complex may in fact be more restricted than suggested by previous
 population-genetic analyses of the seals themselves.
DOI: 10.5061/dryad.qjq2bvqj1
title: Climatic refugia and reduced extinction correlate with underdispersion in mammals and birds in Africa

description: Macroevolutionary patterns, often inferred from metrics of community
 relatedness, are often used to ascertain major evolutionary processes
 shaping communities. These patterns have been shown to be informative of
 biogeographic barriers, of habitat suitability and invasibility
 (especially with regards to environmental filtering), and of regions that
 function as evolutionary cradles (i.e., sources of diversification) or
 museums (i.e., regions of reduced extinction). Here, we analysed
 continental datasets of mammal and bird distributions to identify primary
 drivers of community evolution on the African continent for
 mostly-endothermic vertebrates. We find that underdispersion (i.e.,
 relatively low phylogenetic diversity compared to species richness)
 closely correlates with specific ecoregions that have been identified as
 climatic refugia in the literature, regardless of whether these specific
 regions have been touted as cradles or museums. Using theoretical models
 of identical communities that differ only with respect to extinction
 rates, we find that even small suppressions of extinction rates can result
 in underdispersed communities, supporting the hypothesis that climatic
 stability can lead to underdispersion. We posit that large-scale patterns
 of under- and overdispersion between regions of similar species richness
 are more reflective of a particular region’s extinction potential, and
 that the very nature of refugia can lead to underdispersion via the steady
 accumulation of species richness through diversification within the same
 ecoregion during climatic cycles. Thus, patterns of environmental
 filtering can be obfuscated by environments that coincide with
 biogeographic refugia, and considerations of regional biogeographic
 history are paramount for inferring macroevolutionary processes. --
description: Full data processing methodology is available in the associated
 manuscript.
description: Codes are detailed in the attached pdf. This pipeline was
 formatted to run on a Linux operating system; filepaths have been redacted
 and adjustments will need to be made for other operating
 systems.