cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fp0b8
title: Data from: Towards understanding the genetic basis of mouth asymmetry in the scale-eating cichlid Perissodus microlepis

description: How polymorphisms consisting in left–right asymmetries are produced and
 maintained in natural populations is a tantalizing question, which remains
 largely unanswered. The scale-eating cichlid fish Perissodus microlepis is
 a remarkable example of extreme ecological specialization achieved by
 morphological and behavioural laterality. Its asymmetric mouth is
 accompanied by a pronounced lateralized foraging behaviour, where a
 left-bending morph preferentially feeds on the scales of the right side of
 its prey, while the opposite is true for the right morph. This striking
 asymmetry made this fish a textbook example of the astounding degree of
 ecological specialization and negative frequency-dependent selection. Yet,
 the genetic basis underlying this spectacular laterality remains unknown.
 We addressed this question through analyses of wild-caught fish using
 high-throughput DNA sequencing data. A novel array of SNP markers was
 developed by ddRAD sequencing (ddRADseq) and the use of pooled DNA samples
 (PoolSeq). We obtained more than 155 000 SNPs using ddRADseq and 3 900 000
 SNPs with PoolSeq. Among these, we identified one (ddRAD) SNP, and 38 or
 378 (PoolSeq) windows that are differentiated between the left and right
 morphs accounting for spurious associations due to geographic structuring.
 This allowed us to uncover candidate genomic regions that potentially
 contain genes for this trait. Then, this interesting trait has a genetic
 basis that is likely to be influenced by multiple loci. This result
 contributes to a greater understanding of the genetic bases of left–right
 asymmetry and, ultimately, the evolutionary processes governing the
 maintenance of this striking case of laterality.
description: READMEddRAD_SNP_morph.vcfSNP data used for ddRAD analyses of differentiation between morphs; raw Illumina sequences archived to the NCBI Accession no. PRJNA324541; vcf file created using Stacks v. 1.29Poolseq_SNP_morph.vcfSNP data used for PoolSeq analyses of differentiation between morphs; raw Illumina sequences archived to the NCBI Accession no. PRJNA324541; vcf file created using Popoolation v. 1.2.2, Popoolation2 v. 1.2.01, samtools v. 1.3.1, bcftools v. 1.3.1, htslib v. 1.3.1ddRAD_SNP_geo.vcfSNP data used for ddRAD analyses of differentiation between sampling sites; raw Illumina sequences archived to the NCBI Accession no. PRJNA324541; vcf file created using Stacks v. 1.29Poolseq_SNP_geo.vcfSNP data used for PoolSeq analyses of differentiation between sampling sites; raw Illumina sequences archived to the NCBI Accession no. PRJNA324541; vcf file created using Popoolation v. 1.2.2, Popoolation2 v. 1.2.01, samtools v. 1.3.1, bcftools v. 1.3.1, htslib v. 1.3.1Phenotype_scoresValues of mouth bending angle measured in each individual, and samples used to prepare the ddRAD and Poolseq library respectivelyPRJNA324541Link out to NCBI BioProject accession no. PRJNA324541
DOI: 10.5061/dryad.60d18
title: Data from: Violence in the prehistoric period of Japan: the spatiotemporal pattern of skeletal evidence for violence in the Jomon period

description: Whether man is predisposed to lethal violence, ranging from homicide to
 warfare, and how that may have impacted human evolution, are among the
 most controversial topics of debate on human evolution. Although recent
 studies on the evolution of warfare have been based on various
 archaeological and ethnographic data, they have reported mixed results: it
 is unclear whether or not warfare among prehistoric hunter–gatherers was
 common enough to be a component of human nature and a selective pressure
 for the evolution of human behaviour. This paper reports the mortality
 attributable to violence, and the spatio-temporal pattern of violence thus
 shown among ancient hunter–gatherers using skeletal evidence in
 prehistoric Japan (the Jomon period: 13 000 cal BC–800 cal BC). Our
 results suggest that the mortality due to violence was low and
 spatio-temporally highly restricted in the Jomon period, which implies
 that violence including warfare in prehistoric Japan was not common.
description: ESM for Violence in
 Japanese prehistoryDefinition of and
 sources of data for injured individuals in the Jomon period, and detailed
 information of all sites where skeletal remains have been
 recovered.supplement_corrected_final.docx
DOI: 10.5061/dryad.t6m9m
title: Data from: Impact of predicted precipitation scenarios on multitrophic interactions

description: 1. Predicted changes in the frequency and intensity of extreme rainfall
 events in the UK have the potential to disrupt terrestrial ecosystem
 function. However, responses of different trophic levels to these changes
 in rainfall patterns, and the underlying mechanisms, are not well
 characterised. 2. This study aimed to investigate how changes in both the
 quantity and frequency of rainfall events will affect the outcome of
 interactions between plants, insect herbivores (above- and below- ground)
 and natural enemies. 3. Hordeum vulgare L. plants were grown in controlled
 conditions and in the field, and subjected to three precipitation
 scenarios: ambient (based on a local 10 year average rainfall); continuous
 drought (40% reduction compared to ambient); drought/ deluge (40%
 reduction compared to ambient at a reduced frequency). The effects of
 these watering regimes and wireworm (Agriotes species) root herbivory on
 the performance of the plants, aphid herbivores above-ground (Sitobion
 avenae, Metapolophium dirhodum and Rhopalosiphum padi), and natural
 enemies of aphids including ladybirds (Harmonia axyridis) were assessed
 from measurements of plant growth, insect abundance and mass, and assays
 of feeding behaviour. 4. Continuous drought decreased plant biomass,
 whereas reducing the frequency of watering events did not affect plant
 biomass but did alter plant chemical composition. In controlled
 conditions, continuous drought ameliorated the negative impact of
 wireworms on plant biomass. 5. Compared to the ambient treatment, aphid
 mass was increased by 15% when feeding on plants subjected to drought/
 deluge; and ladybirds were 66% heavier when feeding on these aphids but
 this did not affect ladybird prey choice. In field conditions, wireworms
 feeding below-ground reduced the number of shoot-feeding aphids under
 ambient and continuous drought conditions but not under drought/ deluge.
 6. Predicted changes in both the frequency and intensity of precipitation
 events under climate change have the potential to limit plant growth, but
 reduce wireworm herbivory, while simultaneously promoting above-ground
 aphid numbers and mass, with these effects transferring to the third
 trophic level. Understanding the effect of future changes in precipitation
 on species interactions is critical for determining their potential impact
 on ecosystem functioning and constructing accurate predictions under
 global change scenarios.
description: Controlled environment
 and field experimental dataData file containing all
 data reported in the paper including plant, soil and insect data from
 controlled environment and field experiments. First spreadsheet in the
 data file contains a key to explain all abbreviations used throughout the
 file.Experimental
 data.xlsx
DOI: 10.5061/dryad.d715g
title: Data from: Landscape structure and the genetic effects of a population collapse

description: Both landscape structure and population size fluctuations influence
 population genetics. While independent effects of these factors on genetic
 patterns and processes are well studied, a key challenge is to understand
 their interaction, as populations are simultaneously exposed to habitat
 fragmentation and climatic changes that increase variability in population
 size. In a population network of an alpine butterfly, abundance declined
 60–100% in 2003 because of low over-winter survival. Across the network,
 mean microsatellite genetic diversity did not change. However, patch
 connectivity and local severity of the collapse interacted to determine
 allelic richness change within populations, indicating that patch
 connectivity can mediate genetic response to a demographic collapse. The
 collapse strongly affected spatial genetic structure, leading to a
 breakdown of isolation-by-distance and loss of landscape genetic pattern.
 Our study reveals important interactions between landscape structure and
 temporal demographic variability on the genetic diversity and genetic
 differentiation of populations. Projected future changes to both landscape
 and climate may lead to loss of genetic variability from the studied
 populations, and selection acting on adaptive variation will likely occur
 within the context of an increasing influence of genetic drift.
description: DryadData_MatricesData matrices containing: 1. pairwise Fst scores for all 13 populations. 2. geographic distances between each population according to whether the distance occurs over forest or meadow habitat, the sum of which is the total distance. 3. movement indices for individuals before the demographic crash and after.PreCollapseGENEPOP_UpdateGenotypic data for 7 microsatelite loci from individuals collected prior to the demographic collapse.PostCollapseGENEPOP_UpdateGenotypic data from 7 microsatelite loci from individuals collected after the demographic collapse.
DOI: 10.5061/dryad.dr275
title: Data from: Disentangling the relative importance of species occurrence, abundance and intraspecific variability in community assembly: a trait-based approach at the whole-plant level in Mediterranean forests

description: Understanding which factors and rules govern the process of assembly in
 communities constitutes one of the main challenges of plant community
 ecology. The presence of certain functional strategies along broad
 environmental gradients can help to understand the patterns observed in
 community assembly and the filtering mechanisms that take place. We used a
 trait-based approach, quantifying variations in aboveground (leaf and
 stem) and belowground (root) functional traits along environmental
 gradients in Mediterranean forest communities (south Spain). We proposed a
 new practical method to quantify the relative importance of species
 turnover (distinguishing between species occurrence and abundance) versus
 intraspecific variation, which allowed us to better understand the
 assemblage rules of these plant communities along environmental gradients.
 Our results showed that the functional structure of the studied plant
 communities was highly determined by soil environment. Results from our
 modelling approach based on maximum likelihood estimators showed a
 predominant influence of soil water storage on most of the community
 functional traits. We found that changes in community functional structure
 along environmental gradients were mainly promoted by species turnover
 rather than by intraspecific variability. Specifically, our new method of
 variance decomposition demonstrated that between-site trait variation was
 the result of changes in species occurrence rather than in the abundance
 of certain dominant species. In conclusion, this study showed that water
 availability promoted the predominance of specific trait values (both in
 above and belowground fractions) associated to a resource acquisition or
 conservation strategy. In addition, we provided evidence that changes on
 community functional structure along the environmental gradient were
 mainly promoted by a process of species replacement, which represent a
 crucial step towards a more general understanding of the relative
 importance of intraspecific versus interspecific trait variation in these
 woody Mediterranean communities.
description: Woody plant traits
 databaseFunctional traits at
 whole plant level for woody mediterranean plants on three different areas
 from Córdoba region (Spain)Dryad_database.xls
DOI: 10.18160/xjar-dnrx
title: Biogenic in-situ observations (L2), Munich Soil respiration, 2024-03-26–2024-11-27

description: Soil respiration data from Munich, Germany. Details of the measurements, file contents etc are described in ICOS Cities deliverable report D3.13.
DOI: 10.5061/dryad.4350cp14
title: Data from: Persistent genetic signatures of historic climatic events in an Antarctic octopus

description: Repeated cycles of glaciation have had major impacts on the distribution
 of genetic diversity of the Antarctic marine fauna. During glacial
 periods, ice cover limited the amount of benthic habitat on the
 continental shelf. Conversely, more habitat and possibly altered seaways,
 were available during interglacials when the ice receded and the sea level
 was higher. We used microsatellites and partial sequences of the
 mitochondrial cytochrome oxidase c subunit 1 (MT-CO1) gene to examine
 genetic structure in the direct-developing, endemic Southern Ocean octopod
 Pareledone turqueti Joubin, 1905 sampled from a broad range of areas that
 circumvent the Antarctic continent. We find that, unusually for a species
 with poor dispersal potential, P. turqueti has a circumpolar distribution
 and is also found off the islands of South Georgia and Shag Rocks. The
 overriding pattern of spatial genetic structure can be explained by
 hydrographic (with ocean currents both facilitating and hindering gene
 flow) and bathymetric features. The Antarctic Peninsula region displays a
 complex population structure, consistent with its varied topographic and
 oceanographic influences. Genetic similarities between the Ross and
 Weddell Seas, however, are interpreted as a persistent historic genetic
 signature of connectivity during the hypothesized Pleistocene Western
 Antarctic Ice Sheet collapses. A calibrated molecular clock indicates two
 major lineages within P. turqueti, a continental lineage and a
 subAntarctic lineage, that diverged in the mid-Pliocene with no subsequent
 gene flow. Both lineages survived subsequent major glacial cycles. Our
 data are indicative of potential refugia around the Antarctic continent
 within the Ross Sea, Weddell Sea and off Adélie Land, with mean age of
 mtDNA diversity within these main continental lineages coinciding with
 Pleistocene glacial cycles.
description: Pareledone_turqueti_microsatsPareledone_turquetiCOI sequence data for Pareledone turqueti individuals from Antarctica.
DOI: 10.5061/dryad.ds543
title: Data from: A new phylogeny of Stegosauria (Dinosauria, Ornithischia)

description: The stegosaurs are some of the most easily recognizable dinosaurs, but are
 surprisingly rare as fossils. Consequently much remains unknown about
 their palaeobiology, and every new stegosaurian find contributes to our
 understanding of the evolution of the clade. Since the last attempt to
 examine the evolutionary relationships of Stegosauria, new specimens have
 come to light, including the most complete individual of Stegosaurus ever
 found, new taxa have been described and, perhaps most importantly, new
 methods for analysis of cladistic datasets have been produced. In the
 light of these new data and technological advances, the phylogenetic
 relationships of the stegosaurs and basal armoured dinosaurs are
 investigated. The inclusion of continuous data results in much better
 resolution than was previously obtained, and the resulting single most
 parsimonious tree supports re-erection of the genera Miragaia and
 Hesperosaurus, which had previously been synonymized with Dacentrurus and
 Stegosaurus respectively. The recently described genus Alcovasaurus is
 resolved as a basal thyreophoran, but this is most likely a consequence of
 a very high degree of missing data and the questionable ontogenetic stage
 of the specimen. Examination of the effects of continuous data on the
 analysis suggest that while it contains a phylogenetic signal congruent
 with that of discrete data and provides better resolution than discrete
 data alone, it can affect topologies in unpredictable ways, particularly
 in areas of the tree where there are large amounts of missing data. The
 phylogeny presented here will form the basis for future work on the
 palaeobiology of the plated dinosaurs.
description: Character Taxon
 MatrixA character-taxon matrix
 for analysis of stegosaurian dinosaur relationshipsCharacter
 ListA
 character list to accompany the character-taxon matrixRaven&MaidmentOSIA file containing characters, justifications for changes made to characters, and synapomorphiesRaven&Maidment_2017_OSI.docx
DOI: 10.5061/dryad.dv2q6
title: Data from: Microclimate variability in alpine ecosystems as stepping stones for non-native plant establishment above their current elevational limit

description: Alpine environments are currently relatively free from non-native plant
 species, although their presence and abundance have recently been on the
 rise. It is however still unclear whether the observed low invasion levels
 in these areas are due to an inherent resistance of the alpine zone to
 invasions or whether an exponential increase in invasion is just a matter
 of time. Using a seed-addition experiment on north- and south-facing
 slopes (cf. microclimatic gradient) on two mountains in subarctic Sweden,
 we tested the establishment of six non-native species at an elevation
 above their current distribution limits and under experimentally enhanced
 anthropogenic pressures (disturbance, added nutrients and increased
 propagule pressure). We found a large microclimatic variability in
 cumulative growing degree days (GDD) (range = 500.77 °C, SD = 120.70 °C)
 due to both physiographic (e.g. aspect) and biophysical (e.g. vegetation
 cover) features, the latter being altered by the experimental disturbance.
 Non-native species establishment and biomass production were positively
 correlated with GDD along the studied microclimatic gradient. However,
 even though establishment on the north-facing slopes caught up with that
 on the south-facing slopes throughout the growing season, biomass
 production was limited on the north-facing slopes due to a shorter growing
 season. On top of this microclimatic effect, all experimentally imposed
 anthropogenic factors enhanced non-native species success. The observed
 microclimatic effect indicates a potential for non-native species to use
 warm microsites as stepping stones for their establishment towards the
 cold end of the gradient. Combined with anthropogenic pressures this
 result suggests an increasing risk for plant invasion in cold ecosystems,
 as such stepping stones in alpine ecosystems are likely to be more common
 in a future that will combine a warming climate with persistent
 anthropogenic pressures.
description: Lembrechts2017_Ecography_DataDatasets (Plot GDD, species establishment and species biomass) associated with the experiment described in Lembrechts et al. (2017) Microclimate variability in alpine ecosystems as stepping stones for non-native plant establishment above their current elevational limit. Ecography 40: 001–009. doi: 10.1111/ecog.03263Lembrechts2017_Ecography_DryadData_v2.zipLembrechts2017_Ecography_README.docx
DOI: 10.5061/dryad.7jv4466
title: Data from: Ocean warming and acidification may challenge the riverward migration of glass eels

description: The dramatic decline of European eel (Anguilla anguilla) populations over
 recent decades has attracted considerable attention and concern.
 Furthermore, little is known concerning the sensitivity of eel’s early
 stages to projected future environmental change. Here we investigated, for
 the first time, the potential combined effects of ocean warming (OW; ∆ +
 4oC; 18oC) and acidification (OA; ∆ - 0.4 pH units) on the survival and
 migratory behaviour of A. anguilla glass eels, namely their preference
 towards riverine cues (freshwater and geosmin). Recently arrived
 individuals were exposed to isolated and combined OW- and OA–conditions
 for 100 days, adjusting for the salinity gradients associated with
 upstream migration. A two-choice test was used to investigate migratory
 activity and shifts in preference towards freshwater environments. While
 OW decreased survival and increased migratory activity, OA appears to
 hinder migratory response, reducing the preference for riverine cues. Our
 results suggest that future conditions could potentially favor an early
 settlement of glass eels, reducing the proportion of fully-migratory
 individuals. Further research into the effects of climate change on eel
 migration and habitat selection is needed to implement efficient
 conservation plans for this critically endangered species.
description: Santos&Borges_etal_DataIn this file, the data from our study on the influence of ocean warming and ocean acidification on the riverward migration of glass eels is present. These include survival and behavioural outputs as well as a code sheet for easier table read. The tables are R software ready and can be exported as '.csv' in order to run in the Rscript.BorgesSantos_etal_Data.xlsxSantos&Borges_etal_RscriptThis is the code for the Rscript of the statistical analysis performed in our study.BorgesSantos_etal_Rscript.txt
DOI: 10.5061/dryad.6rb12hk
title: Data from: Predation risk determines pigmentation phenotype in nuthatches by melanin-related gene expression effects

description: Pigments determine the appearance of organisms. However, pigment
 production can be associated to physiological constraints as in the case
 of pheomelanin, the sulphurated form of melanin whose synthesis in
 melanocytes consumes cysteine and consequently reduces the availability of
 glutathione (GSH) to exert antioxidant protection. Pheomelanogenesis may
 thus increase the susceptibility to suffer chronic oxidative stress. I
 investigated the possibility that environmental lability in the expression
 of genes regulating pheomelanogenesis protects from oxidative stress, a
 situation in which GSH is most required. By broadcasting adult alarm
 calls, I manipulated the perception of predation risk, a natural source of
 oxidative stress, in free-living Eurasian nuthatch Sitta europaea
 nestlings developing pheomelanin-pigmented flank feathers. The
 manipulation affected the consumption of GSH that resulted from the
 expression of two genes (Slc7a11 and Slc45a2) influencing cysteine/GSH
 availability in cells, as these genes were downregulated in the feather
 melanocytes of the nestlings with lowest intracellular antioxidant
 capacity (i.e., lowest GSH levels). Systemic oxidative damage increased
 with Slc7a11 expression in feather melanocytes, suggesting that the
 observed downregulation was physiologically advantageous. The nestlings
 exposed to an increased perception of predation risk developed flank
 feathers of reduced color intensity. These results indicate that perceived
 predation risk can determine the pigmentation phenotype by (probably
 epigenetic) effects on gene expression that protect from physiological
 constraints imposed by pheomelanin production.
description: Dataset used in the
 studyPredation risk -
 Dryad.xlsPredation risk - Dryad
 readme.txt