cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8sf7m0ctt
title: Data for: Sex-specific transgenerational plasticity: Developmental temperatures of mothers and fathers have different effects on sons and daughters

description: Each parent can influence offspring phenotypes via provisioning of the
 zygote or sex-specific DNA methylation. Transgenerational plasticity may
 therefore depend on environmental conditions experienced by each parent.
 We tested this hypothesis by conducting a fully factorial experiment
 across three generations of guppies (Poecilia reticulata), determining the
 effects of warm (28°C) and cold (21°C) thermal backgrounds of mothers and
 fathers on mass and length, and thermal performance (sustained [Ucrit] and
 sprint swimming speeds, citrate synthase and lactate dehydrogenase
 activities; 18, 24, 28, 32 and 36°C test temperatures) of sons and
 daughters. Offspring sex was significant for all traits except for sprint
 speed. Warmer mothers produced sons and daughters with reduced mass and
 length, and warmer fathers produced shorter sons. Ucrit of male offspring
 was greatest when both parents were raised at 28°C, and warmer fathers
 produced daughters with greater Ucrit. Similarly, warmer fathers produced
 sons and daughters with greater metabolic capacities. We show that thermal
 variation experienced by parents can modify offspring phenotypes, and that
 predicting the impacts of environmental change on populations would
 require knowledge of the thermal background of each mothers and fathers,
 particularly where sexes are spatially segregated.
DOI: 10.5061/dryad.dncjsxm4v
title: Supplementary tables for: Dependent variable selection in phylogenetic generalized least squares regression analysis under Pagel’s lambda model

description: Phylogenetic generalized least squares (PGLS) regression is widely used to
 detect evolutionary correlations. In contrast to the equal treatment of
 analyzed traits in conventional correlation methods such as Pearson and
 Spearman's rank tests, we must designate one trait as the independent
 variable and the other as the dependent variable. However, in our PGLS
 regression analyses (using Pagel’s λ model) of both empirical and
 simulated datasets, switching independent and dependent variables yielded
 many conflicting results. A serious problem with PGLS regression that has
 not been noticed before is that selecting an inappropriate trait as the
 dependent variable will often result in an error. To assess correlations
 in simulated data, we established a gold standard by analyzing changes in
 traits along phylogenetic branches. Next, we tested seven potential
 criteria for dependent variable selection: log-likelihood, Akaike
 information criterion, R2, p-value, Pagel’s λ, Blomberg et al.’s K, and
 the estimated λ in Pagel’s λ model. We determined that the last three
 criteria performed equally well in selecting the dependent variable and
 were superior to the other four. For practicality, we suggest using the
 trait with a higher λ or K value as the dependent variable in future PGLS
 regressions. In analyzing the evolutionary relationship between two
 traits, we should designate the trait with a stronger phylogenetic signal
 as the dependent variable even if it could logically assume the cause in
 the relationship.
description: Using different models and variances, we
 conducted 16,000 simulations of the evolution of two traits
 (<em>X<sub>1</sub></em> and
 <em>X<sub>2</sub></em>) along a binary tree with
 100 terminal nodes.  Supplementary Table S1 includes all the PGLS
 regression analysis results, the gold standard for the correlation of each
 simulation established by analyzing changes in traits along phylogenetic
 branches, and the values of log-likelihood, Akaike
 information
 criterion, <em>R</em><sup>2</sup>, <em>p</em>-value, Pagel’s <em>λ</em>, Blomberg et al.’s <em>K</em>, and the estimated <em>λ</em> in Pagel’s <em>λ</em> model of each simulated trait or each PGLS regression. Supplementary Table S2 shows the differences in the performance of the models selected by seven criteria observed in the analysis of all 16,000 simulations.
DOI: 10.25430/researchdata.cab.unipd.it.00001750
title: Laboratory Experiments on Stony Debris Flow Countermeasures

description: Results about the evaluation of the effectiveness of a novel open-type dam with drainage system for mitigating stony debris flows using small-scale experiments
DOI: 10.5061/dryad.dv41ns23z
title: Data from: Hybridization and adaptive introgression in a marine invasive species in native habitats

description: Hybridization of distinct populations or species is an important
 evolutionary driving force. For invasive species, hybridization can
 enhance their competitive advantage in the non-native range as a source of
 adaptive novelty by introgression of selectively favoured alleles. We use
 single-nucleotide polymorphism arrays (SNP-chips) to assess genetic
 diversity and population structure in the invasive ctenophore Mnemiopsis
 leidyi in native habitats along the USA east coast. Hybrids are present at
 the distribution border of the two lineages. However, our data suggests
 selection against hybrids in stable habitats, while hybrids are selected
 for in fluctuating environments. Hybrid populations thriving in extreme
 and unstable environments of the native range, such as the Chesapeake Bay,
 could accelerate the invasion success if translocated. For M.
 leidyi, this is especially relevant as low salinity currently limits its
 invasion range in western Eurasia. Hybridization status is thus
 important but currently disregarded to determine high-risk areas for
 ballast water exchange.
description: All individuals were genotyped
 at a total of 96 single nucleotide polymorphisms (SNPs) using a high
 throughput low-density SNP-chip array developed from whole-genome re-sequencing data (Pujolar et al. 2022). SNP genotyping was
 performed using Fluidigm
 96.96 Dynamic Arrays (Fluidigm Corporation, San Francisco,
 CA, USA). The Fluidigm system uses nano-fluidic circuitry to allow for the simultaneous
 genotyping of up to 96
 samples with 96 loci (described in Seeb
 et al. 2009). Genotypes were called and compiled using the Fluidigm SNP
 Genotyping Analysis software.
DOI: 10.5061/dryad.18931zd2t
title: Data for: Prediction in cultured cortical neural networks

description: Theory suggest that networks of neurons may predict their input.
 Prediction may underlie most aspects of information processing, and is
 believed to be involved in motor and cognitive control and decision
 making. Retinal cells have been shown to be capable of predicting visual
 stimuli, and there is some evidence for prediction of input in the visual
 cortex and hippocampus. However, there is no proof that the ability to
 predict is a generic feature of neural networks. We investigated whether
 random in vitro neuronal networks can predict stimulation, and how
 prediction is related to short and long-term memory. To answer these
 questions we applied two different stimulation modalities. Focal
 electrical stimulation has been shown to induce long term memory traces,
 whereas global optogenetic stimulation did not. We used mutual information
 to quantify how much activity recorded from these networks reduces the
 uncertainty of upcoming stimuli (prediction) or recent past stimuli
 (short-term memory).      Cortical
 neural networks did predict future stimuli, with the majority of all
 predictive information provided by the immediate network response to the
 stimulus. Interestingly, prediction strongly depended on short-term memory
 of recent sensory inputs during focal as well as global stimulation.
 However, prediction required less short-term memory during focal
 stimulation. Furthermore, the dependency on short-term memory decreased
 during 20h of focal stimulation, when long-term connectivity changes were
 induced. These changes are fundamental for long-term memory formation,
 suggesting that besides short-term memory the formation of long-term
 memory traces may play a role in efficient prediction.
DOI: 10.5061/dryad.qjq2bvqmv
title: Effects of plant traits and ecosystem properties on wave attenuation and soil carbon content

description: Understanding the relationships among the environment, species traits and
 ecosystem properties is important for developing management measures that
 optimize the delivery of ecosystem services (ESs). Here, we identify the
 most important relationships responsible for the delivery of two key ESs
 provided by tidal marshes: (1) nature-based shoreline protection through
 wave attenuation and (2) mitigation of climate change through soil carbon
 storage. In two tidal zones below and above the mean high water (MHW, Elbe
 Estuary, Germany) level, we measured environmental parameters, such as
 soil salinity and inundation, as well as plant traits representing
 adaptations to hydrodynamic stress and strongly influencing decomposition
 rates. Multiple linear regression results showed that wave attenuation
 rates were positively related to aboveground community biomass and stem
 bending resistance, and soil organic carbon was positively related to
 stem-specific density (below the MHW level). In the tidal zone above the
 MHW level, soil carbon density was governed by inundation duration and
 decomposition rates. Our study highlights that (1) ES delivery is not
 equally spread across tidal marshes and (2) ecosystem management should
 stimulate the development and persistence of habitat diversity (here, low
 and high marsh zones) to maximize ES delivery potential. Securing the
 delivery of the two studied ESs under climate change will depend on
 providing suitable (landward) space to sustain the functioning of the two
 marsh zones. In the studied marshes, these services are highly dependent
 on a few species (i.e., wave attenuation on Schoenoplectus tabernaemontani
 and Bolboschoenus maritimus and carbon storage on Phragmites australis),
 and as such, current and future ESs strongly depend on specific species’
 responses to changing environmental conditions.
description: Microsoft Excel
DOI: 10.5061/dryad.xsj3tx9mj
title: Data from: Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

description: Subgenome dominance after whole-genome duplication generates distinction
 in gene number and expression at the level of chromosome sets, but it
 remains unclear how this process may be involved in evolutionary novelty.
 Here, we generated a chromosome-scale genome assembly of the Asian pitcher
 plant Nepenthes gracilis to analyze how its novel traits (dioecy and
 carnivorous pitcher leaves) are linked to genomic evolution. We found a
 decaploidal karyotype with a complete set of syntenic chromosomes
 (2n=10x=80) yet with a clear indication of subgenome dominance and highly
 diploidized gene contents. The male-linked and pericentromerically located
 region on the putative sex chromosome was identified in a recessive
 subgenome and harbored three transcription factors involved in flower and
 pollen development, including a likely neofunctionalized LEAFY duplicate.
 Transcriptomic and syntenic analyses suggested that the
 paleopolyploidization events seeded genes that subsequently formed tandem
 clusters in recessive subgenomes with the specific expression in the
 digestive zone, where specialized cells digest prey and absorb derived
 nutrients. Novel gene evolution in recessive subgenomes is likely to be
 prevalent there because duplicates were enriched with Nepenthes-specific
 genes with tissue-specific expression, including those expressed in
 pitcher-specific tissues. Thus, subgenome dominance likely contributed to
 evolutionary novelty by allowing recessive subgenomes to serve as a
 preferred host of novel tissue-specific duplicates. Our results provide
 insight into how polyploids, which may frequently be evolutionary
 dead-ends, have given rise to novel traits in exceptionally thriving
 high-ploidy lineages.
DOI: 10.6086/d18t16
title: Dataset for: Untangling the assassin’s web: Phylogeny and classification of the spider-associated Emesine complex (Hemiptera: Reduviidae)

description: Web-building spiders are formidable predators, yet assassin bugs in the
 Emesine Complex (Hemiptera: Reduviidae: Emesinae, Saicinae, and
 Visayanocorinae) prey on spiders. The Emesine Complex comprises
 &gt;1,000 species and these web-associated predatory strategies may
 have driven their diversification. However, lack of natural history data
 and a robust phylogenetic framework currently preclude tests of this
 hypothesis. We combine Sanger (207 taxa, 3,865 bp) and high-throughput
 sequencing data (15 taxa, 381 loci) to generate the first taxon- and
 data-rich phylogeny for this group. We discover rampant paraphyly among
 subfamilies and tribes, necessitating revisions to the classification. We
 use ancestral character state reconstructions for 40 morphological
 characters to identify diagnostic features for a revised classification.
 Our new classification treats Saicinae Stål and Visayanocorinae Miller as
 junior synonyms of Emesinae Amyot and Serville, synonymizes the emesine
 tribes Ploiariolini Van Duzee and Metapterini Stål with Emesini Amyot and
 Serville, and recognizes six tribes within Emesinae (Collartidini
 Wygodzinsky, Emesini, Leistarchini Stål, Oncerotrachelini trib. nov.,
 Saicini Stål stat. nov., and Visayanocorini Miller stat. nov.). We show
 that a pretarsal structure putatively involved in web-associated behaviors
 evolved in the last common ancestor of Emesini, the most species-rich
 clade within Emesinae, suggesting that web-associations could be
 widespread in Emesinae.
DOI: 10.5061/dryad.xwdbrv1jn
title: Impact of multiple soil microbial inoculants on biomass and biomass allocation of the legume crop field pea (Fabaceae: Pisum sativum L.)

description: Food production is a global challenge and consequently, there is
 considerable interest in manipulating the rhizobiome using microbial
 inoculants (MI) to support sustainable agriculture. We investigated how
 three commercially-available types of plant growth-promoting MI, alone and
 in combination (B5: five species of Bacillus bacteria, GP: four species of
 Trichoderma fungi, N2: Paenibacillus polymyxa bacteria) impacted field pea
 (Fabales: Fabaceae, Pisum sativum L.) in the greenhouse and a two-year
 field experiment in the United States, North Dakota, NDSU Field Research
 station at Prosper ND. CON indicates controls that did not receive any MI
 and FC is the fertilizer control in the field experiment which also did
 not receive any MI. The dataset consists of data plant data from a 2-wk
 greenhouse experiment (GH 2wk), a 4-wk greenhouse experiment (GH 4wk), and
 a two-year field experiment (field). In the greenhouse, we found that
 effects of MI on plant performance varied, with positive effects of MI
 only apparent when plants were grown in the winter and likely under
 greater stress because they lacked nodules. Plants grown in the summer had
 nodules, and two-week-old MI plants had less root biomass and total plant
 weight than non-inoculated controls, but weight of four-week-old MI plants
 was similar to or greater than controls. In the field, the root-to-shoot
 biomass ratio was highest in non-inoculated controls, and positive effects
 of N2 on shoots and B5 on shoots and pod densities didn’t translate into
 differences in pod weight or total plant weight. In most cases, plants
 inoculated with all three inoculants performed similarly to those
 receiving a single inoculant, while root colonization by arbuscular
 mycorrhizal fungi (AMF) was higher for B5 plants than plants in the other
 treatments. This research underscores the need to consider microbial and
 environmental context when evaluating MI.
DOI: 10.5061/dryad.05qfttf7x
title: Data and R script for: Barriers to chimpanzee gene flow at the south‐east edge of their distribution

description: Populations on the edge of a species' distribution may represent an
 important source of adaptive diversity, yet these populations tend to be
 more fragmented and are more likely to be geographically isolated. Lack of
 genetic exchanges between such populations, due to barriers to animal
 movement, can not only compromise adaptive potential but also lead to the
 fixation of deleterious alleles. The south‐eastern edge of chimpanzee
 distribution is particularly fragmented, and conflicting hypotheses have
 been proposed about population connectivity and viability. To address this
 uncertainty, we generated both mitochondrial and MiSeq‐based
 microsatellite genotypes for 290 individuals ranging across western
 Tanzania. While shared mitochondrial haplotypes confirmed historical gene
 flow, our microsatellite analyses revealed two distinct clusters,
 suggesting two populations currently isolated from one another. However,
 we found evidence of high levels of gene flow maintained within each of
 these clusters, one of which covers an 18,000 km2 ecosystem.
 Landscape genetic analyses confirmed the presence of barriers to gene flow
 with rivers and bare habitats highly restricting chimpanzee movement. Our
 study demonstrates how advances in sequencing technologies, combined with
 the development of landscape genetics approaches, can resolve ambiguities
 in the genetic history of critical populations and better inform
 conservation efforts of endangered species.
DOI: 10.5061/dryad.2jm63xsv9
title: Pollinator sharing and hybridization in a pair of dioecious figs sheds light on the pathways to speciation

description: The dynamics and processes underlying the co-diversification of
 plant–pollinator interactions are of great interest to researchers of
 biodiversity and evolution. Co-speciation is generally considered
 to be a key process in generating the diversity of figs and
 their pollinating wasps. Groups of closely-related
 figs pollinated by separate wasps occur
 frequently and represent excellent opportunities to study ongoing
 diversification in this textbook mutualism. We study two closely-related
 sympatric
 dioecious figs (F. heterostyla and F. squamosa) in Xishuangbanna, southwest China, and aim to document what is likely to be the final stages of speciation between these species using a combination of trait data and experimental manipulation. Thirty-seven and 29 floral volatile compounds were identified from receptive F. heterostyla and F. squamosa figs respectively, with 25 compounds shared by both species. Interspecific variation in chemical dissimilarity was significant but relatively low. Ovipositor lengths lie well within the range required for access to heterospecific ovules, facilitating hybridization. Cross-introduction of wasps into figs was conducted and hybrid seeds were generated for all donor/recipient combinations. Wasps of F. heterostyla produce adult offspring in F. squamosa figs, while wasps of F. squamosa induce gall development in F. heterostyla figs and their offspring fail to mature in synchrony with their novel host. We record limited geographic barriers, limited volatile dissimilarity, compatible morphology, complementary reproductive phenologies and the production of hybrid seeds and wasp offspring. We hypothesize that this incomplete wasp specialization and incomplete reproductive isolation may generalize to other closely-related figs.
description: This data set was collated from manual counting. Methods for data
 acquiring, extracting, inclusion criteria, processing, and analysis are
 described in the paper's Material & Methods
 section.
description: Data are provided as Excel files. Researchers interested in the
 re-use of this data set are asked to contact the authors of the data set
 for collaboration.
DOI: 10.5061/dryad.x95x69pqf
title: Growth of Thalassiosira gravida and Thalassiosira rotula across different levels of temperature, photoperiod, and microbiome presence

description: The provided data represent maximum growth rates of the temperate diatom
 Thalassiosira rotula obtained from the Harder Lab (University of
 Bremen; strain T. rotula_S16) and the polar diatom Thalassiosira gravida
 was obtained from the Norwegian culture collection of algae (NORCCA strain
 number UIO 478). Data were assessed in a nanocosm (microtiter-plate) 7-day
 multi-stressor laboratory experiment conducted in November 2022. The
 experimental design includes different combinations of temperature (4°C;
 9°C; 13.5°C), photoperiod (4:20; 16:8; 24:0) and microbiome presence
 (xenic; axenic) at which growth was assessed to evaluate interactive
 effects of abiotic factors (temperature & photoperiod) and biotic
 facors (interactions with microbiome bacteria). Moreover, the code to
 process the data for statistical analysis is provided.
description: Diatom cultures were pre-acclimatized to
 experimental conditions for 7 days by inoculating 40 ml batch cultures
 with 500 cells ml<sup>-1 </sup>(2000 cells
 ml<sup>-1</sup> for treatments with 4h photoperiod to obtain
 sufficient biomass) which were grown at each of the nine treatment
 conditions to allow acclimatization of fluorophores. The actual subsequent
 multifactorial experiment was conducted in white 96-well plates (Greiner,
 Germany) with 300 µl experimental units and 48 replicates per treatment.
 After chlorophyll-a fluorescence of the acclimatized stock cultures was
 measured with a photo-spectrometric plate reader (ClarioStar Plus BMG
 Labtech, excitation 440 nm, emission 680 nm) plates were inoculated at twice the initial
 fluorescence units of the blank values measured in the growth medium. To
 maintain sterile conditions, the 96-well plates were sealed with a
 gas-permeable membrane (Breathe-Easy, Sigma-Aldrich, United States).
 Plates were incubated in climate cabinets at the respective experimental
 temperature and were placed onto LED tables emitting 50 µmol
 m<sup>-2</sup> s<sup>-1</sup> under the
 photoperiod settings above. Fluorescence intensity was measured daily at
 the same time after 5 minutes of dark acclimation and the experiment was
 terminated after seven days. After blank values of fluorescence in the
 growth medium were subtracted from the experimental fluorescence data,
 maximum growth rates (µ<sub>max</sub>) were calculated for
 each experimental unit by fitting non-linear models to the data using the
 “growthrates” package (Petzoldt, 2020).
description: The dataset (plateassay_growthrates.xlsx) can be opened with
 Excel and the code for running the statistical analysis is an R script
 (giesler23.r).