cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1c59zw3rm
title: Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

description: Asparagus setaceus is a popular ornamental plant cultivated in tropical
 and subtropical regions globally. In this study, a chromosome-level
 reference genome of A. setaceus was constructed to assist in studying the
 genome structure and evolution. A total of 112.52 Gb of long reads was
 produced from Nanopore platform, resulting in 156.28× depth coverage of an
 estimated genome size of 720 Mb. The combination of Illumina-short reads,
 10× Genomics linked reads, and Hi-C data produced the final chromosome
 quality genome of A. setaceus with a genome size of 710.15 Mb, accounting
 for 98.63% of the estimated genome size. Furthermore, 96.85% of the
 sequences were anchored to 10 super-scaffolds, corresponding to the 10
 chromosomes. The genome of A. setaceus was predicted to have 28,410 genes,
 and 25,649 (90.28%) of these genes were functionally annotated. Genome
 annotation revealed that 65.59% were repetitive sequences, of which long
 terminal repeats were predominant (42.51% of the whole genome). Divergence
 between A. setaceus and its close relative A. officinalis is estimated to
 have occurred ~9.66 million years ago. Genome evolution analysis indicated
 that A. setaceus underwent two rounds of whole genome duplication events.
 In addition, 762 specific gene families, 898 expanded gene families, 96
 positively selected genes, and 76 resistance R genes in A. setaceus were
 identified and functionally annotated. These findings provided insights
 into the structure and evolution of the A. setaceus genome and will
 facilitate the comparative genetic and genomic research on the genus
 Asparagus.
description: Protein-coding
 genes were predicted using strategies that integrated <i>de
 novo</i> gene prediction, experimental evidence obtained from
 transcriptomic data, and homology-based gene models. For homology
 prediction, GeMoMa was used with a protein sequence from <i>A.
 officinalis</i>, a relative species of <i>A.
 setaceus</i>. For RNA-seq-based prediction, PASA was used on the
 basis of the assembled RNA-seq unigenes. Augustus was used for <i>de
 novo</i> prediction. Then, genes predicted by various methods were
 integrated into a non-redundant gene set by using EVM. For the annotation
 of the protein-coding genes, the sequences of the predicted genes were
 searched against the commonly used databases SwissProt, GO, KEGG, KOG, Nr,
 and InterPro.
DOI: 10.5061/dryad.cvdncjt0c
title: Data from: Individual differences in behaviour explain variation in survival: a meta-analysis

description: Research focusing on among-individual differences in behaviour (“animal
 personality”) has been blooming for over a decade. One of the central
 theories explaining the maintenance of such behavioural variation posits
 that individuals expressing greater “risky” behaviours should suffer
 higher mortality. Here, for the first time, we synthesize the existing
 empirical evidence for this key prediction. Our results did not support
 this prediction as there was no directional relationship between riskier
 behaviour and greater mortality; however there was a significant absolute
 relationship between behaviour and survival. In total, behaviour explained
 a significant, but small, portion (5.8%) of the variance in survival. We
 also found that risky (versus “shy”) behavioural types live significantly
 longer in the wild, but not in the laboratory. This suggests that
 individuals expressing risky behaviours might be of overall higher quality
 but the lack of predation pressure and resource restrictions mask this
 effect in laboratory environments. Our work implies that individual
 differences in behaviour explain important differences in survival but not
 in the direction predicted by theory. Importantly, this suggests that the
 models predicting survival trade-offs may need revision and/or empiricists
 may need to reconsider their proxies of risky behaviours when testing such
 theory.
DOI: 10.6075/j0707ztm
title: Early removal of senescent cells protects retinal ganglion cells loss in experimental ocular hypertension

description: Experimental ocular hypertension induces senescence of retinal ganglion
 cells (RGCs) that mimicks events occurring in human glaucoma.
 Senescence-related chromatin remodeling leads to profound transcriptional
 changes including the upregulation of a subset of genes that encode
 multiple proteins collectively referred to as the senescenceassociated
 secretory phenotype (SASP). Emerging evidence suggests that the presence
 of these proinflammatory and matrix-degrading molecules has deleterious
 effects in a variety of tissues. In the current study, we demonstrated in
 a transgenic mouse model that early removal of senescent cells induced
 upon elevated intraocular pressure (IOP) protects unaffected RGCs from
 senescence and apoptosis. Visual evoked potential (VEP) analysis
 demonstrated that remaining RGCs are functional and that the treatment
 protected visual functions. Finally, removal of endogenous senescent
 retinal cells after IOP elevation by a treatment with senolytic drug
 dasatinib prevented loss of retinal functions and cellular structure.
 Senolytic drugs may have the potential to mitigate the deleterious impact
 of elevated IOP on RGC survival in glaucoma and other optic neuropathies.
DOI: 10.5061/dryad.3tx95x6bn
title: Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP

description: We here report the phylogenetic position of barthelonids, small anaerobic
 flagellates previously examined using light microscopy alone. Barthelona
 spp. were isolated from geographically distinct regions and we established
 five laboratory strains. Transcriptomic data generated from one Barthelona
 strain (PAP020) were used for large-scale, multi-gene phylogenetic
 (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the
 base of the Fornicata clade, indicating that barthelonids represent a
 deep-branching Metamonad clade. Considering the anaerobic/microaerophilic
 nature of barthelonids and preliminary electron microscopy observations on
 strain PAP020, we suspected that barthelonids possess functionally and
 structurally reduced mitochondria (i.e. mitochondrion-related organelles
 or MROs). The metabolic pathways localized in the MRO of strain PAP020
 were predicted based on its transcriptomic data and compared with those in
 the MROs of fornicates. We here propose that strain PAP020 is incapable of
 generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in
 substratelevel phosphorylation were detected. Instead, we detected the
 putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase),
 suggesting that strain PAP020 depends on ATP generated in the cytosol. We
 propose two separate losses of substrate-level phosphorylation from the
 MRO in the clade containing barthelonids and (other) fornicates.
DOI: 10.5061/dryad.bk3j9kd6s
title: Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection

description: Natural environments are rarely static; rather selection can fluctuate on
 time scales ranging from hours to centuries. However, it is unclear how
 adaptation to fluctuating environments differs from adaptation to constant
 environments at the genetic level. For bacteria, one key axis of
 environmental variation is selection for planktonic or biofilm modes of
 growth. We conducted an evolution experiment with Burkholderia
 cenocepacia, comparing the evolutionary dynamics of populations evolving
 under constant selection for either biofilm formation or planktonic growth
 with populations in which selection fluctuated between the two
 environments on a weekly basis. Populations evolved in the fluctuating
 environment shared many of the same genetic targets of selection as those
 evolved in constant biofilm selection, but were genetically distinct from
 the constant planktonic populations. In the fluctuating environment,
 mutations in the biofilm-regulating genes wspA and rpfR rose to high
 frequency in all replicate populations. A mutation in wspA first rose
 rapidly and nearly fixed during the initial biofilm phase but was
 subsequently displaced by a collection of rpfR mutants upon the shift to
 the planktonic phase. The wspA and rpfR genotypes coexisted via negative
 frequency-dependent selection around an equilibrium frequency that shifted
 between the environments. The maintenance of coexisting genotypes in the
 fluctuating environment was unexpected. Under temporally fluctuating
 environments coexistence of two genotypes is only predicted under a narrow
 range of conditions, but the frequency-dependent interactions we observed
 provide a mechanism that can increase the likelihood of coexistence in
 fluctuating environments.
DOI: 10.15468/dl.qc9xyf
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Polygala evolvulacea"
 ]
}

 The dataset includes 10 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002044-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.xsj3tx99s
title: Data from: Toward a standardised protocol for the stable isotope analysis of scleractinian corals

description: Rationale: The stable isotope analysis of carbon and nitrogen is a
 powerful tool in many ecological studies, but different sample treatments
 may affect stable isotope ratios and hamper comparisons among studies. The
 goal of this study was to determine whether treatments that are commonly
 used to prepare scleractinian coral samples for stable isotope analysis
 yield different δ15N and δ13C values, and to provide guidelines toward a
 standardised protocol.  Methods: The animal tissues and
 Symbiodiniaceae of two symbiotic scleractinian coral species (Stylophora
 pistillata and Porites lutea) were divided into subsamples to test the
 effects of the drying method, lipid extraction, acidification treatment
 and water washing. All the subsamples were analysed for their δ15N and
 δ13C values, using continuous flow elemental analyser/isotope ratio mass
 spectrometry. Results: The drying method and lipid extraction treatment
 had no substantial effects on the δ15N and δ13C values of Symbiodiniaceae
 and animal tissues. Acid treatment did cause significant differences in
 δ13C values (mean differences ≤0.5‰, with individual samples becoming up
 to 2.0‰ more negative), whereas no ecologically significant differences
 were observed in δ15N values. Animal tissue δ13C values may vary depending
 on whether samples are washed or not.  Conclusions: To move
 towards a standardised protocol in coral research, we recommend using an
 available drying method (as they are equally acceptable) for the stable
 isotope analysis of scleractinian corals, examining the need for lipid
 extraction on a case‐by‐case basis, performing a direct acidification of
 Symbiodiniaceae and animal tissues, and avoiding washing animal tissue
 with distilled water.
DOI: 10.5061/dryad.wh70rxwj1
title: Data from: Reduced CTGF Expression Promotes Cell Growth, Migration, and Invasion in Nasopharyngeal Carcinoma

description: Background The role of CTGF varies in different types of cancer. The
 purpose of this study is to investigate the involvement of CTGF in tumor
 progression and prognosis of human nasopharyngeal carcinoma (NPC).
 Experimental design CTGF expression levels were examined in NPC tissues
 and cells, nasopharynx (NP) tissues, and NP69 cells. The effects and
 molecular mechanisms of CTGF expression on cell proliferation, migration,
 invasion, and cell cycle were also explored. Results NPC cells exhibited
 decreased mRNA expression of CTGF compared to immortalized human
 nasopharyngeal epithelial cell line NP69. Similarly, CTGF was observed to
 be downregulated in NPC compared to normal tissues at mRNA and protein
 levels. Furthermore, reduced CTGF was negatively associated with the
 progression of NPC. Knocking down CTGF expression enhanced the colony
 formation, cell migration, invasion, and G1/S cell cycle transition.
 Mechanistic analysis revealed that CTGF suppression activated FAK/PI3K/AKT
 and its downstream signals regulating the cell cycle,
 epithelial-mesenchymal transition (EMT) and MMPs. Finally, DNA methylation
 microarray revealed a lack of hypermethylation at the CTGF promoter,
 suggesting other mechanisms are associated with suppression of CTGF in
 NPC. Conclusion Our study demonstrates that reduced expression of CTGF
 promoted cell proliferation, migration, invasion and cell cycle
 progression through FAK/PI3K/AKT, EMT and MMP pathways in NPC.
DOI: 10.15468/dl.bzr8z8
title: Occurrence Download

description: A dataset containing 320 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-51.0",
 "Country is Italy",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Gentiana terglouensis, Phyteuma sieberi, Saxifraga squarrosa, Saxifraga hostii)",
 "Year 2015-2026"
 ]
}

 The dataset includes 320 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002049-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7wm37pvp0
title: Low adaptive potential for tolerance to ethynylestradiol, but also low toxicity, in a grayling population (Thymallus thymallus)

description: Background: The presence of a novel pollutant can induce rapid evolution
 if there is additive genetic variance for the tolerance to the stressor.
 Continuous selection over some generations can then reduce the toxicity of
 the pollutant but also deplete the additive genetic variance for the
 tolerance and thereby slow down adaptation. One common pollutant that has
 been ecologically relevant for some time is 17alpha-ethynyestradiol (EE2),
 a synthetic compound of oral contraceptives since their market launch in
 the 1960s. EE2 is typically found in higher concentrations in rivers than
 in lakes. Recent experimental work revealed significant genetic variance
 for the tolerance to EE2 in two lake-spawning salmonid species but no such
 variance in river-spawning brown trout. We used another river-spawning
 salmonid, the European grayling Thymallus thymallus, to study the toxicity
 of an ecologically relevant concentration of EE2. We also used a
 full-factorial in vitro breeding design and singly rearing of 1,555
 embryos and larvae of 40 sib groups to test whether there is additive
 genetic variance for the tolerance to this pollutant. Results: We found
 that exposure to EE2 reduced larval growth after hatching, but contrary to
 what has been found in the other salmonids, there were no significant
 effects of EE2 on embryo growth and survival. We found additive genetic
 variance for embryo viability, i.e. heritability for fitness. However,
 there was no significant additive variance for the tolerance to EE2.
 Conclusions: Our findings support the hypothesis that continuous selection
 has reduced the toxicity of EE2 and depleted genetic variance for
 tolerance to this synthetic stressor.
description: see Marques da Cunha, Maitre, Wedekind (in review)
DOI: 10.5061/dryad.2280gb5nb
title: Data from: Early plant development depends on embryo damage location: the role of seed size in partial seed predation

description: Data on 1) Observed weevil-infested acorns in the field; 2) Germination
 rates and times, and seedling emergence of control and embryo-damaged
 acorns; 3) Seedling performance and physiology of seedlings
DOI: 10.5061/dryad.s4mw6m93c
title: Data from: Depth moderates loss of marine foundation species after an extreme marine heatwave: could deep temperate reefs act as a refuge?

description: Marine heatwaves have been documented around the world, causing widespread
 mortality of numerous benthic species on shallow reefs (&lt; 15 m
 depth). Deeper habitats are hypothesized to be a potential refuge from
 environmental extremes, though we have little understanding of the
 response of deeper benthic communities to marine heatwaves. Here, we show
 how increasing depth moderates the response of seaweed- and
 coral-dominated benthic communities to an extreme marine heatwave across a
 subtropical-temperate biogeographical transition zone. Benthic community
 composition and key habitat-building species were characterised across
 three depths (15, 25 and 40 m) before and several times after the 2011
 Western Australian marine heatwave to assess resistance during and
 recovery after the heatwave. We found high natural variability in benthic
 community composition along the biogeographic transition zone and across
 depths with a clear shift in the composition after the marine heatwave in
 shallow (15 m) sites but a lot less in deeper communities (40 m). Most
 importantly, key habitat-building seaweeds such as Ecklonia radiata, and
 Syctothalia dorycarpa, which had catastrophic losses on shallow reefs,
 remained and were less affected in deeper communities. Evidently, deep
 reefs have the potential to act as a refuge during marine heatwaves for
 the foundation species of shallow reefs in this region.
DOI: 10.6084/m9.figshare.31164196
title: SI Tables 16, 18, and 19 for Christian et al., Proteomic stress response by a novel methanogen enriched from the Great Salt Lake

description: Proteomics datasets for Christian et al., Proteomic stress response by a novel methanogen enriched from the Great Salt Lake
DOI: 10.6084/m9.figshare.31164196.v1
title: SI Tables 16, 18, and 19 for Christian et al., Proteomic stress response by a novel methanogen enriched from the Great Salt Lake

description: Proteomics datasets for Christian et al., Proteomic stress response by a novel methanogen enriched from the Great Salt Lake
DOI: 10.5061/dryad.1rn8pk0pq
title: Evidence for divergence between sympatric stone charr and Dolly Varden along unique environmental gradients in Kamchatka.

description: Here we describe the biological and ecological differences between
 partially anadromous Dolly Varden and riverine stone charr distributed in
 the Kamchatka River middle course. Endemic stone charr, being the ambush
 predator, is defined by the accelerated growth and prolonged lifespan,
 robust body and large mouth, as well as specific marble colouration since
 an early age. The significant restriction in gene flow between the stone
 charr and benthos-eating Dolly Varden was supported by an allelic
 distribution of eight microsatellite loci. Herewith, the identity of
 mitochondrial DNA control region and intron sequences of growth hormone
 and metallothionine genes confirms a relatively recent diversification of
 the groups within the single basin. We suggest the key role of the
 specific environment for reproduction isolation of stone charr. It
 occupies coniferous taiga zone with dark-coloured water, whereas Dolly
 Varden spawns uppercourse in the zone of stunted, windblown forest.
 Conifer litter decomposition products could drive natural selection of
 stone charr via metabolism acceleration and resistance to toxicants. The
 metabolic difference could promote piscivory and development of the
 specific morphological peculiarities of the stone charr. Therefore, we
 present the first evidence in favour of trophic-based sympatric
 diversification in a river basin at high latitudes.
DOI: 10.5061/dryad.fbg79cnr3
title: Multiple paternity in a lek mating system: females mate multiply when they choose inexperienced sires

description: 1.    Multiple mating by females is common and
 often driven by social constraints on female mate choice. However, females
 mate with multiple males even in systems without these social constraints
 and rates of multiple mating tend to be highly variable within and between
 populations. In lek mating systems, females are able to assess multiple
 males and their choice is unrestricted by pair bonds or the need for
 biparental care, yet some females mate with multiple males. 
 2.    To better understand the factors
 affecting variation in multiple mating, we investigated the occurrence of
 multiple paternity within clutches in a highly polygynous lek mating
 system.  3.    Using long-term data on
 genetic paternity, survival, social status, and individual age from a
 population of lance-tailed manakins (Chiroxiphia lanceolata), a species
 where males lek in cooperative alpha-beta pairs, we tested five
 non-exclusive hypotheses about causes of variation in multiple mating and
 its benefits to females.  4.    We
 found that inexperienced males, including new alphas and rare beta sires,
 were disproportionately likely to share paternity when they sired any
 chicks. In contrast, female age (experience) was unrelated to multiple
 paternity. Multiple mating did not result in higher reproductive success
 or reduced variance in success for females, and there were neither
 consistently promiscuous females nor males that consistently shared
 paternity. 5.    The occurrence of multiple
 paternity in this lek mating system was best explained by female choice
 related to male characteristics that change with male experience. Our
 results support the hypothesis that there is a developmental component to
 the occurrence of multiple mating, and suggest females choose to mate
 multiply when their choices are not optimal.
DOI: 10.5061/dryad.tb2rbnzwj
title: Data from: Assessing biological factors affecting post-speciation introgression

description: An increasing number of phylogenomic studies have documented a
 clear ‘footprint’ of post-speciation introgression
 among closely-related species. Nonetheless, systematic
 genome-wide studies of factors that determine the
 likelihood of introgression remain rare. Here,
 we propose an a
 priori hypothesis-testing framework that uses introgression
 statistics—including a new metric of
 estimated introgression, Dp —to evaluate general patterns of introgression prevalence and direction across multiple closely related species. We demonstrate this approach using whole genome sequences from 32 lineages in 11 wild tomato species to assess the effect of three factors on introgression—genetic relatedness, geographical proximity, and mating system differences—based on multiple trios using the ‘ABBA-BABA’ test. Our analyses suggest each factor affects the prevalence of introgression, although our power to detect these is limited by the number of comparisons currently available. We find that of 14 species pairs with geographically ‘proximate’ versus ‘distant’ population comparisons, 13 showed evidence of introgression; in ten of these cases, this was more prevalent between geographically-closer populations. We also find modest evidence that introgression declines with increasing genetic divergence between lineages, is more prevalent between lineages that share the same mating system, and—when it does occur between mating systems—tends to involve gene flow from more inbreeding to more outbreeding lineages. While our analysis indicates that recent post-speciation introgression is frequent in this group—detected in 15 of 17 tested trios—estimated levels of genetic exchange are modest (0.2-2.5% of the genome), so the relative importance of hybridization in shaping the evolutionary trajectories of these species could be limited. Regardless, similar clade-wide analyses of genomic introgression would be valuable for disentangling the major ecological, reproductive, and historical determinants of post-speciation gene flow, and for assessing the relative contribution of introgression as a source of genetic variation