cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0k6djh9z6
title: A single heat stress bout induces rapid and prolonged heat acclimation in the California mussel, Mytilus californianus

description: Climate change is not only causing steady increases in average global
 temperatures but also increasing the frequency with which extreme heating
 events occur. These extreme events may be pivotal in determining the
 ability of organisms to persist in their current habitats. Thus, it is
 important to understand how quickly an organism’s heat tolerance can be
 gained and lost relative to the frequency with which extreme heating
 events occur in the field. We show that the California mussel, Mytilus
 californianus—a sessile intertidal species that experiences extreme
 temperature fluctuations and cannot behaviorally thermoregulate—can
 quickly (in 24-48 h) acquire improved heat tolerance after exposure to a
 single sublethal heat-stress bout (2 h at 30 or 35°C) and can maintain
 this improved tolerance for up to 3 weeks without further exposure to
 elevated temperatures. This adaptive response improved survival rates by
 ~75% under extreme heat stress bouts (2 h at 40°C). To interpret these
 laboratory findings in an ecological context, we evaluated four years of
 mussel body temperatures recorded in the field. The majority (~64%) of
 consecutive heat stress bouts were separated by 24-48 h, but several
 consecutive heat bouts were separated by as much as 22 days. Thus, the
 ability of M. californianus to maintain improved heat tolerance for up to
 three weeks after a single sublethal heat-stress bout significantly
 improves their probability of survival, as ~33% of consecutive heat events
 are separated by 3-22 days. As a sessile animal, mussels likely evolved
 the capability to rapidly gain and slowly lose heat tolerance to survive
 the intermittent, and often unpredictable, heat events in the intertidal
 zone. This adaptive strategy will likely prove beneficial under the
 extreme heat events predicted with climate change.
description: See Methods section of paper for details on how it was analyzed
 and the overall experimental design.
description: The analysis code in R is for the survival curve and chi square
 analyses; you will need to import that dataset
 "HHStudy_Days1-28_New.csv". The Temp column is a factor for
 either 25, 30, 35C sublethal temperatures or the control group.
 "Days_PostHH" indicates how many recovery days were between the
 sublethal and extreme heat stress bouts. The body mass and shell length
 are recorded for each individual - however there are some missing data for
 this-- see Supplmental Info Table 1 for which data are missing. The
 "LethalHeat_Date" is the date when the extreme heat stress bout
 was given to the mussels. The "EndDate" is when the mussels died
 or finished out the 4 week monitoring period. The last column,
 "status" is whether the mussel survived or died after the
 Extreme heat stress bout: TRUE = died; FALSE = survived (at 4 week time
 point they were still alive).
DOI: 10.5061/dryad.7pvmcvdrp
title: Integrated analysis of circRNA-miRNA-mRNA of Sebastes schlegelii following Edwardsiella tarda challenge

description: Sebastes schlegelii, an important aquaculture species, has been widely
 cultured in East Asian countries. With the increase in the cultivation
 scale, various diseases have become major threats to the industry.
 Evidence has shown that non-coding RNAs (ncRNAs) have remarkable functions
 in the interactions between pathogens and their hosts. However, little is
 known about the mechanisms of circular RNAs (circRNAs) and coding RNAs in
 the process of preventing pathogen infection in the intestine in teleosts.
 In this study, we aimed to uncover the global landscape of mRNAs,
 circRNAs, and microRNAs (miRNAs) in response to Edwardsiella tarda
 infection at different time points (0, 2, 6, 12, and 24 h), and to
 construct regulatory networks for exploring the immune regulatory
 mechanism in the intestine of S. schlegelii. In total, 1,794 mRNAs, 87
 circRNAs, and 79 miRNAs were differentially expressed. Some of the
 differentially expressed RNAs were quantitatively validated using qRT-PCR.
 Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed
 that most of the differentially expressed mRNA genes and the target genes
 of ncRNAs were related to immune signaling pathways, such as the NF-κB
 signal pathway, pathogen recognition receptors related to signaling
 pathways (Toll-like receptors and Nod-like receptors), and the chemokine
 signaling pathway. Based on these differentially expressed genes, 624
 circRNA-miRNA pairs and 2,694 miRNA-mRNA pairs were predicted using the
 miRanda software. Integrated analyses generated 25 circRNA-miRNA-mRNA
 interaction networks. In a novel_circ_0004195/novel-530/IκB interaction
 network, novel_530 was upregulated, while its two targets,
 novel_circ_0004195 and IκB, were downregulated after E. tarda infection.
 In addition, two circRNA-miRNA-mRNA networks related to apoptosis
 (novel_circ_0003210/novel_152/apoptosis-stimulating of p53 protein
 1) and interleukin (novel_circ_0001907/novel_127/interleukin-1
 receptor type 2) were also identified in our study. We thus
 speculated that the downstream NF-κB signaling pathway, p53 signaling
 pathway, and apoptosis might play vital roles in the immune response in
 the intestine of S. schlegelii. This study revealed a landscape of RNAs in
 the intestine of S. schlegelii during E. tarda infection and provided
 clues for further study on the immune mechanisms and signaling networks
 based on the circRNA-miRNA-mRNA axis in S. schlegelii.
description: High-Throughput Sequencing
DOI: 10.5061/dryad.vq83bk3r6
title: Multilevel selection on offspring size and the maintenance of variation

description: Multilevel selection on offspring size occurs when offspring fitness
 depends on both absolute size (hard selection), and size relative to
 neighbours (soft selection). We examined multilevel selection on egg size
 at two biological scales: within clutches and among females, for an
 external fertilising tubeworm. We exposed clutches of eggs to two sperm
 environments (limiting and saturating) and measured their fertilisation
 success. We then modelled environmental (sperm) differences in hard and
 soft selection on individual eggs, as well as selection on clutch-level
 traits (means and variances). Hard and soft selection differed in strength
 and form depending on sperm availability – hard selection was consistently
 stabilising; soft selection was directional and favoured eggs relatively
 larger (sperm limitation) or smaller (sperm saturation) than the
 clutch-mean. At the clutch-level, selection on mean-egg size was largely
 stabilising; whilst selection on within-clutch variance was weak, but
 generally negative – although some correlational selection occurred
 between these two traits. Importantly, we found that the optimal
 clutch-mean egg size differed for mothers and offspring, suggesting some
 antagonism between the levels of selection. We thus identify several
 pathways that may maintain offspring-size variation: environmentally
 (sperm)-dependent soft selection; antagonistic multilevel selection; and
 correlational selection on clutch-means and variances. Multilevel
 approaches are powerful, but seldom used, tools for studies of offspring
 size and we encourage their future use.
description: Data used to model multilevel selection on egg size under sperm
 saturating (H) and sperm limiting (L) conditions for the broadcast
 spawning polycheate, <em>Galeolaria caespitosa</em>. We used a
 split-clutch design to conduct <em>in vitro</em>
 fertilisations, whereby each female's clutch was split across 2
 replicate fertilisations (Rep) per sperm treatment. We then measured the
 size-specific fertilisation success of all eggs within these clutch
 subsamples as a binary response variable (0 = unsuccessful eggs; 1 =
 successfully fertilised eggs). Note that values of clutch-mean in the
 dataset represents the mean-egg size of each female's clutch measured
 from photographs taken prior to fertilisation. Egg size represents the
 inital size of each indiviual egg prior to fertilisation, and has been
 back-calculated from measurements taken after fertilisation using
 equations that describe these relationships.
DOI: 10.5061/dryad.5qfttdz3m
title: Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population

description: Hybridization between divergent lineages generates new allelic
 combinations. One mechanism that can hinder the formation of hybrid
 populations is mitonuclear incompatibility, i.e. dysfunctional
 interactions between proteins encoded on the nuclear and mitochondrial
 genomes (mitogenomes) of diverged lineages. Theoretically, selective
 pressure due to mitonuclear incompatibility can affect genotypes in a
 hybrid population in which nuclear genomes and mitogenomes from divergent
 lineages admix. To directly and thoroughly observe this key process,
 we de novo sequenced the 747 Mb genome of the coastal
 goby, Chaenogobius annularis, and investigated its integrative
 genomic phylogeographics using RNA‐sequencing, RAD‐sequencing, genome
 re‐sequencing, whole mitogenome sequencing, amplicon‐sequencing, and small
 RNA‐sequencing. Chaenogobius annularis populations have
 been geographically separated into Pacific Ocean (PO) and Sea of Japan
 (SJ) lineages by past isolation events around the Japanese archipelago.
 Despite the divergence history and potential mitonuclear incompatibility
 between these lineages, the mitogenomes of the PO and SJ lineages have
 coexisted for generations in a hybrid population on the Sanriku Coast. Our
 analyses revealed accumulation of nonsynonymous substitutions in the
 PO‐lineage mitogenomes, including two convergent substitutions, as well as
 signals of mitochondrial lineage‐specific selection on
 mitochondria‐related nuclear genes. Finally, our data implied that a
 microRNA gene was involved in resolving mitonuclear incompatibility. Our
 integrative genomic phylogeographic approach revealed that mitonuclear
 incompatibility can affect genome evolution in a natural hybrid
 population.
description: <strong>PASA annotation file</strong>
 sample_mydb_pasa.pasa_assemblies.gff3
 <strong>AUGUSTUS annotation file</strong>
 agohaze_sspac_x1.abinitio.gff
DOI: 10.5061/dryad.b5mkkwhc1
title: Data from: A predictive model for improving placement of wind turbines to minimise collision risk potential for a large soaring raptor

description: 1. With the rapid growth of wind energy developments worldwide, it is
 critical that the negative impacts on wildlife are considered and
 mitigated. This includes minimising the numbers of large soaring raptors
 which are killed when they collide with wind turbines. 2. To reduce the
 likelihood of raptor collisions, turbines should be placed at locations
 which are least used by sensitive species. For resident or breeding
 species, this is often delineated crudely through the use of circular
 buffers centred on nest sites, which assume uniform habitat use around a
 nest site. 3. Using GPS tracking data together with a digital elevation
 model we build and cross-validate a simple generalizable model, to
 classify the spatial likelihood of wind turbine collisions for resident
 adult Verreaux’s eagles in any landscape where there are known nests. We
 apply our methods to operational developments in South Africa to validate
 the model and demonstrate its ability in predicting actual collision
 mortalities. 4. Our Collision Risk Potential (CRP) model included the
 variables distance to nest, distance to conspecific nest, slope, distance
 to slope and elevation. Using our model, rather than a circular buffer,
 resulted in ca. 4–5% improvement in eagle protection while excluding
 development from the same amount (but not shape) of area. For an equal
 level of eagle protection, our model can make ca. 20–21% more area
 available for wind energy development compared to a circular buffer. 5.
 Exploring collisions at operational wind farms in South Africa we show
 that our CRP model correctly predicted 87% of known collisions, while
 circular buffers (5.2km radius) only captured 50% of collisions.
 6. Synthesis and applications: We show that by using predictive
 models to account for habitat use, a greater area of land can be made
 available for wind energy development without increased mortality risk to
 raptors. Our predictive model can be used to provide robust guidance on
 wind turbine placement in South Africa in a way which minimizes the
 conflict between a vulnerable raptor species and the development of
 renewable energy. 
description: This data set is derived from GPS tracking data of 15 adult
 Verreaux's eagles subsetted to 10 minute intervals.
 It includes the variables elevation, slope, vector ruggedness
 measure (vrm), distance to slope (dist2slope), distance to nest
 (nest_dist) and distance to conspecific nest (nearest_nest_dist) and their
 re-scaled counterparts (suffix '_rs') for all tracking locations
 (bin 1) and for three times as many pseudoabsence points (bin 0) per
 eagle. 'Name' is the unique identifier per eagle.
DOI: 10.5061/dryad.ncjsxkst0
title: Refugia during the last glacial period and the origin of the disjunct distribution of the insular plant Microtropis japonica (Celastraceae)

description: Aim: While many phylogeographical studies have focused on continental
 refugia, the function of islands as refugia has been long overlooked. In
 this study, we examined the biogeographic history of Microtropis japonica
 and its insular distribution to elucidate the hidden status of islands on
 the range expansion of plants. Location: Two disjunct island areas of
 Japan (the Izu and Ryukyu Islands) and their adjacent areas (the Japanese
 mainlands Honshu and Kyushu, and Taiwan). Taxon: Microtropis japonica
 (Celastraceae). Methods: Phylogeographic and population genetic analyses
 were performed using chloroplast DNA (cpDNA) and nuclear single-nucleotide
 polymorphism (SNP) data. In addition, ecological niche modeling of current
 suitable habitats and those during the last glacial maximum were conducted
 using occurrence and climate data. Results: Both cpDNA and nuclear SNP
 data showed genetic differentiation between two disjunct regions (mainly
 the Izu and Ryukyu Islands). However, at the intra-regional level, the
 genetic structures revealed by different markers showed different
 geographic patterns. While cpDNA data indicated genetic differentiation
 within the Ryukyu Islands but not within the Izu Islands, nuclear SNP data
 indicated genetic differentiation within both island groups. Ecological
 niche modeling showed that both the Izu and Ryukyu Islands have
 continuously been potential distribution areas regardless of historical
 climate oscillations. Main conclusions: Genetic data suggest that the
 current disjunct distribution pattern of M. japonica strongly reflects the
 refugia locations during the last glacial period and the subsequent range
 expansion. Ecological niche modeling revealed the importance of islands as
 refugia in the disjunct distribution of M. japonica.
DOI: 10.5061/dryad.0p2ngf204
title: Data for: Male coercion and female injury in a sexually cannibalistic mantis

description: Sexual conflict can generate male traits that enhance mating success but
 lead to injury in females. Pre-copulatory sexual cannibalism—where females
 eat males without mating—has the potential to select for harmful coercive
 traits as well, but few examples are known. Here, we show that males of
 the highly cannibalistic Springbok mantis, Miomantis caffra, wrestle
 females during pre-mating interactions. We find that most initial contacts
 between males and females involve a violent struggle whereby each sex
 tries be the first to grasp hold of the other with their raptorial
 forelegs. When females win the struggle, they always cannibalise males.
 However, when males grasp females first, they dramatically increase the
 chance of mating. We also find striking evidence that males wound females
 with their fore-tibial claws during struggles, resulting in haemolymph
 loss and scar tissue formation. Taken together, our results show how males
 can overcome the threat of cannibalism by coercively wrestling females. We
 argue that pre-copulatory injury in this species is likely a negative
 pleiotropic side-effect of selection on claws to capture prey.
description: Data are tallies of behaviours observed during male-female
 encounters.
DOI: 10.5061/dryad.7m0cfxpsh
title: Data from: All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment

description: AbstractMonitoring marine resource exploitation is a key activity in
 fisheries science and biodiversity conservation. Since research surveys
 are time-consuming and costly, fishery-dependent data (i.e. derived
 directly from fishing vessels) are increasingly credited with a key role
 in expanding the reach of ocean monitoring. Fishing vessels may be seen as
 widely ranging data-collecting platforms, which could act as a fleet of
 sentinels for monitoring marine life, in particular exploited stocks.
 Here, we investigate the possibility of assessing catch composition of
 single hauls carried out by trawlers by applying DNA metabarcoding to the
 “slush” collected from fishing nets just after the end of hauling
 operations. We assess the performance of this approach in portraying
 β-diversity and examining the quantitative relationship between species
 abundances in the catch and DNA amount in the slush (reads counts
 generated by amplicon sequencing). We demonstrate that the assemblages
 identified using DNA in the slush mirror those returned by visual
 inspection of net content and detect a strong relationship between read
 counts and species abundances in the catch. We therefore argue that this
 approach could be upscaled to serve as a powerful source of information on
 the structure of demersal assemblages and the impact of fisheries.
description: <b>COI_R1.fastq</b> and <b>COI_R2.fastq</b>: COI paired-end FastQ files from the Illumina HiSeq 2x250 bp run. <b>COI_tag&primers.txt</b>: COI primers and unique dual-tag combinations (forward and reverse) for 63 COI amplicons (54 slush samples, 2 extraction blanks, 1 PCR negative control, 6 seawater blanks). <b>12S_R1.fastq</b> and <b>12S_R2.fastq</b>: 12S paired-end FastQ files from the Illumina MiSeq 2x150 bp run. <b>12S_tag&primers.txt</b>: 12S primers and unique dual-tag combinations (forward and reverse) for 63 12S amplicons (54 slush samples, 2 extraction blanks, 1 PCR negative control, 6 seawater blanks). <b>metabarcoding_COI_data.xlsx</b>: number of reads per species/replicate/site after data post-processing and cleaning. Data refer to analyzed taxa: teleosts, elasmobranchs, cephalopods and decapods. <b>metabarcoding_12S_data.xlsx</b>: number of reads per species/replicate/site after data post-processing and cleaning. Data refer to analyzed taxa: teleosts and elasmobranchs.
DOI: 10.5061/dryad.08kprr51n
title: The sodium/proton exchanger NHA2 regulates blood pressure through a WNK4-NCC dependent pathway in the kidney

description: NHA2 is sodium/hydrogen exchanger that was associated with arterial
 hypertension in humans, but the role of NHA2 in kidney function and blood
 pressure homeostasis is currently unknown. Here we show that NHA2
 localizes almost exclusively to distal convoluted tubules in the kidney.
 NHA2 knock-out mice displayed reduced blood pressure, normocalcemic
 hypocalciuria and an attenuated response to the thiazide diuretic
 hydrochlorothiazide. Phosphorylation of the thiazide-sensitive
 sodium/chloride cotransporter NCC and its upstream activating kinase
 Ste20/SPS1-related proline/alaninerich kinase (SPAK), as well as the
 abundance of with no lysine [K] kinase 4 (WNK4), were significantly
 reduced in kidneys of NHA2 knock-out mice. In vitro experiments
 recapitulated these findings and revealed increased WNK4 ubiquitylation
 and enhanced proteasomal WNK4 degradation upon loss of NHA2. The effect of
 NHA2 on WNK4 stability was Kelch-like 3 (KLHL3)-dependent. More
 specifically, loss of NHA2 selectively attenuated KLHL3 phosphorylation
 and the physiologically important PKAand PKC-mediated decrease of WNK4
 degradation was blunted upon loss of NHA2. Phenotype analysis of NHA2/NCC
 double knock-out mice supported the notion that NHA2 affects blood
 pressure homeostasis by an intrarenal and NCC-dependent mechanism. In
 summary, our data reveal NHA2 as a critical component of the WNK4-NCC
 pathway and hence as a novel regulator of blood pressure homeostasis in
 the kidney.
description: Detailed description of methods can be found in the original,
 published manuscript
 (https://pubmed.ncbi.nlm.nih.gov/32956652/). 1.
 Uncropped immunoblots of all immunoblots published in the manuscript
 (incl. Supplemental Information). For details of SDS-PAGE and
 immunoblotting see Materials and Methods section of the published
 manuscript. Developed X-ray films were scanned. Unedited scans were safed
 as TIF files and compiled in a Word Document. 2. Basic
 data of normalized expression (immunoblots or real-time PCR, for details
 of quantification see Materials and Methods section of the published
 manuscript) were imported in Graph Pad Prism (Version 9) for statistical
 analysis and visualization.
description: A readme.txt file with detailed re-use instructions has been
 uploaded. Uncropped blots can be visualized using Word
 (Version 2003 or higher), derived expression data can be visualized by
 Graph Pad Prism (Version 9 or higher).
DOI: 10.5061/dryad.kwh70rz2m
title: Data from: Multidimensional plasticity in the Glanville fritillary butterfly: larval performance is temperature, host and family specific

description: Variation in environmental conditions during development can lead to
 changes in life-history traits with long-lasting effects. Here, we study
 how variation in temperature and host plant, i.e. the consequences of
 potential maternal oviposition choices, affects a suite of life-history
 traits in pre-diapause larvae of the Glanville fritillary butterfly. We
 focus on offspring survival, larval growth rates and relative fat
 reserves, and pay specific attention to intraspecific variation in the
 responses (GxExE). Globally, thermal performance and survival curves
 varied between diets of two host plants, suggesting that host modifies the
 temperature impact, or vice versa. Additionally, we show that the relative
 fat content has a host-dependent, discontinuous response to developmental
 temperature. This implies that a potential switch in resource allocation,
 from more investment in growth at lower temperatures to storage at higher
 temperatures, is dependent on the larval diet. Interestingly, a large
 proportion of the variance in larval performance is explained by
 differences among families, or interactions with this variable. Finally,
 we demonstrate that these family-specific responses to the host plant
 remain largely consistent across thermal environments. Altogether, the
 results of our study underscore the importance of paying attention to
 intraspecific trait variation in the field of evolutionary ecology.
description: See README text files for detailed information
description: See README text files for detailed information