cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gtht76hmd
title: Temperature mesocosm data

description: Predicting the effects of climate change requires understanding complex
 interactions among multiple abiotic and biotic factors. By influencing key
 interactions among host species, parasites can affect community and
 ecosystem structuring. Yet, our understanding of how multiple parasites
 and abiotic factors interact to alter ecosystem structure remains limited.
 To empirically test the role of temperature variation and parasites in
 shaping communities, we used a multigenerational mesocosm experiment
 composed of four sympatric freshwater crustacean species (isopods and
 amphipods) that share up to four parasite species. Mesocosms were assigned
 to one of four different treatments with contrasting seasonal temperatures
 (normal and elevated) and parasite exposure levels (continuous and
 arrested (presence or absence of parasite larvae in mesocosm)). We found
 that parasite exposure and water temperature had interactive effects on
 the host community. Continuous exposure to parasites altered the community
 structure and differences in water temperature altered species abundance.
 The abundance of the amphipod Paracalliope fluviatilis decreased
 substantially when experiencing continuous parasite exposure and elevated
 water temperatures. Elevated temperatures also led to parasite-induced
 mortality in another amphipod host, Paracorophium excavatum.
 Contrastingly, isopod hosts were affected much less, suggesting increasing
 temperatures in conjunction with higher parasite exposure might increase
 their relative abundance in the community. Changes in invertebrate host
 populations have implications for other species such as fish and birds
 that consume crustaceans as well as having impacts on ecosystem processes,
 such as aquatic primary production and nutrient cycling. In light of
 climate change predictions, parasite exposure and rise in average
 temperatures may have substantial impacts on communities and ecosystems,
 altering ecosystem structure and dynamics.
description: The data set represents a mesocosm experiment with four
 treatments. Each mesocosm was composed of four sympatric freshwater
 crustacean species (isopods (<i>Austridotea annectens
 </i>and<i> A. lacustris) </i>and amphipods
 (<i>Paracalliope fluviatilis</i> and <i>Paracorophium
 excavatum)</i>) that share up to four parasite species (trematodes
 <i>Coitocaecum</i> <i>parvum</i> and
 <i>Maritrema</i> <em>poulini</em>,
 nematode, <em>Hedruris spinigera</em>, and acanthocephalan,
 <i>Acanthocephalus</i>
 <em>galaxii</em>). Mesocosms were assigned to one of four
 different treatments with contrasting seasonal temperatures (normal and
 elevated) and parasite exposure levels (continuous and arrested (presence
 or absence of parasite larvae in mesocosm)). We had 6 replicates per
 treatment for a total of 24 mesocosms. The data set presented here
 represents the host and parasite community by mesocosm.
DOI: 10.5061/dryad.jh9w0vtbv
title: Data for: Age structure eliminates the impact of coinfection on epidemic dynamics in a freshwater zooplankton system

description: Parasites often coinfect host populations, and, by interacting within
 hosts, might change the trajectory of multi-parasite epidemics. However,
 host-parasite interactions often change with host age, raising the
 possibility that within-host interactions between parasites might also
 change, influencing the spread of disease. We measured how heterospecific
 parasites interacted within zooplankton hosts and how host age changed
 these interactions. We then parameterized an epidemiological model to
 explore how age-effects altered the impact of coinfection on epidemic
 dynamics. In our model, we found that in populations where
 epidemiologically relevant parameters did not change with age, the
 presence of a second parasite altered epidemic dynamics. In contrast, when
 parameters varied with host age (based on our empirical measures), there
 was no longer a difference in epidemic dynamics between singly and
 coinfected populations, indicating that variable age structure within a
 population eliminates the impact of coinfection on epidemic dynamics.
 Moreover, infection prevalence of both parasites was lower in populations
 where epidemiologically relevant parameters changed with age. Given that
 host-population age structure changes over time and space, these results
 indicate that age-effects are important for understanding epidemiological
 processes in coinfected systems and that studies focused on a single age
 group could yield inaccurate insights.
description: This experiment was conducted by infected zooplankton hosts with
 bacterial and fungal pathogens over a range of host ages, to see how host
 age mediates interactions between parasites within hosts. Full details can
 be found in the related manuscript. 
description: A readme file has been uploaded with the data and scripts.
DOI: 10.5061/dryad.6hdr7sr15
title: Pygmy rabbit landscape genomics in the southern Great Basin

description: Local adaptation can occur when spatially separated populations are
 subjected to contrasting environmental conditions. Historically,
 understanding the genetic basis of adaptation has been difficult, but
 increased availability of genome-wide markers facilitates studies of local
 adaptation in non-model organisms of conservation concern. The pygmy
 rabbit (Brachylagus idahoensis) is an imperiled lagomorph that relies on
 sagebrush for forage and cover. This reliance has led to widespread
 population declines following reductions in the distribution of sagebrush,
 leading to geographic separation between populations. In this study, we
 used &gt;20,000 single nucleotide polymorphisms (SNPs),
 genotype-environment association methods, and demographic modeling to
 examine neutral genetic variation and local adaptation in the pygmy rabbit
 in Nevada and California. We identified 308 loci as outliers, many of
 which had functional annotations related to metabolism of plant secondary
 compounds. Likewise, patterns of spatial variation in outlier loci were
 correlated with landscape and climatic variables including proximity to
 streams, sagebrush cover, and precipitation. We found that populations in
 the Mono Basin of California likely diverged from other Great Basin
 populations during late Pleistocene climate oscillations, and that this
 region is adaptively differentiated from other regions in the southern
 Great Basin despite limited gene flow and low effective population size.
 Our results demonstrate that peripherally isolated populations can
 maintain adaptive divergence.
DOI: 10.5061/dryad.18931zcxg
title: Surface deformation associated with fractures near the 2019 Ridgecrest earthquake sequence

description: Contemporary earthquake hazard models hinge on an understanding of how
 strain is distributed in the crust and the ability to precisely detect
 millimeter-scale deformation over broad regions of active faulting.
 Satellite radar observations revealed hundreds of previously unmapped
 linear strain concentrations (or fractures) surrounding the 2019
 Ridgecrest earthquake sequence. We documented and analyzed displacements
 and widths of 169 of these fractures. Although most fractures are
 displaced in the direction of the prevailing tectonic stress (prograde), a
 large number of them are displaced in the opposite (retrograde) direction.
 We developed a model to explain the existence and behavior of these
 displacements. A major implication is that much of the prograde tectonic
 strain is accommodated by frictional slip on many preexisting faults.
DOI: 10.5061/dryad.d51c5b039
title: Molecular determinants of phase separation for Drosophila DNA replication licensing factors

description: Liquid-liquid phase separation (LLPS) of intrinsically disordered regions
 (IDRs) in proteins can drive the formation of membraneless compartments in
 cells. Phase-separated structures enrich for specific partner proteins and
 exclude others. Previously, we showed that the IDRs of metazoan DNA
 replication initiators drive DNA-dependent phase separation in vitro and
 chromosome binding in vivo, and that initiator condensates selectively
 recruit partner proteins (Parker et al., 2019). How initiator IDRs
 facilitate LLPS and maintain compositional specificity is unknown. Here,
 using D. melanogaster (Dm) Cdt1 as a model initiation factor, we show that
 phase separation results from a synergy between electrostatic DNA-bridging
 interactions and hydrophobic inter-IDR contacts. Both sets of interactions
 depend on sequence composition (but not sequence order), are resistant to
 1,6-hexanediol, and do not depend on aromaticity. These findings
 demonstrate that distinct sets of interactions drive condensate formation
 and specificity across different phase-separating systems and advance
 efforts to predict IDR LLPS propensity and partner selection a priori.
DOI: 10.25349/d9wp5d
title: Data from: Fossil dermal denticles reveal the pre-exploitation baseline of a Caribbean coral reef shark community

description: Pre-exploitation shark baselines and the history of human impact on coral
 reef-associated shark communities in the Caribbean are poorly understood.
 We recovered shark dermal denticles from mid-Holocene (~7 ka) and modern
 reef sediments in Bocas del Toro, Caribbean Panama to reconstruct an
 empirical shark baseline before major human impact and quantify how much
 the modern shark community in the region had shifted from this historical
 reference point. We found that denticle accumulation rates, a proxy for
 shark abundance, declined by 71% since the mid-Holocene. All denticle
 morphotypes, which reflect shark community composition, experienced
 significant losses, but those morphotypes found on fast swimming, pelagic
 sharks (e.g., families Carcharhinidae and Sphyrnidae) declined the most.
 Analysis of historical records suggested that the steepest decline in
 shark abundance occurred in the late 20th century, coinciding with the
 advent of a targeted shark fishery in Panama. Although the
 disproportionate loss of denticles characterizing pelagic sharks was
 consistent with overfishing, the large reduction in denticles
 characterizing demersal species with low commercial value (i.e., the nurse
 shark Ginglymostoma cirratum) indicated that other stressors could have
 exacerbated these declines. We demonstrate that the denticle record can
 reveal changes in shark communities over long ecological timescales,
 helping to contextualize contemporary abundances and inform shark
 management and ecology.
description: <b>DillonPNAS_SupData_Bocas_Denticles</b> This dataset includes: (1) mid-Holocene and modern shark dermal denticle (shark scale) assemblage data; (2) recent shark catch data; and (3) semi-quantitative perceptions of shark abundance through time based on historical records in Caribbean Panama. Denticles were recovered from bulk samples of fine sediments collected from a subaerially exposed ~7000-year-old coral reef and from nearby modern reefs within a sheltered, semi-enclosed lagoonal system in Bocas del Toro, Panama. The rate of denticle accumulation in these sediments serves as a proxy for shark abundance. These data were collected to reconstruct a shark baseline before major human impact in this region of Caribbean Panama and quantify how much the modern shark community had changed over time. Insight from the denticle record was supplemented with archaeological evidence, historical narratives, and modern ecological and fisheries data to independently reconstruct the ecological history of sharks in the region, help constrain the timing of shark declines, and make inferences about the drivers and ecological consequences of those declines. This dataset contains five csv files: "abundances", "taphonomy", "sorting", "ecol_state_scores", and "shark_catches". Field attributes for each csv file are described in the accompanying Metadata ReadMe file.
DOI: 10.5061/dryad.xd2547dgx
title: Resource partitioning is not coupled with assortative mating in sympatrically divergent ricefish in a Wallacean ancient lake

description: Sympatric speciation is considered to be difficult without the coupling
 between ecological traits that allow resource partitioning and
 reproductive traits that allow assortative mating. Such “magic traits” are
 known to be involved in most of the compelling examples of sympatric
 speciation. In this study, we report a possible case of sympatric
 speciation without magic traits. Three species of ricefish
 (genus Oryzias) are suggested to have diverged sympatrically
 within Lake Poso, an ancient lake in Sulawesi. An analysis of genome-wide
 single-nucleotide polymorphisms showed that these three species are
 reproductively isolated from each other throughout the lake. Stable
 isotope analyses revealed that the three species use different food
 resources, which reflect differences in their feeding morphologies (gill
 rakers and digestive tracts) and feeding sites. Field and laboratory
 observations showed that O. nebulosus and O.
 orthognathus share a mating habitat of cobbles, where they
 scatter fertilized eggs, whereas this site is never used by O.
 nigrimas, indicating that assortative mating is partly achieved by spatial
 isolation. The small, less-adhesive eggs of O.
 nebulosus and O. orthognathusprobably reflect their
 adaptation to spawning on cobble beaches. Laboratory mating experiments
 showed strong prezygotic isolation between O.
 nebulosus and O. orthognathus, which is achieved by
 strong species recognition presumably by both sexes based on
 species-specific mating dances and nuptial coloration. In summary, the
 assortative mating of O. nebulosus and O.
 orthognathus is probably not coupled to resource partitioning. We
 discussed how sympatric speciation among these species might have been
 achieved even without magic traits.
description: Poso_Oryzias.vcf The VCF file containing 916
 biallelic SNPs among the three Poso species.
DOI: 10.5061/dryad.7d7wm37v8
title: Gene alterations, clinical informations and survival data of gliomas with/without corpus callosum involvement

description: The raw dataset of this study contained the gene alterations, clinical
 informations and survival data of glioma patients. Gene alterations data
 were obtained by Next-generation DNA sequencing of glioma samples of
 patients. Clinical informations were obtained from Electronic medical
 records and follow-up. The survival data were obtained by follow-up of
 patients. In order to explore gene alterations and their correlation with
 the survival of glioblastoma (GBM) of corpus callosum (CC) involvement
 (ccGBM), this dataset was analyzed in detail. A total of 30 ccGBM and 88
 non-ccGBM were finally included. The ccGBM had higher incidence of PDGFRA
 (33.3% versus 9.1%, P=0.004) alterations than non-ccGBM. PDGFRA
 amplification (PDGFRAamp, 33.3% versus 9.1%, P=0.004) and missense
 mutation (PDGFRAmut, 20.0% versus 3.4%, P=0.011) both had higher incidence
 in ccGBM than in non-ccGBM. PDGFRA alteration was significantly associated
 with the occurrence of ccGBM (OR=4.91 [95%CI: 1.55-15.52], P=0.007). The
 ccGBM of PDGFRAamp achieved shorter median PFS (8.6 versus 13.5 months,
 P=0.025) and OS (12.4 versus 17.9 months, P=0.022) than non-ccGBM of
 PDGFRAnon-amp. The ccGBM of PDGFRAamp combined with PDGFRAmut
 (PDGFRAamp-mut) had shorter median PFS (7.6 versus 8.9 months, P=0.022)
 and OS (9.6 versus 17.8 months, P=0.006) than non-ccGBM of PDGFRA wild
 type and non-amplification (PDGFRA-w, non-amp). Compared to ccGBM of
 PDGFRA-w, non-amp, the ccGBM of PDGFRAamp and PDGFRAamp-mut both had
 shorter median PFS and OS (P&lt;0.05). Hazard ratios (HRs) of
 PDGFRAamp for PFS and OS of ccGBM were 3.08 (95%CI: 1.02-9.35, P=0.047)
 and 5.07 (95%CI: 1.52-16.89, P=0.008) respectively, HRs of PDGFRAamp-mut
 for PFS and OS were 13.16 (95%CI: 3.19-54.40, P&lt;0.001) and 16.36
 (95%CI: 2.66-100.70, P=0.003) respectively. The PDGFRA alterations is
 significantly associated with the occurrence and poor prognosis of ccGBM.
description: The dataset was collected during a glioma study at the
 Neurosurgery department of First Medical Centre of Chinese PLA General
 Hospital. To get the results of gene alterations status of glioma invading
 corups callosum or not, the gene alterations of glioma were tested using
 Next-generation DNA sequencing by Genetron Health of China.
description: The readme file contains an explanation of each of the variables
 in the dataset, its measurement units. Information on how the measurements
 were done can be found in the associated manuscript referenced
 above.
DOI: 10.5061/dryad.rn8pk0p9q
title: Legacies of historic charcoal production affect the forest flora in a Swedish mining district: survey data

description: Iron production was historically associated with one of the major impacts
 on forests worldwide, as vast amounts of wood were harvested to produce
 the charcoal needed for reducing iron oxides in the ore to iron. This
 impact has left abundant legacies which potentially may remain in the
 present-day vegetation. We investigated how remains of historic charcoal
 production, mainly from the 18th to the early 20th century, at still
 remaining charcoal kiln platforms (CKPs), affect the current species
 richness, species occurrences, and cover of field layer vascular plants in
 a Swedish mining district located in the boreo-nemoral forest zone. CKPs
 have a significantly higher species richness than the surrounding forest,
 and they also affect cover (negatively) for ericaceous species typically
 dominating the forest field-layer. Several forest species are more
 frequent at CKPs, and these also harbor significantly more uncommon
 species, of which many are typical for traditionally managed grasslands;
 these latter species are likely to represent remnants in present-day
 forests reflecting former land-use such as livestock grazing. The soil
 chemistry at CKPs is strongly deviating from the surrounding forest, and
 this, together with a lower cover of ericaceous shrubs, are the most
 likely mechanisms behind the higher species richness. CKPs represent
 conspicuous and abundant historic anthropogenic habitats in the forest
 vegetation. As far as we are aware, the flora at CKPs in boreal and
 boreo-nemoral forests has not previously been investigated in detail, and
 they deserve more attention, both from a biological and a
 cultural-historical perspective.
description: Methods are described in the article published in Nordic Journal
 of Botany.
DOI: 10.5061/dryad.mw6m905ws
title: Otolith microstructures analysis of juveniles sole (Solea solea L.) in the Southern North Sea

description: The dataset contains the individual fish and otolith measurements
 necessary to analyse the early-life history stages of juvenile common sole
 in the Southern North Sea. Samples were collected at three major nursery
 grounds, the Belgian coast, the Dutch coast and the UK coast between 2013
 and 2016. The analysis of the otolith microstructures (daily growth rings)
 allows the back calculation of hatching and settlement periods as well as
 the investigation of growth conditions. The dataset includes three types
 of data associated to each sampled fish: 1) the individual age/counts
 associated to the early-life stages including larval period,
 metamorphosis, juvenile period, total PLD and total age; 2) the otolith
 size dimensions in terms of radius, diameter and PLD size which associated
 to ages allow the analysis of growth rates; 3) other supplementary data
 for the analysis of the relationship of otolith and somatic growth
 including total lengths and weights.
description: See the uploaded
 file SOLEASOLEAotolithmicrostructuresREADME.txt
DOI: 10.5061/dryad.8sf7m0cnc
title: Phylogenetic results of 6 morphological character matrices

description: The construction of morphological character matrices is central to
 paleontological systematic study, which extracts paleontological
 information from fossils. Although the word information has been
 repeatedly mentioned in a wide array of paleontological systematic
 studies, its meaning has rarely been clarified and there has not been a
 standard to measure paleontological information due to the incompleteness
 of fossils, difficulty of recognizing homologous and homoplastic
 structures, etc. Here, based on information theory, we show the deep
 connections between paleontological systematic study and communication
 system engineering. It is information, the decrease of uncertainty, in
 morphological characters that distinguishes operational taxonomic units
 (OTUs) and reconstructs evolutionary history. We propose that concepts in
 communication system engineering such as source coding and channel coding
 correspond in paleontological studies to the construction of diagnostic
 features and the entire character matrices, which should be distinguished
 as how typical communication systems are engineered because these two
 steps serve dual purposes. With character matrices from six different
 vertebrate groups, we analyzed their information properties including
 source entropy, mutual information, and channel capacity. Estimation of
 channel capacity shows upper limits of all matrices in transmitting
 paleontological information, indicating that, due to the presence of
 noise, too many characters not only increase the burden in character
 scoring, but also may decrease quality of matrices. Information entropy,
 which measure how informative a variable is, of each character is tested
 as a weighting criterion in parsimony-based systematic studies, the
 results show high consistence with existing knowledge with both good
 resolution and interpretability.
description: This dataset contains a .rar file with 24 .nex files that belong
 to 6 different vertebrate groups: Ornithischia (Han et al., 2017),
 Ceratopsia (Yu et al., 2020), Diplodocidae (Tschopp & Mateus
 2017), multituberculata (Wang et al., 2019), Carnivoramorpha (Spaulding
 & Flynn 2012), and lizards (Tschopp et al., 2018). The original
 character matrices including morphological characters and encoded states
 can be found in the references above.  For each group,
 there are 4 .nex files with names of
 GroupName_equal_weighting/_implied_weight_3/_implied_weight_12/_info_entropy, indicating the parsimony-based phylogenetic analysis was run under equal weighting, implied weighting (k=3), implied weighting(k=12), and information entropy weighting proposed in this study. The tree results are appended after the character matrix in each .nex file, and the strict consensus tree was appended as the last tree. For information entropy weighting, the weights keep the first two digits after the decimal point. Phylogenetic analysis was done in TNT 1.5 (Goloboff & Catalano 2016). The strict consensus tree was appended to the last of tree list in each method.
description: See Methods above.