cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b2pg468
title: Data from: Quantifying in situ phenotypic variability in the hydraulic properties of four tree species across their distribution range in Europe

description: Many studies have reported that hydraulic properties vary considerably
 between tree species, but little is known about their intraspecific
 variation and, therefore, their capacity to adapt to a warmer and drier
 climate. Here, we quantify phenotypic divergence and clinal variation for
 embolism resistance, hydraulic conductivity and branch growth, in four
 tree species, two angiosperms (Betula pendula, Populus tremula) and two
 conifers (Picea abies, Pinus sylvestris), across their latitudinal
 distribution in Europe. Growth and hydraulic efficiency varied widely
 within species and between populations. The variability of embolism
 resistance was in general weaker than that of growth and hydraulic
 efficiency, and very low for all species but Populus tremula. In addition,
 no and weak support for a safety vs. efficiency trade-off was observed for
 the angiosperm and conifer species, respectively. The limited variability
 of embolism resistance observed here for all species except Populus
 tremula, suggests that forest populations will unlikely be able to adapt
 hydraulically to drier conditions through the evolution of embolism
 resistance.
description: Cost hydraulic
 datasetThis file contains all
 traits (hydraulic and growth) and climate values per population and site
 across Europe.Gonzales Munoz cost action
 database.xlsx
DOI: 10.5061/dryad.p9f5160
title: Data from: Light regulates tropical symbiotic nitrogen fixation more strongly than soil nitrogen

description: Nitrogen limits primary production in almost every biome on Earth1,2.
 Symbiotic nitrogen fixation, conducted by certain angiosperms and their
 endosymbiotic bacteria, is the largest potential natural source of new
 nitrogen into the biosphere3, influencing global primary production,
 carbon sequestration and element cycling. Because symbiotic nitrogen
 fixation represents an alternative to soil nitrogen uptake, much of the
 work on symbiotic nitrogen fixation regulation has focused on soil
 nitrogen availability4,5,6,7,8. However, because symbiotic nitrogen
 fixation is an energetically expensive process9, light availability to the
 plant may also regulate symbiotic nitrogen fixation rates10,11. Despite
 the importance of symbiotic nitrogen fixation to biosphere functioning,
 the environmental factors that most strongly regulate this process remain
 unresolved. Here we show that light regulates symbiotic nitrogen fixation
 more strongly than does soil nitrogen and that light mediates the response
 of symbiotic nitrogen fixation to soil nitrogen availability. In a
 shadehouse experiment, low light levels (comparable with forest
 understories) completely shut down symbiotic nitrogen fixation, whereas
 soil nitrogen levels that far exceeded plant demand did not fully
 downregulate symbiotic nitrogen fixation at high light. For in situ forest
 seedlings, light was a notable predictor of symbiotic nitrogen fixation
 activity, but soil-extractable nitrogen was not. Light as a primary
 regulator of symbiotic nitrogen fixation is a departure from decades of
 focus on soil nitrogen availability. This shift in our understanding of
 symbiotic nitrogen fixation regulation can resolve a long-standing
 biogeochemical paradox12, and it will improve our ability to predict how
 symbiotic nitrogen fixation will fuel the global forest carbon sink and
 respond to human alteration of the global nitrogen cycle.
description: Shadehouse seedling
 dataData on plant biomass
 and delta 15N values for seedlings grown in full-factorial light x soil
 nitrogen shadehouse experiment. Experiment duration: July 2015 - Jan
 2016.Taylor
 & Menge 2018_Shadehouse Data for
 Dryad.csv
DOI: 10.5061/dryad.pm620
title: Data from: Defensive symbionts mediate species coexistence in phytophagous insects

description: 1. Competition of two species for the same resource is expected to result
 in competitive exclusion of the inferior competitor. In natural
 communities, however, other antagonists and symbionts moderate
 competition. Thus we have to go beyond studying pairwise interactions. 2.
 Natural enemies may facilitate coexistence if they affect the superior
 competitor more strongly, or they can hinder coexistence via apparent
 competition. Less well studied is the role of symbionts, which may
 influence species coexistence in conjunction with enemies. 3. Eukaryotes
 commonly harbor microbial endosymbionts that provide protection against
 natural enemies, but are costly in their absence. Such defensive symbionts
 could thus mediate coexistence of species competing for the same resource,
 both in the presence and in the absence of enemies, but as yet there is
 little evidence for this claim. 4. We addressed this proposed role of
 defensive symbionts in replicated simple communities consisting of two
 aphid species sharing the same host plant and the same natural enemy, a
 parasitoid wasp. Both, one, or neither species were infected with a
 resistance-conferring symbiont, and they competed in the absence as well
 as the presence of parasitoids. 5. The symbiont had significant effects in
 the absence of parasitoids by lowering competitive ability especially in
 one species, but the effects were more dramatic in the presence of
 parasitoids. With both species protected by the symbiont, parasitoid
 densities remained low and both aphid species persisted. When neither
 species was protected, parasitoids drove both species to extinction.
 Surprisingly, the same outcome was observed when only one species was
 protected. The susceptible species supported high densities of parasitoids
 that also killed the resistant aphids via mechanisms other than
 parasitism, presumably by disturbing them to the point of starvation. This
 is an intriguing form of apparent competition. 6. Our results demonstrate
 an important role of defensive symbionts in insect communities through
 modifying species interactions. This highlights the need for experimental
 data when studying species coexistence in competitive networks.
 Furthermore, the observation that a susceptible host can negatively affect
 a resistant host via a shared parasitoid is an instructive insight for
 biological control.
description: aphid and mummy
 countsSee detailed description
 in README file.aphid_and_mummy_counts_for_DRYAD.txt
DOI: 10.5061/dryad.hj6r1
title: Data from: Integrative taxonomy and species delimitation in harvestmen: a revision of the western North American genus Sclerobunus (Opiliones: Laniatores: Travunioidea)

description: Alpha taxonomy, and specifically the delimitation of species, is becoming
 increasingly objective and integrative. The use of coalescent-based
 methods applied to genetic data is providing new tools for the discovery
 and delimitation of species. Here, we use an integrative approach via a
 combination of discovery-based multivariate morphological analyses to
 detect potential new species. These potential species are then used as a
 priori species in hypothesis-driven validation analyses with genetic data.
 This research focuses on the harvestmen genus Sclerobunus found throughout
 the mountainous regions of western North America. Based on our analyses,
 we conduct a revision of Sclerobunus resulting in synonymy of Cyptobunus
 with Sclerobunus including transfer of S. cavicolens comb. nov. and
 elevation of both subspecies of S. ungulatus: S. ungulatus comb. nov. and
 S. madhousensis comb. nov., stat. nov. The three subspecies of S. robustus
 are elevated, S. robustus, S. glorietus stat. nov., and S. idahoensis
 stat. nov. Additionally, five new species of Sclerobunus are described
 from New Mexico and Colorado, including S. jemez sp. nov., S. klomax sp.
 nov., S. skywalkeri sp. nov., S. speoventus sp. nov., and S. steinmanni
 sp. nov. Several of the newly described species are single-cave endemics,
 and our findings suggest that further exploration of western North
 American cave habitats will likely yield additional new species.
description: Sclerobunus_PhasedMatrices_Derkarabetian&Hedin2014Zip file containing fasta files for individual phased matrices for all genes used in this study.Sclerobunus_GeneTrees_Derkarabetian&Hedin2014Zip file containing individual gene trees estimated via RAxML for all genes used in this study.Sclerobunus_SpeciesTree_Derkarabetian&Hedin2014Species tree estimated with *BEAST.
DOI: 10.5061/dryad.j3j5t
title: Data from: Horses give functionally relevant responses to human facial expressions of emotion: a response to Schmoll (2016)

description: [No description entered]
description: Raw
 DataSmith et
 al Supporting Data.xlsx
DOI: 10.15468/dl.me32qu
title: Occurrence Download

description: A dataset containing 161 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Grubbia rosmarinifolia",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 161 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001047-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.31154320
title: <b>Two chromosome-level genome assemblies and annotations of Yorkshire pigs (Sus scrofa)</b>

description: <b>This project conducted genome assembly and annotation for two male Yorkshire pigs.</b>
DOI: 10.6084/m9.figshare.31154320.v1
title: <b>Two chromosome-level genome assemblies and annotations of Yorkshire pigs (Sus scrofa)</b>

description: <b>This project conducted genome assembly and annotation for two male Yorkshire pigs.</b>
DOI: 10.5061/dryad.s6f0p
title: Data from: Individual consistency and phenotypic plasticity in rockhopper penguins: female but not male body mass links environmental conditions to reproductive investment

description: In marine habitats, increasing ocean temperatures due to global climate
 change may distinctly reduce nutrient and consequently food availability
 for seabirds. Food availability is a known driver of body mass and
 reproductive investment in birds, but these traits may also depend on
 individual effects. Penguins show extreme intra-annual body mass variation
 and rely on accumulated body reserves for successful breeding. However, no
 study so far has tested individual consistency and phenotypic responses in
 body mass and reproductive investment in this taxon. Using a unique
 dataset on individually marked female and male southern rockhopper
 penguins (Eudyptes chrysocome chrysocome) across six years, we
 investigated 1) the individual consistency in body mass (measured at egg
 laying), body condition and reproductive investment across years,
 subsequently 2) identified the best-explanatory temperature-related
 environmental variables for female and male body mass, and 3) tested the
 effect of female and male body mass on reproductive investment. Body mass,
 body condition and reproductive investment were all highly repeatable. As
 body condition should control for the structural size of the birds, the
 similarly high repeatability estimates for body mass and body condition
 suggested that the consistent between-individual body mass differences
 were independent of structural size. This supported the use of body mass
 for the subsequent analyses. Body mass was higher under colder
 environmental conditions (positive Southern Annular Mode), but the overall
 phenotypic response appeared limited. Reproductive investment increased
 with female but not male body mass. While environmental effects on body
 mass in our study period were rather small, one can expect that ongoing
 global climate change will lead to a deterioration of food availability
 and we might therefore in the long-term expect a phenotypical decline in
 body mass and reproductive investment.
description: Dehnhard_2015_PLoS_ONE_dataBody mass, body condition and egg mass data of individually marked male and female southern rockhopper penguins breeding on New Island, Falkland / Malvinas Islands. Analyses in Dehnhard et al. 2015 PLoS ONE were based on this dataset.
DOI: 10.5061/dryad.sp4bd705
title: Data from: Post Permo-Triassic terrestrial vertebrate recovery southwestern United States

description: Recovery of marine biodiversity following the Permo-Triassic extinction is
 thought to have been delayed relative to other mass extinctions.
 Terrestrial vertebrate biodiversity is said to have taken as much as 15
 Myr longer to recover than the marine. The present study tests, at the
 scale of an individual fossil community, whether a disparity in
 biodiversity existed in the American Southwest, between the Moenkopi
 Formation, containing an early Middle Triassic (Anisian) terrestrial
 tetrapod fauna, and the Chinle Formation, containing a successor Late
 Triassic (Norian) tetrapod fauna. Taking Chinle faunal biodiversity to
 represent full biotic recovery, comparison of taxonomic and guild
 diversity of faunas from similar depositional and taphonomic environments
 in these two formations allowed us to assess the possibility of incipient
 terrestrial recovery of biodiversity in the Anisian. Comparisons were made
 between the Holbrook Member fauna of the Moenkopi, a unit best
 characterized as a low-sinuosity medium- to coarse-grained fluvial
 deposit, and each of four Chinle stratigraphic units, representing fluvial
 settings from sandy low-sinuosity to muddy high-sinuosity. Three metrics
 were applied: generic and familial taxonomic diversity and guild
 diversity; these were compared by rarefaction. Simpson and Shannon
 diversity metrics augmented the analysis. Units of extraordinary
 preservation in the Chinle—the so-called blue layers—were removed from the
 analysis. In all tests the biodiversity of the Holbrook Member fauna is
 within the variation seen in Chinle faunas. If the results of our study
 represent global conditions, they suggest that by at least early Anisian
 time (6 Myr after the P/T extinction) biodiversity had reached levels
 comparable to those seen in the Late Triassic. This potentially brings the
 terrestrial vertebrate recovery in line with the 4–8 Myr it took for
 recovery in the marine realm.
description: Specimen
 ListList of all fossil
 specimens used in this study including specimen number (when known),
 source locality, and published source (when available).Supplementary
 Material.xls
DOI: 10.5061/dryad.dc14n
title: Data from: Distribution of MICB diversity in the Zhejiang Han population: PCR sequence-based typing for exons 2–6 and identification of five novel MICB alleles

description: The polymorphism of major histocompatibility complex class I chain-related
 gene B (MICB) and variations in MICB alleles in a variety of populations
 have been characterized using several genotyping approaches. In the
 present study, a novel polymerase chain reaction sequence-based typing
 (PCR-SBT) method was established for the genotyping of MICB exons 2–6, and
 the allelic frequency of MICB in the Zhejiang Han population was
 investigated. Among 400 unrelated healthy Han individuals from Zhejiang
 Province, China, a total of 20 MICB alleles were identified, of which
 MICB*005:02:01, MICB*002:01:01, and MICB*004:01:01 were the most
 predominant alleles, with frequencies of 0.57375, 0.1225, and 0.08375,
 respectively. Nine MICB alleles were detected on only one occasion, giving
 a frequency of 0.00125. Of the 118 distinct MICB ∼ HLA-B haplotypes
 identified, 42 showed significant linkage disequilibrium
 (P &lt; 0.05). Haplotypes MICB*005:02:01 ∼ B*46:01,
 MICB*005:02:01 ∼ B*40:01, and MICB*008 ∼ B*58:01 were the most common
 haplotypes, with frequencies of 0.0978, 0.0761, and 0.0616, respectively.
 Five novel alleles, MICB*005:07, MICB*005:08, MICB*027, MICB*028, and
 MICB*029 were identified. Compared with the MICB*005:02:01 sequence, a G
 &gt; A substitution was observed at nucleotide position 210 in
 MICB*005:07, and a 1,134 T &gt; C substitution in MICB*005:08 and an
 862 G &gt; A substitution in MICB*027 were detected. In addition, it
 appears that MICB*028 probably arose from MICB*004:01:01 with an A to G
 substitution at position 1,147 in exon 6. MICB*029 had a G &gt; T
 transversion at nucleotide position 730 in exon 4, compared with that of
 MICB*002:01:01. On the basis of the new PCR-SBT assay, these observed
 results demonstrated MICB allelic variations in the Zhejiang Han
 population.
description: MICB~HLA-BThe data we have uploaded includes the MICB genotypes and the HLA-B genotypes of 400 unrelated healthy Han individuals from Zhejiang province, China.MICB-HLA-B.xls
DOI: 10.5061/dryad.qh53c
title: Data from: Is the tree of life the best metaphor, model or heuristic for phylogenetics?

description: Mindell (2013) [henceforth simply “Mindell”] has provided a claim that the
 Tree of Life (ToL) is still useful in phylogenetics as a model, a
 metaphor, and a heuristic. Here I examine all three of these claims.
 Mindell noted that what biologists have long discussed as the ToL is in
 fact reticulate, and always has been. He therefore objected to simplistic
 declarations that there is no ToL, in the sense of no recoverable
 phylogenetic history for recognized taxa. Mindell argued that a “tree with
 reticulations” is still basically a tree, and that the ToL therefore
 continues to be a useful metaphor, model, and heuristic for phylogenetics.
 Here, I argue an alternative point of view, in which a “tree with
 reticulations” is a network, and that therefore a network will be a better
 metaphor, model, and heuristic for phylogenetics, in the sense that it
 will be more inclusive and more powerful. This distinction between tree
 and network in the face of reticulations is not a semantic one. The tree
 metaphor/model/heuristic pre-supposes tree-like data, whereas the network
 allows the data to determine the tree-likeness of the
 metaphor/model/heuristic—some networks are more tree-like than are others.
 So, the network view does not deny the importance of the ToL, but simply
 makes it a special case of something much more general. In this Point of
 View I will point out, first, that the tree as a metaphor is actually
 pre-dated by the network as a phylogenetic metaphor, and that many of the
 current debates in phylogenetics are not new and actually date back to the
 beginnings of phylogenetic analysis. We can learn from this history.
 Second, I point out that the use of a tree as a model pre-supposes a
 particular approach to data modeling that has serious limitations for
 phylogenetic analysis. Modeling from complex to simple, rather than simple
 to complex, has benefits for the analysis. Finally, I note that, as a
 heuristic, an unrooted network has many advantages over the use of a
 rooted tree. Data exploration and display is a sorely under-valued part of
 phylogenetics. Note that I am not arguing that a tree cannot be used as a
 model, heuristic, or metaphor for phylogenetics, because it surely can,
 but I am arguing instead that it is not the best model, heuristic, or
 metaphor—a network is better. Thus, one does not need “a pluralistic view
 of the ToL” (Mindell, p. 479) but a rather simplistic view of a network,
 instead. Mindell sees the ToL as basically a tree even though he
 recognizes that parts of it are not tree-like; but instead we should see
 an evolutionary history in which some parts are more tree-like than are
 others.
description: Appendix1
DOI: 10.5061/dryad.3b17f
title: Data from: Empirical evidence for species-specific export of fish naïveté from a no-take marine protected area in a coastal recreational hook and line fishery

description: No-take marine protected areas (MPAs) are assumed to enhance fisheries
 catch via the “spillover” effect, where biomass is exported to adjacent
 exploited areas. Recent studies in spearfishing fisheries suggest that the
 spillover of gear-naïve individuals from protected to unprotected sites
 increases catch rates outside the boundaries of MPAs. Whether this is a
 widespread phenomenon that also holds for other gear types and species is
 unknown. In this study, we tested if the distance to a Mediterranean MPA
 predicted the degree of vulnerability to hook and line in four
 small-bodied coastal fish species. With the assistance of underwater video
 recording, we investigated the interaction effect of the distance to the
 boundary of an MPA and species type relative to the latency time to ingest
 a natural bait, which was considered as a surrogate of fish naïveté or
 vulnerability to fishing. Vulnerability to angling increased (i.e.,
 latency time decreased) within and near the boundary of an MPA for an
 intrinsically highly catchable species (Serranus scriba), while it
 remained constant for an intrinsically uncatchable control species
 (Chromis chromis). While all of the individuals of S. scriba observed
 within the MPA and surrounding areas were in essence captured by angling
 gear, only one fifth of individuals in the far locations were captured.
 This supports the potential for the spillover of gear-naïve and
 consequently more vulnerable fish from no-take MPAs. Two other species
 initially characterized as intermediately catchable (Coris julis and
 Diplodus annularis) also had a shorter latency time in the vicinity of an
 MPA, but for these two cases the trend was not statistically significant.
 Overall, our results suggest that an MPA-induced naïveté effect may not be
 universal and may be confined to only intrinsically highly catchable fish
 species. This fact emphasizes the importance of considering the
 behavioural dimension when predicting the outcomes of MPAs, otherwise the
 effective contribution may be smaller than predicted for certain highly
 catchable species such as S. scriba.
description: Data
 baseLatency time (in
 seconds) and event (bite=1 or not=0) measured in the four species
 evaluated in the study (Chromis chromis, Coris julis, Serranus scriba and
 Diplodus annularis) at different distances (in m) to the no-take of Palma
 Bay. The covariates of the habitat (PCA1 and PCA2) and density of other
 fish are also included.Alos et al 2015
 data.xls
DOI: 10.5061/dryad.1th15
title: Data from: Understanding geographic origins and history of admixture among chimpanzees in European zoos, with implications for future breeding programmes

description: Despite ample focus on this endangered species, conservation planning for
 chimpanzees residing outside Africa has proven a challenge because of the
 lack of ancestry information. Here, we analysed the largest number of
 chimpanzee samples to date, examining microsatellites in &gt;100
 chimpanzees from the range of the species in Africa, and 20% of the
 European zoo population. We applied the knowledge about subspecies
 differentiation throughout equatorial Africa to assign origin to
 chimpanzees in the largest conservation management programme globally. A
 total of 63% of the genotyped chimpanzees from the European zoos could be
 assigned to one of the recognized subspecies. The majority being of West
 African origin (40%) will help consolidate the current breeding programme
 for this subspecies and the identification of individuals belonging to the
 two other subspecies so far found in European zoos can form the basis for
 breeding programmes for these. Individuals of various degree of mixed
 ancestry made up 37% of the genotyped European zoo population and thus
 highlight the need for appropriate management programmes guided by genetic
 analysis to preserve maximum genetic diversity and reduce hybridization
 among subspecies.
description: Hvilsom2013