cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mcvdncjw6
title: Does operational sex ratio influence relative strength of purging selection in males vs. females?

description: According to theory, sexual selection in males may
 efficiently purge mutation load of sexual
 populations, reducing or fully compensating “the cost of males”.
 For this to occur, mutations not only need to be deleterious to both
 sexes, they also must affect males more than females. A frequently
 overlooked problem is that relative strength
 of selection on males vs. females may vary between
 environments, with social
 conditions being particularly likely to affect selection
 in males and females differently. Here we induced mutations in red flour
 beetles (Tribolium castaneum) and tested their effect in both
 sexes under three different operational sex ratios (1:2, 1:1,
 2:1). Induced mutations decreased fitness of both males
 and females, but their effect
 was not stronger in males. Surprisingly, operational sex
 ratio did not affect selection against deleterious mutations nor its
 relative strength in the sexes. Thus, our results show
 no support for the role of sexual selection in
 the evolutionary maintenance of sex.
DOI: 10.5061/dryad.ns1rn8png
title: Shrub encroachment decreases soil inorganic carbon stocks in Mongolian grasslands

description: 1. Widespread shrub encroachment in global drylands may increase plant
 biomass and change soil organic carbon stocks of grassland ecosystems.
 However, the response of soil inorganic carbon (SIC), which is a major
 component of dryland carbon pools, to this vegetation shift remains
 unknown. 2. We conducted a systematic field survey in 75 pairs of
 shrub-encroached grassland and control plots at 25 sites in the grasslands
 of the Inner Mongolia Plateau to evaluate how shrub encroachment affects
 SIC density (SICD) in these ecosystems. 3. We found that shrub
 encroachment significantly reduced SICD in the upper 100 cm (3.85 vs. 4.74
 kg C m-2, P &lt; 0.05), especially in the subsurface soil (20-50 cm
 layer). The magnitude of SICD changes was related to the change in soil
 pH, shrub patch size, and initial SICD, reflecting that the reduction in
 SICD might be attributed to the shrub encroachment-related soil
 acidification. Our results also revealed that the lost SIC was mainly
 released into the atmosphere rather than redistributed into deeper soil
 layers. 4. Synthesis. We provide the first evidence for the soil
 acidification-induced SIC loss caused by shrub encroachment. Our findings
 highlight the non-negligible role of SIC dynamics in the C budget of
 shrub-encroached grassland ecosystems and the need to consider these
 dynamics in terrestrial C cycle research.
DOI: 10.5061/dryad.931zcrjfm
title: Species diversity and composition drive the aesthetic value of coral reef fish assemblages

description: Data set corresponding to the manuscript : "Species diversity and
 composition drive the aesthetic value of coral reef fish
 assemblages".
DOI: 10.5061/dryad.dv41ns1t8
title: Sexual isolation with and without ecological isolation in marine isopods Jaera albifrons and J. praehirsuta

description: Sexual barriers associated with mate choice are often found to be
 associated with some level of ecological isolation between species. The
 independence and relative strength of sexual isolation are thus difficult
 to assess. Here we take advantage of a pair of marine isopod species
 (Jaera albifronsand J. praehirsuta) that show sexual isolation
 and coexist in populations where they share the same microhabitat or not
 (i.e. without or with ecological isolation). We estimated the strength of
 sexual isolation between J. albifronsand J.
 praehirsutausing no-choice trials and a multiple-choice experimental
 population. We found that sexual isolation is strong in both the presence
 and absence of ecological isolation, but that it is asymmetric and fails
 to prevent interspecific gene flow entirely. First-generation intrinsic
 post-zygotic barriers were low, and there was no sexual isolation
 within J. praehirsutaacross habitats. The J.
 albifrons/ J. praehirsutaspecies pair thus provides an example
 where the role of sexual isolation as a barrier to gene flow i) does not
 depend upon current ecological isolation, ii) seems to have evolved
 independently of local ecological conditions, but iii) is insufficient to
 complete speciation entirely on its own.
DOI: 10.15468/dl.2h6x6v
title: Occurrence Download

description: A dataset containing 1917 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-98.50879 19.10171,-98.33154 19.10171,-98.33154 19.22256,-98.50879 19.22256,-98.50879 19.10171))",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata"
 ]
}

 The dataset includes 1917 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001925-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m63xsj3x5
title: Data from: Limited thermal plasticity and geographic divergence in the ovipositor of Drosophila suzukii

description: Phenotypic plasticity has been repeatedly suggested to facilitate
 adaptation to new environmental conditions, as in invasions. Here we
 investigate this possibility by focusing on the worldwide invasion of
 Drosophila suzukii: an invasive species that has rapidly colonized all
 continents over the last decade. This species is characterized by a highly
 developed ovipositor, allowing females to lay eggs through the skin of
 ripe fruits. Using a novel approach based on the combined use of SEM and
 photogrammetry, we quantified the ovipositor size and 3D shape,
 contrasting invasive and native populations raised at three different
 developmental temperatures. We found a small but significant effect of
 temperature and geographic origin on the ovipositor shape, showing the
 occurrence of both geographic differentiation and plasticity to
 temperature. The shape reaction norms are in turn strikingly similar among
 populations, suggesting very little difference in shape plasticity among
 invasive and native populations, and therefore rejecting the hypothesis of
 a particular role for plasticity of the ovipositor in the invasion
 success. Overall, the ovipositor shape seems to be a fairly robust trait,
 indicative of stabilizing selection. The large performance spectrum rather
 than the flexibility of the ovipositor would thus contribute to the
 success of D. suzukii worldwide invasion.
DOI: 10.5061/dryad.n5tb2rbrb
title: Supplemental figures from: Role of the thyroid gland in expression of the thyroid phenotype of SBP2 deficient mice

description: Selenocysteine insertion sequence binding protein 2, SBP2 (SECISBP2), is
 required for selenoprotein synthesis. Partial SBP2 deficiency syndrome
 manifests characteristic thyroid function tests. The Sbp2 deficiency mouse
 model, Sbp2 iCKO, replicates this thyroid phenotype and was used for
 pathophysiologic investigations. As selenoproteins have antioxidative role
 in thyroid gland function, their deficiencies have potential to affect
 thyroid hormone (TH) synthesis. Sbp2 iCKO mice had larger thyroids
 relative to body weight and increased thyroidal T4 and T3 content while 5’
 deiodinases enzymatic activities were decreased. Possible mechanisms for
 the discrepancy between the increased thyroidal T3 and normal circulating
 T3 were investigated in dynamic experiments. Treatment with bovine TSH
 resulted in increased delta T4 in Sbp2 iCKO mice, indicating increased
 availability of preformed thyroidal TH. Next, the recovery of TH levels
 was evaluated after withdrawal of chemical suppression. At one day, Sbp2
 iCKO had higher serum and thyroidal T3 concomitant with lower TSH,
 confirming increased capacity of TH synthesis in Sbp2 deficiency.
 Decreased TH secretion was ruled out, as serum and thyroidal TH were high
 in Sbp2 iCKO mice. Treatment with low-iodine diet also ruled out thyroidal
 secretion defect as both serum levels and thyroidal TH content similarly
 declined over time in Sbp2 deficient mice compared to Wt. This study
 provides evidence for unsuspected changes in thyroid gland that contribute
 to the thyroid phenotype of Sbp2 deficiency. The increased thyroidal T4
 and T3 content, when circulating T3 levels are normal is due to an
 increased TH synthesis capacity while thyroidal secretion is preserved.
DOI: 10.5061/dryad.5mkkwh71h
title: Stepwise shifts underlie evolutionary trends in morphological complexity of the mammalian vertebral column

description: A fundamental concept in evolutionary biology is that life tends to become
 more complex through geologic time, but empirical examples of this
 phenomenon are controversial. One debate is whether increasing complexity
 is the result of random variations, or if there are evolutionary processes
 which actively drive its acquisition, and if these processes act uniformly
 across clades. The mammalian vertebral column provides an opportunity to
 test these hypotheses because it is composed of serially-repeating
 vertebrae for which complexity and organization can be readily measured.
 Here we test seven competing hypotheses for the evolution of vertebral
 complexity by incorporating fossil data from the mammal stem lineage into
 evolutionary models. Based on these data, we reject Brownian motion (a
 random walk) and uniform increasing trends in favor of stepwise shifts for
 explaining increasing complexity. We hypothesize that clade-specific
 adaptations associated with increased aerobic capacity in non-mammalian
 cynodonts may have provided impetus for increasing vertebral complexity in
 mammals.
description: Vertebral complexity and organization across synapsids. Dataset
 includes: 1. Complexity and organization metrics
 calculated from raw vertebral measures available from https://doi.org/10.5061/dryad.jm820mg. Range, polarization, irregularity, concentration and smoothness calculated following McShea (1991) on logged data. Clustering calculated as 1-the Hopkins Statistic. 2. Age ranges of non-mammalian synapsid species gathered from the literature, used for callibrating phylogeny 3. Phylogenetic trees as .Rdata files saved in the multiPhylo format. 60 phylogenetic trees generated using 'bin_timePaleophy' function with minimum branch length method and occurence dates randomly sampled from withing their time bin. The master tree reflects the most complete sampling (444 species), while the subsampled tree reflects taxa included in the analysis.
DOI: 10.5061/dryad.7pvmcvdpc
title: Dr (Colon Cancer)

description: Colon adenocarcinoma (COAD) is the commonest colon cancer exhibiting high
 mortality. Due to the association with cancers progression, long noncoding
 RNAs (lncRNAs) become prognostic biomarkers. This study, using relevant
 clinic information and expression profiles of lncRNA originating in The
 Cancer Genome Atlas database, aims to construct a prognostic lncRNA
 signature to estimate the prognosis for patients. In the training cohort,
 prognosis related lncRNAs were selected from differently expressed lncRNAs
 by univariate Cox analysis. Furthermore, the least absolute shrinkage and
 selection operator (LASSO) regress and multivariate Cox analysis were
 employed for identifying prognostic lncRNAs. The prognostic signature was
 constructed by those lncRNAs. Prognostic model was able to calculate each
 COAD patient’s risk score and split the patients to groups of low and high
 risk. Compared to the low-risk group, the high-risk group had significant
 poor prognosis. Then, the prognostic signature was validated in validation
 and all cohorts. The receiver operating characteristic (ROC) curve and
 c-index were performed in all cohort. Moreover, those prognostic lncRNAs
 signature were combined with clinicopathological risk factors to construct
 a nomogram for predicting the prognosis of COAD in clinic. Finally, 7
 lncRNAs (CTC-273B12.10, AC009404.2, AC073283.7, RP11-167H9.4, AC007879.7,
 RP4-816N1.7, RP11-400N13.2) were identified and validated by different
 cohorts. The Kyoto Encyclopedia of Genes and Genomes analysis of the mRNAs
 co-expressed with 7 prognostic lncRNAs suggested 4 significantly
 up-regulated pathways, which are AGE-RAGE signaling pathway, focal
 adhesion, ECM-receptor interaction and PI3K/Akt signaling pathway. To sum
 up, our study verified that the mentioned 7 lncRNAs can be biomarkers to
 predict the prognosis of COAD patients and design personalized treatment.
description: On TCGA (https://cancergenome.nih.gov/) official website, we
 obtained the RNA-Seq (level 3, HTSeq-FPKM data) with 473 colon
 adenocarcinoma patients’ relevant clinical information. The approve from
 the ethics committee was not needed due to clinical data and the RNA‐Seq
 expression data were obtained from TCGA. Further, the quality of clinical
 data was assessed, and a part of patients were not included in our studies
 for following reasons: (a) The clinical prognostic information of some
 patients is not available; (b) Patients were dead in the first month after
 diagnosis; (c) The death was caused by other diseases and
 accidents.
DOI: 10.5061/dryad.qz612jm8x
title: Negative feedback: ants choose unoccupied over occupied food sources and lay more pheromone to them

description: In order to make effective collective decisions, ants lay pheromone trails
 to lead nestmates to acceptable food sources. The strength of a trail
 informs other ants about the quality of a food source, allowing colonies
 to exploit the most profitable resources. However, recruiting too many
 ants to a single food source can lead to over-exploitation, queuing, and
 thus decreased food intake of the colony. The non-linear nature of
 pheromonal recruitment can also lead colonies to become trapped in
 suboptimal decisions, if the environment changes. Negative feedback
 systems can ameliorate these problems. We investigated a potential source
 of negative feedback: whether the presence of nestmates makes food sources
 more or less attractive. Lasius niger workers were trained to food sources
 of identical quality, scented with different odours. Ants fed alone at one
 odour. At the other odour ants fed either with other feeding nestmates, or
 with dummy ants (black cuticular hydrocarbon-coated glass beads). Ants
 avoided food sources at which other nestmates were present. They also
 deposited less pheromone to occupied food sources, suggesting an active
 avoidance behavior, and potentiating negative feedback. However, ants did
 not avoid the food associated with dummy ants, suggesting that cuticular
 hydrocarbons and static visual cues alone may not be sufficient for
 nestmate recognition in this context. This effect may prevent crowding at
 a single food source when other profitable food sources are available
 elsewhere, leading to a higher collective food intake. It could also
 potentially protect colonies from becoming trapped in local feeding
 optima.
DOI: 10.5061/dryad.w0vt4b8m3
title: Museum epigenomics: characterizing cytosine methylation in historic museum specimens

description: Museum genomics has transformed the field of collections-based research,
 opening up a range of new research directions for paleontological
 specimens as well as natural history specimens collected over the past few
 centuries. Recent work demonstrates that it is possible to characterize
 epigenetic markers such as DNA methylation in well preserved ancient
 tissues. This approach has not yet been tested in traditionally prepared
 natural history specimens such as dried bones and skins, the most common
 specimen types in vertebrate collections. In this study, we developed and
 tested methods to characterize cytosine methylation in dried skulls up to
 76 years old. Using a combination of ddRAD and bisulphite treatment, we
 characterized patterns of cytosine methylation in two species of deer
 mouse (Peromyscus spp.) collected in the same region in Michigan in 1940,
 2003, and 2013–2016. We successfully estimated methylation in specimens of
 all age groups, although older specimens yielded less data and showed
 greater interindividual variation in data yield than newer specimens.
 Global methylation estimates were reduced in the oldest specimens (76
 years old) relative to the newest specimens (1–3 years old), which may
 reflect post-mortem hydrolytic deamination. Methylation was reduced in
 promoter regions relative to gene bodies and showed greater bimodality in
 autosomes relative to female X chromosomes, consistent with expectations
 for methylation in mammalian somatic cells. Our work demonstrates the
 utility of historic specimens for methylation analyses, as with genomic
 analyses; however, studies will need to accommodate the large variance in
 the quantity of data produced by older specimens.
description: These are double digest RADseq libraries that have undergone
 bisulfite treatment for methylation analysis. The DNA was extracted from
 dried bone tissue (microturbinates) sampled from <em>Peromyscus
 maniculatus </em>and <em>Peromyscus leucopus
 </em>specimens collected between 1940 and 2016. The libraries were
 digested with SphI and MluCI and individually tagged using a combinatorial
 barcoding system with barcodes on the forward adapter and indices on the
 reverse primer. All samples contain a spike-in of fully unmethylated
 lambda phage DNA - these reads can be used to calculate the
 sample-specific bisulfite conversion rate. The raw sequence data is
 uploaded here, as well as a document linking specimen ID to the barcode
 and index sequences. Detailed specimen information is available in the
 supplementary material of the associated manuscript.
DOI: 10.5281/zenodo.18392638
title: Seismic moment tensor results in support of "The influence of 3D velocity models on seismic moment tensor estimation in Alaska"

description: This collection includes figures and results from a catalog of 5 estimated moment tensors forevents Alaska for 6 Earth models, for both double-couple and full moment tensor inversions.
DOI: 10.5281/zenodo.18392637
title: Seismic moment tensor results in support of "The influence of 3D velocity models on seismic moment tensor estimation in Alaska"

description: This collection includes figures and results from a catalog of 5 estimated moment tensors forevents Alaska for 6 Earth models, for both double-couple and full moment tensor inversions.
DOI: 10.5061/dryad.5qfttdz11
title: Populations of a widespread invader and co-occurring native species vary in phenotypic plasticity

description: Phenotypic plasticity can promote plant invasions and enhance impacts on
 native species but little is known about variation in plasticity among
 invader populations compared to native species. Variation in plasticity
 among invader populations could inform more precise predictions of invader
 spread and impacts across heterogeneous resource environments.
  We used a common garden experiment with sun and shade treatments
 to test for variation in plasticity among 12 populations of an invasive
 grass, and to determine if the invader exhibited greater plasticity than
 six native species that co-occur in the Southeast US. Principal component
 analysis revealed that invader populations from different native ranges
 consistently varied from each other and native species in traits linked to
 more favorable phenotypes under resource limitation. Overall, the invader
 exhibited greater plasticity than native species, as demonstrated by
 higher plasticity index values for traits such as plant height, leaf mass
 ratio, and root shoot ratio. Variation in phenotypic plasticity among
 invader populations suggests the potential for evolution of plasticity,
 and greater plasticity of invader populations than native species may
 underlie invader dominance. Differences in plasticity among populations
 appears to play an important role in predictions of the spread and
 potentially the impacts of invasive species.
DOI: 10.5061/dryad.dfn2z34w6
title: A new species of croton (Euphorbiaceae) from a Madagascan lineage discovered in coastal Kenya

description: Croton kinondoensis, a new species from Kenya, is described and
 illustrated here with photographs. It is found in the sacred Kaya Kinondo
 Forest, one of the last remaining coastal forests patches in Kenya. Its
 morphology and systematic position based on ITS and trnL-F DNA sequence
 data clearly place it within the Adenophorus Group of Croton, a clade of
 ca. 15 species otherwise known only from Madagascar and the Comoros
 Archipelago. Its closest affinities appear to lie with Croton mayottae,
 from the island of Mayotte, and C. menabeensis, from northwestern
 Madagascar. This new species likely represents an independent dispersal of
 Croton from Madagascar to mainland Africa.
description: DNA was extracted from leaf fragments obtained from the holotype
 specimen <i>Ngumbau & Nyange SAJIT-V-0520 </i>(HIB)
 using the Mag-MK Plant Genomic DNA extraction kit (Sangon Biotech,
 Shanghai) following the manufacturer’s protocol. For Malagasy accessions,
 DNA was extracted using the DNeasy plant mini kit (Qiagen, Valencia,
 California) following the manufacturer’s protocol. The ITS and
 <i>trnL-F</i> regions were amplified using the same primers
 (White et al. 1990; Taberlet et al. 1991) and the same PCR procedures as
 in Van Ee et al. (2015) and Haber et al. (2017). Sequence formatting and
 editing were conducted in Geneious v. 5.6.4 (Kearse et al.
 2012).
DOI: 10.5061/dryad.cz8w9ghzm
title: A Test of the Repeatability of Measurements of Relative Fitness in the Long-Term Evolution Experiment with Escherichia coli

description: Experimental studies of evolution using microbes have a long tradition,
 and these studies have increased greatly in number and scope in recent
 decades. Most such experiments have been short in duration, typically
 running for weeks or months. A venerable exception, the long-term
 evolution experiment (LTEE) with Escherichia coli has continued for 30
 years and 70,000 bacterial generations. The LTEE has become one of the
 cornerstones of the field of experimental evolution, in general, and the
 BEACON Center for the Study of Evolution in Action, in particular. Science
 laboratories and experiments usually have finite lifespans, but we hope
 that the LTEE can continue far into the future. There are practical issues
 associated with maintaining such a long-term experiment. One issue, which
 we address here, is whether key measurements made at one time and place
 are reproducible, within reasonable limits, at other times and places.
 This issue comes to the forefront when one considers moving an experiment
 like the LTEE from one lab to another. To that end, the Barrick lab at the
 University of Texas at Austin, measured the fitness values of samples from
 the 12 LTEE populations at 2,000, 10,000, and 50,000 generations and
 compared the new data to data previously obtained at Michigan State
 University. On balance, the datasets agree very well. More generally, this
 finding shows the value of simplicity in experimental design, such as
 using a chemically defined growth medium and appropriately storing samples
 from microbiological experiments. Even so, one must be vigilant in
 checking assumptions and procedures given the potential for uncontrolled
 factors (e.g., water quality) to affect outcomes. This vigilance is
 perhaps especially important for a trait like fitness, which integrates
 all aspects of organismal performance and may therefore be sensitive to
 any number of subtle environmental influences.
description: <strong>LTEE.fitness.repeatability.csv</strong> This data file contains colony counts and relative fitness values to compare the reproducibility of new competition assays conducted at The University of Texas at Austin (UTA) with competition assays previously conducted at Michigan State University (MSU). The file also contains fitness values predicted by a power law model (PLM) for comparison.