cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.905qfttr3
title: The effect of prey abundance and fisheries on the survival, reproduction, and social structure of killer whales (Orcinus orca) at subantarctic Marion Island

description: Most marine apex predators are keystone species that fundamentally
 influence their ecosystems through cascading top-down processes.
 Reductions in worldwide predator abundances, attributed to environmental
 and anthropogenic-induced changes to prey availability and negative
 interactions with fisheries, can have far-reaching ecosystem impacts. We
 tested whether the survival of killer whales (Orcinus orca) observed at
 Marion Island in the Southern Indian Ocean correlated with social
 structure and prey variables (direct measures of prey abundance,
 Patagonian toothfish fishery effort, and environmental proxies) using
 multistate models of capture-recapture data spanning 12 years (2006 to
 2018). We also tested the effect of these same variables on killer whale
 social structure and reproduction measured over the same period. Indices
 of social structure had the strongest correlation with survival, with
 higher sociality associated with increased survival probability. Survival
 was also positively correlated to Patagonian toothfish fishing effort
 during the previous year, suggesting that fishery-linked resource
 availability is an important determinant of survival. No correlation
 between survival and environmental proxies of prey abundance was found.
 At-island prey availability influenced the social structure of Marion
 Island killer whales, but none of the variables explained variability in
 reproduction. Future increases in legal fishing activity may benefit this
 population of killer whales through the artificial provisioning of
 resources they provide.
DOI: 10.5061/dryad.3r2280gn2
title: Data for: Interspecific interactions between gray woolly monkeys (Lagothrix lagotricha cana) and nine syntopic primate species

description: Assemblage structure and acquisition of high-value resources will usually
 be affected by changes in resource availability and differential
 competitive abilities of assemblage members. In fragmented habitats where
 carrying capacity limits are exceeded due to high population densities and
 biomass, interspecific interactions can be expected to occur at a high
 frequency, potentially turning into an important cost for coexistence. We
 studied assemblage- and guild-level patterns of interspecific interactions
 in two highly diverse isolated primate assemblages in southern Amazonia.
 Specifically, we assessed the effects of temporal variation in fruit
 availability on the rates of interspecific interactions between gray
 woolly monkeys (Lagothrix lagotricha cana), one of the largest
 tree-dwelling mammals of the Amazon forests, and nine syntopic primate
 species. This dataset includes the rates of interactions at the
 guild-level and assemblage-level, as well as the rates of interactions
 with each individual species. Additionally, the dataset provides
 estimations of fruit availability at both study sites.
DOI: 10.5061/dryad.v15dv421j
title: Experimental manipulation of scavenger and herbivore functional role and their effects on plant communities following mass mortality events

description: We designed an experiment to measure the relative importance of bottom-up
 forces (nutrient addition) and top-down forces (impairment of obligate
 scavenger and herbivore functional roles) generated by experimental
 carrion deployment to simulate mass mortality events on the local plant
 community. In our experimental plots, we measured changes in plant
 functional groups before and for three years after experimental carrion
 deployment. Additionally, we monitored cherrybark oak (Quercus pagoda)
 seedlings' growth and survival three years after being transplanted
 in the experimental plots. 
description: Details for each dataset are provided in the README
 file. Datasets include: 
 Plant
 community transects run before carrion deployment, and one and two years
 after carrion deployment Experimental treatments of
 experimental plots Year of data
 collection Plant functional group
 abundance 
 Plant community quadrats
 run three years after carrion deployment Experimental treatments of
 experimental plots Plant functional group
 abundance 
 Growth of transplanted
 cherrybark oak seedlings three years after experimental carrion
 deployment<br> Experimental treatments of
 experimental plots Length of cherrybark oak
 seedlings 
 Survival of transplanted
 cherrybark oak seedlings three years after experimental carrion
 deployment Experimental treatments of
 experimental plots Survival of cherrybark oak
 seedlings
DOI: 10.7291/d19x13
title: Giant clam nitrogen isotopic data and code for N isotope model

description: Giant clams are reef-dwelling bivalves that reach unusual sizes through a
 partnership with photosymbiotic algae. To date, no shell-based
 biogeochemical proxy has been found which directly records the
 photosymbiotic development and health of these animals. We present new
 results showing a size-related decline in nitrogen isotopic values of
 shell-bound organic matter from the hinge layers of giant clams from the
 Northern Red Sea. In three of four tested shells, δ15N values decline from
 &gt; 4‰ at the juvenile stage to between 0 and -2.5‰ at maturity,
 consistent with a transition from heterotrophic nutrition early in the
 bivalve’s life to receiving most of their nutrition from photosynthetic
 symbionts and external dissolved inorganic nitrogen at maturity. We find
 less extreme declines or no change within the outer shell layer, with more
 inter-individual variability, which is likely related to the greater
 influence of the symbionts in the adjacent siphonal mantle of the animals.
 We use a von Bertalanffy-linked trophic model that uses δ15N of nitrate
 and particulate organic matter to corroborate and explain the trophic
 transition in the ontogeny of the clams, and propose that high-resolution
 δ15N measurements in bivalves could be used as a proxy for photosymbiosis
 and reef paleoenvironmental conditions in the fossil record.
DOI: 10.5061/dryad.q573n5tp9
title: Data for: Butterfly eyespots exhibit unique patterns of open chromatin

description: How the precise spatial regulation of genes is correlated with spatial
 variation in chromatin accessibilities is not yet clear. Previous studies
 that analysed chromatin from homogenates of whole-body parts of insects
 found little variation in chromatin accessibility across those parts, but
 single-cell studies of Drosophila brains showed extensive spatial
 variation in chromatin accessibility across that organ. In this work we
 studied the chromatin accessibility of butterfly wing tissue fated to
 differentiate distinct colors and patterns in pupal wings of Bicyclus
 anynana. We observed that three dissected wing regions showed unique
 chromatin accessibilities. Open chromatin regions specific to eyespot
 color patterns were highly enriched for binding motifs recognized by
 Suppressor of Hairless (Su(H)), Krüppel (Kr), Buttonhead (Btd) and Nubbin
 (Nub) transcription factors. Genes in the vicinity of the eyespot-specific
 open chromatin regions included those involved in wound healing and SMAD
 signal transduction pathways, previously proposed to be involved in
 eyespot development. We conclude that eyespot and non-eyespot bits of
 tissue taken from the same wing have distinct patterns of chromatin
 accessibility, possibly driven by the eyespot-restricted expression of
 potential pioneer factors, such as Kr.
description: We dissected small eyespot and adjacent control tissues from 3hr
 pupae and performed ATAC-Seq to identify the chromatin accessibility
 differences between different sections of the wings.
DOI: 10.5061/dryad.qv9s4mwkq
title: Biomass temporal stability increases at two spatial scales during secondary succession

description: Ecological stability has long been considered to change over succession,
 but how secondary succession influences the relationship between diversity
 and temporal stability of biomass production at different spatial scales
 is poorly understood. We studied changes in plant diversity, functional
 temporal stability (biomass production) and compositional temporal
 stability (the latter two are hereafter referred to as functional
 stability and compositional stability) and explored the stabilizing roles
 of plant diversity at two spatial scales (small plots of 0.25 m2 area and
 large transects of 1.25 m2 area) during secondary succession in a
 subalpine meadow from 2003-2010. Our results showed that both plant
 diversity and functional and compositional stability increased at the
 small plot scale and large transect scale during secondary succession. As
 secondary succession proceeded, higher average alpha diversity (i.e.,
 species diversity at the plot scale) led to higher functional and
 compositional stability at the plot scale by mainly species stability,
 predominantly contributing to higher functional and compositional
 stability at the large transect scale. In addition, Simpson-based beta
 diversity (i.e., compositional dissimilarity among communities within the
 same transect), while unaffected by succession, contributed to functional
 stability at the large transect scale by promoting asynchronous dynamics
 among communities. Synthesis: Our study highlights the stabilizing effects
 of plant diversity across the two spatial scales during secondary
 succession. Our findings provide the first empirical evidence that
 biodiversity-mediated effects on ecosystem temporal stability strengthen
 over successional time, suggesting that the stabilizing effects of
 biodiversity should be considered across spatial and temporal scales in
 the face of global changes and biodiversity loss.
DOI: 10.5061/dryad.02v6wwq7h
title: Genomes of the extinct Bachman’s Warbler show high divergence and no evidence of admixture with other extant Vermivora Warblers

description: Bachman’s Warbler (Vermivora bachmanii) – last sighted in 1988 – is one of
 the only North American passerines to have gone extinct. Given extensive
 ongoing hybridization of its two extant congeners – the Blue-Winged
 Warbler (V. cyanoptera) and Golden-Winged Warbler (V. chrysoptera) – and
 shared patterns of plumage variation between Bachman’s Warbler and hybrids
 between those extant species, it has been suggested that Bachman’s Warbler
 might have also had a component of hybrid ancestry. Here, we use historic
 DNA (hDNA) and whole genomes of Bachman’s Warblers collected at the turn
 of the 20th century to address this. We combine these data with the two
 extant Vermivora species to examine patterns of population
 differentiation, inbreeding, and gene flow. In contrast to the admixture
 hypothesis, the genomic evidence is consistent with V. bachmanii having
 been a highly divergent, reproductively isolated species, with no evidence
 of introgression. We show that these three species have similar levels of
 runs of homozygosity (ROH), consistent with effects of a small long-term
 effective population size or population bottlenecks, with one V. bachmanii
 outlier showing numerous long ROH and an FROH greater than 5%. We also
 found—using population branch statistic estimates—previously undocumented
 evidence of lineage-specific evolution in V. chrysoptera near a
 pigmentation gene candidate, CORIN, which is a known modifier of ASIP,
 which is in turn involved in melanic throat and mask coloration in this
 family of birds. Together, these genomic results also highlight how
 natural history collections are such invaluable repositories of
 information about extant and extinct species.
description: The dataset includes detailed sample information for the genomic
 samples included in the study. The information comes from collection
 databases (for museum samples) and field data for the wild caught birds in
 the study.
description: The files include a README (accessible via Microsoft Word) and a
 .CSV file which can be opened in any spreadsheet software.
DOI: 10.5061/dryad.zpc866td7
title: Data for: Human atlastin-3 is a constitutive ER membrane fusion catalyst (phylogenetic and sequence analysis)

description: Homotypic membrane fusion catalyzed by the atlastin (ATL) GTPase sustains
 the branched endoplasmic reticulum (ER) network in metazoans. Our recent
 discovery that two of the three human ATL paralogs (ATL1/2) are
 C-terminally autoinhibited implied that relief of autoinhibition would be
 integral to the ATL fusion mechanism. An alternative hypothesis is that
 the third paralog ATL3 promotes constitutive ER fusion with relief of
 ATL1/2 autoinhibition used conditionally. However, published studies
 suggest ATL3 is a weak fusogen at best. Contrary to expectations, we
 demonstrate here that purified human ATL3 catalyzes efficient membrane
 fusion in vitro and is sufficient to sustain the ER network in triple
 knockout cells. Strikingly, ATL3 lacks any detectable C-terminal
 autoinhibition, like the invertebrate Drosophila ATL ortholog.
 Phylogenetic analysis of ATL C-termini indicates that C-terminal
 autoinhibition is a recent evolutionary innovation. We suggest that ATL3
 is a constitutive ER fusion catalyst and that ATL1/2 autoinhibition likely
 evolved in vertebrates as a means of upregulating ER fusion activity on
 demand.
description: Sequences were retrieved from public data bases.
DOI: 10.5061/dryad.s1rn8pkd7
title: Data from: Strength of female mate preferences in temperature manipulation study supports the signal reliability hypothesis

description: Both sexually selected traits and mate preferences for these traits can be
 condition dependent, yet how variation in preferred traits could select
 for condition dependent preferences has rarely been examined. The signal
 reliability hypothesis predicts that mate preferences vary across
 environments in relation to the reliability of the information preferred
 traits provide in those environments. Extensive variation in the mc4r gene
 on the Y-chromosome that influences male size in Xiphophorus multilineatus
 allowed us to use a split-sibling design to determine if male size is more
 likely to provide information about male genotype (i.e., dam) when males
 were reared in a warm as compared to a cold environment. We then examined
 strength of preference for male size by females reared in the same two
 environments. We found that males were larger in the cold environment, but
 male size was more variable across dams and therefore a more reliable
 indicator of dam in the warm environment. Females reared in the warm
 environment had stronger mate preferences for male size, in addition to a
 relationship between their strength of preference and growth rates that
 was not detected in the cold reared females. These results suggest that
 female preference for male size was influenced by the temperature in which
 they were reared, with the direction of the difference across treatments
 supporting the reliability hypothesis. Understanding how the reliability
 of male traits can select for conditional variation in the strength of the
 female mate preferences will further our discovery of adaptive mate
 preferences. For example, the relationship between the strength of a
 female’s mate preference and their growth rates supports previous work
 with this species of swordtail fish hypothesizing disassortative mating in
 relation to growth rates to mitigate a documented growth-mortality
 tradeoff.
description: Photos of all fish in study were taken to calculate growth rates
 by measuring their standard length (SL) in ImageJ (Rasband, W.S., NIH, Maryland, USA). Growth rate
 (GR) was calculated by subtracting the first SL measurement from the
 second SL measurement, and dividing by the number of days between the two
 measurements. Strength of preference (SOP) for females was calculated by
 subtracting the time she spent with the smaller animation from the time
 she spent with the larger animation.
DOI: 10.5061/dryad.b8gtht7j0
title: High physiological function for corals with thermally tolerant, host-adapted symbionts

description: The flexibility to associate with more than one symbiont may considerably
 expand a host's niche breadth. Coral animals and dinoflagellate
 micro-algae represent one of the most functionally integrated and
 widespread mutualisms between two eukaryotic partners. Symbiont identity
 greatly affects a coral's ability to cope with extremes in
 temperature and light. Over its broad distribution across the Eastern
 Pacific, the ecologically dominant branching coral, Pocillopora
 grandis, depends on mutualisms with the
 dinoflagellates Durusdinium
 glynnii and Cladocopium latusorum. Measurements of
 skeletal growth, calcification rates, total mass increase, calyx
 dimensions, reproductive output and response to thermal stress were used
 to assess the functional performance of these partner combinations. The
 results show both host–symbiont combinations displayed similar phenotypes;
 however, significant functional differences emerged when exposed to
 increased temperatures. Negligible physiological differences in colonies
 hosting the more thermally tolerant D. glynnii refute the
 prevailing view that these mutualisms have considerable growth tradeoffs.
 Well beyond the Eastern Pacific, pocilloporid colonies with D.
 glynnii are found across the Pacific in warm, environmentally variable,
 near-shore lagoonal habitats. While rising ocean temperatures threaten the
 persistence of contemporary coral reefs, lessons from the Eastern Pacific
 indicate that co-evolved thermally tolerant host–symbiont combinations are
 likely to expand ecologically and spread geographically to dominate reef
 ecosystems in the future.
DOI: 10.5061/dryad.280gb5mtx
title: Data from: Keep numbers in view: Red-eared sliders (Trachemys scripta elegans) learn to discriminate relative quantities

description: The ability to discriminate relative quantities, one of the numerical
 competences, is considered as an adaptive trait in uncertain environments.
 Besides humans, previous studies have reported this capacity in several
 non-human primates and birds. Here, we test whether red-eared sliders
 (Trachemys scripta elegans) can discriminate different relative
 quantities. Subjects were first trained to distinguish different stimuli
 with food reward. Then, they were tested with novel stimuli pairs to
 demonstrate how they distinguished the stimuli. The results show that most
 subjects can complete the initial training and use relative quantity
 rather than absolute quantity to make choices during testing phase. This
 study provides behavioural evidence of relative quantity discrimination in
 a reptile species, and suggests that such capacity may be widespread among
 vertebrates.
DOI: 10.57903/uj/3exhgv
title: Spatially Offset Raman Spectroscopy toward In Vivo Assessment of the Adipose Tissue in Cardiometabolic Pathologies, SORS spectra - raw data

description: This dataset contains baseline-corrected SORS spectra acquired from perigonadal white adipose tissue (gWAT) in a murine model of atherosclerosis, heart failure, and high-fat diet (HFD)-induced obesity. The data were collected as part of a research project funded by the National Science Centre (OPUS 17 (no. 2019/33/B/ST4/00878 to A.K.), PRELUDIUM 20 (no. 2021/41/N/ST4/03701 to Z.M.)) and support the publication of the article titled "Spatially Offset Raman Spectroscopy toward In Vivo Assessment of the Adipose Tissue in Cardiometabolic Pathologies."
DOI: 10.5061/dryad.37pvmcvqs
title: Data from: Taxic and morphological diversification during the early radiation of Clupeomorpha (Actinopterygii, Teleostei)

description: Evolutionary radiation is a problematic concept whose definition and
 classification have recently changed. Radiations can be defined as the
 pattern of abrupt increase in diversity of a lineage. It is relevant to
 evaluate the presence and interaction of different types of radiation in
 extant and fossil organisms to adequately delimitate the radiation types
 and to know the diversity in the context of Earth´s history. Here, we
 employed superorder Clupeomorpha in the Early-Late Cretaceous boundary as
 a study case to recognize the radiation types and their interactions,
 using both taxic and morphologic approaches. Clupeomorpha is a diverse and
 ancient teleostean superorder with a wide geographic and ecological
 distribution, that has been extensively studied. We proposed a model to
 calculate rates of origination to analyze the taxic diversification and
 employed geometric morphometrics to analyze the morphological
 diversification that occurred at the time boundary. The results suggest
 the absence of taxic radiation due to the constant increase in the taxa
 origination. However, the expansion of the phylomorphospace occupation and
 the disparity increase suggest the presence of a
 climatic-geographical-disparification and broad diversification-like,
 according to the current classifications. This exhibits the
 incompatibility of the current radiation classifications with the case
 study. 
description: Data are part of a geometric
 morphometric analysis of the body shape diversity of the clupeomorph
 fishes during the Cretaceous. We digitalized twice 15 landmarks and 35
 semilandmarks on TPS software (Clupeomorpha_2_14ene22.tps;
 Clupeomorpha_3_14ene22.tps). The code used can be consulted on the Paper
 Supporting Information and next to these files.  
 As more phylogenetic-related
 taxa tend to resemble morphologically each other and lose data
 independence, phylogeny was considered in the analysis. Clupeomorph
 phylogeny was obtained from the character matrix of Than-Marchese
 & Alvarado-Ortega (2022). A Bayesian inference analysis of 56 taxa
 and 71 characters was performed with 20 million generations, 2 runs, 4
 strings, and 0.2 temperature. Bayesian analysis was performed with MrBayes
 software and the unrooted consensus tree was cut with Mesquite software.
 The phylogeny obtained was attached to this repository
 (Matriz_11ene22_Bayes_JAO_tax_fil.con.tre)
description: -Clupeomorpha_2_14ene22.tps
 and Clupeomorpha_3_14ene22.tps files can be read with R software using
 geomorph package and
 others.  -Matriz_11ene22_Bayes_JAO_tax_fil.con.tre can be
 read with R software using ape package
 and other phylogenetic packages. Also, it can be read in other software
 like Mesquite and FigTree.
DOI: 10.5061/dryad.6t1g1jx45
title: Data from: Genome engineering allows selective conversions of terephthalaldehyde to multiple valorized products in bacterial cells

description: Deconstruction of polyethylene terephthalate (PET) plastic waste generates
 opportunities for valorization to alternative products. We recently
 designed an enzymatic cascade that could produce terephthalaldehyde (TPAL)
 from terephthalic acid. Here, we showed that the addition of TPAL to
 growing cultures of Escherichia coli wild-type strain MG1655 and
 an engineered strain for reduced aromatic aldehyde rection (RARE) strain
 resulted in substantial reduction. We then investigated if we could
 mitigate this reduction using multiplex automatable genome engineering
 (MAGE) to create an E. coli strain with 10 additional knockouts in RARE.
 Encouragingly, we found this newly engineered strain enabled a 2.5-fold
 higher retention of TPAL over RARE after 24h. We applied this new strain
 for the production of para-xylylenediamine (pXYL) and observed a 6.8-fold
 increase in pXYL titer compared to RARE. Overall, our study demonstrates
 the potential of TPAL as a versatile intermediate in microbial
 biosynthesis of chemicals that derived from waste PET.