cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hg549
title: Data from: The global distribution of diet breadth in insect herbivores

description: Understanding variation in resource specialization is important for
 progress on issues that include coevolution, community assembly, ecosystem
 processes, and the latitudinal gradient of species richness. Herbivorous
 insects are useful models for studying resource specialization, and the
 interaction between plants and herbivorous insects is one of the most
 common and consequential ecological associations on the planet. However,
 uncertainty persists regarding fundamental features of herbivore diet
 breadth, including its relationship to latitude and plant species
 richness. Here we use a global dataset to investigate host range for over
 7,500 insect herbivore species covering a wide taxonomic breadth and
 interacting with more than 2,000 species of plants in 165 families. We ask
 whether relatively specialized and generalized herbivores represent a
 dichotomy, rather than a continuum from few to many host families and
 species attacked, and whether diet breadth changes with increasing plant
 species richness towards the tropics. Across geographic regions and
 taxonomic subsets of the data, we find that the distribution of diet
 breadth is fit well by a discrete, truncated Pareto power law
 characterized by the predominance of specialized herbivores and a long,
 thin tail of more generalized species. Both the taxonomic and phylogenetic
 distributions of diet breadth shift globally with latitude, consistent
 with a higher frequency of specialized insects in tropical regions. We
 also find that more diverse lineages of plants support assemblages of
 relatively more specialized herbivores, and that the global distribution
 of plant diversity contributes to, but does not fully explain, the
 latitudinal gradient in insect herbivore specialization.
description: dietBreadthArchivedDiet breadth data: each row indicates the number of herbivores ("Count") with a given diet breadth at a given site. Further details (such as species or family-level diet breadth) under the "Data" column.
DOI: 10.5061/dryad.8083
title: Data from: Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine-mapping by selective sweep analysis

description: Drosophila melanogaster is a cosmopolitan species that colonizes a great
 variety of environments. One trait that shows abundant evidence for
 naturally segregating genetic variance in different populations of D.
 melanogaster is cold tolerance. Previous work has found quantitative trait
 loci (QTL) exclusively on the second and the third chromosomes. To gain
 insight into the genetic architecture of cold tolerance on the X
 chromosome and to compare the results with our analyses of selective
 sweeps, a mapping population was derived from a cross between substitution
 lines that solely differed in the origin of their X chromosome: one
 originates from a European inbred line, the other one from an African
 inbred line. We found a total of six QTL for cold tolerance factors on the
 X chromosome of D. melanogaster. Although the composite interval mapping
 revealed slightly different QTL profiles between sexes, a coherent model
 suggests that most QTL overlapped between sexes and each explained around
 5-14% of the genetic variance (which may be slightly overestimated). The
 allelic effects were largely additive, but we also detected two
 significant interactions. Taken together, this provides evidence for
 multiple QTL that are spread along the entire X chromosome and whose
 effects range from low to intermediate. One detected transgressive QTL
 influences cold tolerance in different ways for the two sexes. While
 females benefit from the European allele increasing their cold tolerance,
 males tend to do better with the African allele. Finally, using selective
 sweep mapping the candidate gene CG16700 for cold tolerance co-localizing
 with a QTL was identified.
description: Svetec et
 alR
 input file for QTL analysis: 1 column: ID of fly line, 2 column: female
 CCRT, 3 column: male CCRT, 4-26 column: Genotype (African=2, European=0),
 1 row: female, male, marker ID (25-444), 2 row: Chromosome ID (X), 3 row:
 Marker position in cM (for actual position in base pairs see Supplementary
 Table 1)
DOI: 10.5061/dryad.8ss7096
title: Data from: Fish in habitats with higher motorboat disturbance show reduced sensitivity to motorboat noise

description: Anthropogenic noise can negatively impact many taxa worldwide. It is
 possible that in noisy, high-disturbance environments the range and
 severity of impacts could diminish over time, but the influence of
 previous disturbance remains untested in natural conditions. This study
 demonstrates effects of motorboat noise on the physiology of an endemic
 cichlid fish in Lake Malaŵi. Exposure to motorboats driven 20–100 m from
 fish and loudspeaker-playback of motorboat noise both elevated
 oxygen-consumption rate at a single lower-disturbance site, characterised
 by low historic and current motorboat activity. Repeating this assay at
 further lower-disturbance sites revealed a consistent effect of elevated
 oxygen consumption in response to motorboat disturbance. However, when
 similar trials were repeated at four higher-disturbance sites, no effect
 of motorboat exposure was detected. These results demonstrate that
 disturbance history can affect local population responses to noise. Action
 regarding noise pollution should consider the past, as well as the
 present, when planning for the future.
description: Harding et al.
 dataData collected in the
 field from Lake Malawi and includes three corresponding excel tabs for the
 respective elements of the manuscript (Single lower-disturbance site,
 lower-disturbance sites, higher-disturbance sites).
DOI: 10.15468/dl.b8drf5
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Protoschwenkia mandonii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 36 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000980-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hm304
title: Data from: Genetic diversity of the imperiled bath sponge Spongia officinalis Linnaeus, 1759 across the Mediterranean Sea: patterns of population differentiation and implications for taxonomy and conservation

description: The Mediterranean bath sponge Spongia officinalis is an iconic species
 with high socio-economic value and imperiled present and future status due
 to unregulated harvesting, mortality incidents and lack of established
 knowledge regarding its ecology. This study aims to assess genetic
 diversity and population structure of the species at different geographic
 sectors and levels of geographic distance along its distribution. For this
 purpose, 11 locations in the eastern Mediterranean (Aegean Sea), western
 Mediterranean (Provence coast), and the Strait of Gibraltar were sampled;
 specimens were analysed using partial mitochondrial cytochrome oxidase
 subunit I (COI) sequences, along with a set of 8 microsatellite loci.
 According to our results (i) no genetic differentiation exists among the
 acknowledged Mediterranean morphotypes and presumably S. officinalis can
 be viewed as a single, morphologically variable species; (ii) a notable
 divergence was recorded in the Gibraltar region, indicating the possible
 existence of a cryptic species; (iii) restriction to gene flow was
 evidenced between the Aegean Sea and Provence giving two well-defined
 regional clusters, thus suggesting the existence of a phylogeographic
 break between the two systems; (iv) low levels of genetic structure, not
 correlated to geographic distance, were observed inside geographic
 sectors, implying mechanisms (natural or anthropogenic) that enhance
 dispersal and gene flow, promoting population connectivity; (v) the
 genetic diversity of S. officinalis is maintained high in most studied
 locations despite pressure from harvesting and the influence of
 devastating epidemics. These findings provide a basis towards the
 effective conservation and management of the species.
description: Microsatellite scores of
 Spongia officinalis, genetic diversity in the Mediterranean
 SeaDailianis
 et al 2011 MolEcol msats.txt
DOI: 10.5061/dryad.4qq6v
title: Data from: Fine-scale forest variability and biodiversity in the boreal mixedwood forest

description: Local spatial variation in species distributions is driven by a mix of
 abiotic and biotic factors, and understanding such hierarchical variation
 is important for conservation of biodiversity across larger scales. We
 sought to understand how variation in species composition of understory
 vascular plants, spiders, and carabid beetles is associated with
 concomitant spatial variation in forest structure on a 1-ha permanent plot
 in a never-cut mixedwood forest in central Alberta (Canada). Using
 correlations among dendrograms produced by cluster analysis we associated
 data about mapped distribution of all living and dead stems &gt; 1 cm
 diameter at breast height with distributions of the three focal taxa
 sampled from regular grids across the plot. Variation in each of these
 species assemblages were significantly associated with several forest
 structure variables at various spatial scales, but the scale of the
 associations varied among assemblages. Variation in species richness and
 abundance was explained mostly by changes in basal area of trees across
 the plot; however, other variables (e.g., snag density and tree density)
 were also important, depending on assemblage. We conclude that fine-scale
 habitat variation is important in structuring spatial distribution of the
 species of the forest floor, even within a relatively homogeneous natural
 forest. Thus, assessments that ignore within-stand heterogeneity and
 management that ignores its maintenance will have limited utility as
 conservation measures for these taxa, which are major elements of forest
 biodiversity.
description: Biodiversity and Forest
 Structure at George Lake PSPData from a permanent
 sampling plot (PSP) in central Alberta (Canada). All live and dead stems
 with DBH &gt; 1.0 cm were identified and mapped within a 1 Ha (100m x
 100m) plot. The plot was subdivided into 25 non-overlapping subplots (20m
 x 20m) and stem data summarized at this level. In addition, from each of
 these 25 subplots, biodiversity data (ground-dwelling spiders and carabid
 beetles, foliage-dwelling spiders, and understory vascular plants) were
 collected. The data consists of six spreadsheets. The first sheet contains
 univariate summaries of forest structure for each subplot (live and dead
 stem density and basal area, and in three DBH classes: DBH1: 1.0-4.9 cm;
 DBH2: 5-20 cm; DBH3: &gt; 20 cm). The second sheed contains multivariate
 summaries of forest structure for each subplot (live and dead stem density
 and basal area by species). The remaining sheets contain raw abundances
 (ground-dwelling spiders and carabid beetles, and foliage-dwelling
 spiders) or percent cover (understory vascular plants) for species
 collected and/or observed in each of the 25 subplots.Pinzon et
 al_DOI_10.1111ecog.03379.xlsx
DOI: 10.5061/dryad.s3k34
title: Data from: Heritable variation in host tolerance and resistance inferred from a wild host– parasite system

description: Hosts have evolved two distinct defence strategies against parasites:
 resistance (which prevents infection or limit parasite growth) and
 tolerance (which alleviates the fitness consequences of infection).
 However, heritable variation in resistance and tolerance and the genetic
 correlation between these two traits have rarely been characterized in
 wild host populations. Here, we estimate these parameters for both traits
 in Leuciscus burdigalensis, a freshwater fish parasitized by Tracheliastes
 polycolpus. We used a genetic database to construct a full-sib pedigree in
 a wild L. burdigalensis population. We then used univariate animal models
 to estimate inclusive heritability (i.e. all forms of genetic and
 non-genetic inheritance) in resistance and tolerance. Finally, we assessed
 the genetic correlation between these two traits using a bivariate animal
 model. We found significant heritability for resistance (H = 17.6%; 95%
 CI: 7.2–32.2%) and tolerance (H = 18.8%; 95% CI: 4.4–36.1%), whereas we
 found no evidence for the existence of a genetic correlation between these
 traits. Furthermore, we confirm that resistance and tolerance are strongly
 affected by environmental effects. Our results demonstrate that (i)
 heritable variation exists for parasite resistance and tolerance in wild
 host populations, and (ii) these traits can evolve independently in
 populations.
description: pedigreeThis is the reconstructed pedigree associated with all individuals in the phenotype databasephenotypesIn this file you find all traits measured for each individual (Resistance, Tolerance, Size...).
DOI: 10.5061/dryad.5s8f922
title: Data from: The potential of biochar in improving drainage, aeration and maize yields in heavy clay soils

description: [No abstract entered]
description: Grain and biomass
 yieldsHeavy clay Ksat
 dataHeavy clay water
 retension data
DOI: 10.5061/dryad.pd76f
title: Data from: Misregulation of spermatogenesis genes in Drosophila hybrids is lineage-specific and driven by the combined effects of sterility and fast male regulatory divergence.

description: Hybrid male sterility is a common outcome of crosses between different
 species. Gene expression studies have found that a number of
 spermatogenesis genes are differentially expressed in sterile hybrid
 males, compared with parental species. Late-stage sperm development genes
 are particularly likely to be misexpressed, with fewer early-stage genes
 affected. Thus, a link has been posited between misexpression and
 sterility. A more recent alternative explanation for hybrid gene
 misexpression has been that it is independent of sterility and driven by
 divergent evolution of male-specific regulatory elements between species
 (faster male hypothesis). The faster male hypothesis predicts that
 misregulation of spermatogenesis genes should be independent of sterility
 and approximately the same in both hybrids, whereas sterility should only
 affect gene expression in sterile hybrids. To test the faster male
 hypothesis vs. the effect of sterility on gene misexpression, we analyse
 spermatogenesis gene expression in different species pairs of the
 Drosophila phylogeny, where hybrid male sterility occurs in only one
 direction of the interspecies cross (i.e. unidirectional sterility). We
 find significant differences among genes in misexpression with effects
 that are lineage-specific and caused by sterility or fast male regulatory
 divergence.
description: Misregulation of
 spermatogenesis genes in Drosophila hybridsSperm motility,
 fecundity and gene expressionData_Dryad.xlsx
DOI: 10.5061/dryad.5gc43
title: Data from: Dietary niche variation and its relationship to lizard population density

description: (1) Insular species are predicted to broaden their niches, in response to
 having fewer competitors. They can thus exploit a greater proportion of
 the resource spectrum. In turn, broader niches are hypothesized to
 facilitate (or be a consequence of) increased population densities. (2) We
 tested whether insular lizards have broader dietary niches than mainland
 species, how it relates to competitor and predator richness, and the
 nature of the relationship between population density and dietary niche
 breadth. (3) We collected population density and dietary niche breadth
 data for 36 insular and 59 mainland lizard species, and estimated
 competitor and predator richness at the localities where diet data were
 collected. We estimated dietary niche shift by comparing island species to
 their mainland relatives. We controlled for phylogenetic relatedness, body
 mass, and the size of the plots over which densities were estimated. (4)
 We found that island and mainland species had similar niche breadths.
 Dietary niche breadth was unrelated to competitor and predator richness,
 on both islands and the mainland. Population density was unrelated to
 dietary niche breadth across island and mainland populations. (5) Our
 results indicate that dietary generalism is not an effective way of
 increasing population density nor is it result of lower competitive
 pressure. A lower variety of resources on islands may prevent insular
 animals from increasing their niche breadths even in the face of few
 competitors.
description: Appendix S1 - Data used
 in the studyThe file contains data
 on population density, dietary niche width, study area, predator richness,
 competitor richness, and lizard body mass for 94 species from islands and
 the mainland.
DOI: 10.5061/dryad.tm65d
title: Data from: Historical contingency in a multigene family facilitates adaptive evolution of toxin resistance

description: Novel adaptations must originate and function within an already
 established genome [ 1 ]. As a result, the ability of a species to adapt
 to new environmental challenges is predicted to be highly contingent on
 the evolutionary history of its lineage [ 2–6 ]. Despite a growing
 appreciation of the importance of historical contingency in the adaptive
 evolution of single proteins [ 7–11 ], we know surprisingly little about
 its role in shaping complex adaptations that require evolutionary change
 in multiple genes. One such adaptation, extreme resistance to tetrodotoxin
 (TTX), has arisen in several species of snakes through coevolutionary arms
 races with toxic amphibian prey, which select for TTX-resistant
 voltage-gated sodium channels (Nav) [ 12–16 ]. Here, we show that the
 relatively recent origins of extreme toxin resistance, which involve the
 skeletal muscle channel Nav1.4, were facilitated by ancient evolutionary
 changes in two other members of the same gene family. A substitution
 conferring TTX resistance to Nav1.7, a channel found in small peripheral
 neurons, arose in lizards ∼170 million years ago (mya) and was present in
 the common ancestor of all snakes. A second channel found in larger
 myelinated neurons, Nav1.6, subsequently evolved resistance in four
 different snake lineages beginning ∼38 mya. Extreme TTX resistance has
 evolved at least five times within the past 12 million years via changes
 in Nav1.4, but only within lineages that previously evolved resistant
 Nav1.6 and Nav1.7. Our results show that adaptive protein evolution may be
 contingent upon enabling substitutions elsewhere in the genome, in this
 case, in paralogs of the same gene family.
description: Boa&OphisaurusAnnotations of the coding sequences of three voltage-gated sodium channel genes (SCN4A, SCN8A, and SCN9A) from two species (Boa constrictor and Ophisaurus gracilis) in GenBank format.ReptileTimecalReptile phylogeny with time calibration in Newick format.
DOI: 10.5061/dryad.88t58
title: Data from: Response of subtropical submarine-cave ecosystem to Holocene cave development and Asian monsoon variability

description: A submarine cave is a unique environment that is dark, food limited,
 semi-isolated from the outside, and sheltered from wave action. However,
 our knowledge of the long-term change in submarine-cave ecosystems remains
 limited. We document here the community-scale responses toward long-term
 change in a submarine cave, Daidokutsu in Okinawa in southern Japan. Using
 both metazoans (ostracods and bivalves) and protozoans (larger benthic
 foraminiferans) in two sediment cores obtained from the cave, we
 reconstruct the faunal and diversity changes of the past 7 Kyr. All
 taxonomic groups showed long-term, gradual linear change of faunal
 composition from predominantly open-water taxa to predominantly cave taxa,
 and ostracods showed short-term variability of species diversity. The
 long-term faunal trend probably reflects gradual isolation of the cave
 ecosystem due to coral reef development (i.e., development of the cave
 ceiling) during periods of the Holocene transgression and subsequent
 sea-level highstand. The short-term diversity changes show substantial
 similarity to centennial- to millennial-scale Holocene Asian monsoon
 variability. Ostracod species diversity peaks tend to correspond with
 periods of strong East Asian winter monsoons. The results indicate that
 limestone submarine-cave ecosystems, an important cryptic habitat,
 developed gradually during the Holocene and may be sensitive to rapid
 climate changes
description: Census data of ostracod
 in Daidokutsu Cave and outside of the caveSheet
 "Core06": Census data of ostracod species in Core 06; Sheet
 "Core 19": Census data of ostracod species in Core 19; Sheet
 "IR1": Census data of ostracod species in surface sediment
 IR1census_Daidokutsu_final.xlsx
DOI: 10.5061/dryad.f1170
title: Data from: Influence of oxidative homeostasis on bacterial density and cost of infection in Drosophila–Wolbachia symbioses

description: The evolution of symbioses along the continuum between parasitism and
 mutualism can be influenced by the oxidative homeostasis, i.e. the balance
 between reactive oxygen species (ROS) and antioxidant molecules. Indeed,
 ROS can contribute to the host immune defence to regulate symbiont
 populations, but are also toxic. This interplay between ROS and symbiosis
 is notably exemplified by recent results in arthropod-Wolbachia
 interactions. Wolbachia are symbiotic bacteria involved in a wide range of
 interactions with their arthropods hosts, from facultative, parasitic
 associations to obligatory, mutualistic ones. In the present study, we
 used Drosophila-Wolbachia associations to determine whether the oxidative
 homeostasis plays a role in explaining the differences between
 phenotypically distinct arthropod-Wolbachia symbioses. We used Drosophila
 lines with different Wolbachia infections and measured the effects of
 pro-oxidant (paraquat) and antioxidant (glutathione) treatments on the
 Wolbachia density and the host survival. We show that experimental
 manipulations of the oxidative homeostasis can reduce the cost of the
 infection through its effect on Wolbachia density. We discuss the
 implication of this result from an evolutionary perspective and argue that
 the oxidative homeostasis could underlie the evolution of tolerance and
 dependence on Wolbachia.
description: Monnin_2016_Supporting_DataSurvival data, Wolbachia density data, lipid peroxidation data (tbars), antioxidant capacity data (trolox) and expression data.