cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7d7wm37zf
title: Plasticity of plant silicon and nitrogen concentrations in response to water regimes varies across temperate grassland species

description: Temperate grasslands exhibit strong spatial and temporal variation in
 water regimes. Thus, grassland plants experience potentially stressful
 water regimes, which may influence their tissue silicon (Si) and nitrogen
 (N) concentrations. Plant Si and N concentrations play important
 ecological roles in temperate grasslands, e.g. by influencing plant
 performance and herbivory, yet comparisons of species’ responses to a
 broad range of water regimes, including drought, waterlogging, and
 flooding, are lacking. We conducted a mesocosm experiment with ten
 temperate grassland species of two life forms (grasses and forbs) exposed
 to four different soil water regimes (drought, benign control, waterlogged
 and flooded conditions), and analysed their Si and N concentrations.
 Grasses showed lower Si concentrations under drought and flooding compared
 to the benign control and the highest concentrations emerged under
 waterlogging. Overall, plant Si responses of grasses were more uniform,
 while in forbs, responses varied both in direction and magnitude across
 species. For N concentrations, all species and life forms showed the
 highest concentrations under drought compared to the benign control, while
 half of the species exhibited decreasing concentrations under waterlogging
 and/or flooding. The water regimes, especially waterlogging and flooding,
 induced changes in species rankings of plant Si and N concentrations, with
 stronger shifts in forbs than in grasses. Our results indicate that
 spatial and temporal variation of water regimes may influence plant Si and
 N concentrations in temperate grassland species. Plant Si responses to
 water regimes might be highly species-specific in forbs but more similar
 in grasses, whereas plant N responses are likely to be relatively uniform
 across species and life forms. The strong plasticity in plant Si and N
 concentrations we observed might have pervasive consequences for
 ecological processes, such as herbivory.
DOI: 10.5061/dryad.00000006g
title: Coral bleaching due to cold stress on a central Red Sea reef flat

description: Ocean warming is leading to more frequent coral bleaching events. However,
 cold stress can also induce bleaching in corals. Here, we report
 observations of a boreal winter bleaching event in Jan 2020 in the central
 Red Sea, mainly within a population of the branching
 coral Stylophora pistillata on an offshore reef flat.
 Sea surface temperatures rarely fall below 24°C in this region, but data
 loggers deployed on several nearby reef flats recorded overnight seawater
 temperatures as low as 18°C just three days before the observations. The
 low temperatures coincided with an extremely low tide and cool air
 temperatures, likely resulting in the aerial exposure of the corals during
 the nighttime low tide event. The risk of aerial exposure is rare in
 winter months, as the Red Sea exhibits seasonal fluctuations in sea level
 with winter values typically 0.3-0.4m higher than in summer. These
 observations are notable for a region typically characterized as a
 high-temperature sea, and highlight the need for long-term monitoring
 programs as this rare event may have gone unnoticed.
description: Temperature data was collected with loggers deployed <em>in
 situ</em> as well as publically-available satellite data from ERA5.
 Tidal data was collected with an ADCP (Acoustic doppler current profiler)
 deployed in situ and a tide gauge deployed in the KAUST harbor.
DOI: 10.15468/dl.chs456
title: Occurrence Download

description: A dataset containing 293 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eutaxia myrtifolia",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 293 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003309-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5285/490af551-ae77-2a79-e063-7086abc01bec
title: Low resolution images of four limpet species collected from the Baja California Peninsula, Mexico (January 2024) and from museum collections in California, US

description: This dataset comprises low resolution JPEG images of four limpet species: <em>Fissurella volcano</em>, <em>Lottia gigantea</em>, <em>Lottia conus</em>, and <em>Lottia strigatella</em>. Specimens were collected along the Baja California peninsula and California, either from the field in January 2024 (Baja specimens only) or from the collections of the Los Angeles County Museum of Natural History (including Baja and California specimens). Shells were photographed against a black background using a Panasonic Lumix DC-G9 camera with an OM SYSTEM 90 mm macro lens and categorised based on their orientation (dorsal or ventral views) and whether they were collected within their respective northern or southern genetic clades. These images were used to test computer vision for identifying cryptic morphological differences between genetically distinct populations as part of the NERC funded Discovery Science Project 'CryptoBioVision: Applying Computer Vision for Cryptic Species Discovery' (NE/X011518/1).
DOI: 10.5061/dryad.sf7m0cg9d
title: Hypoxia preconditioned mesenchymal stem cells prevent cardiac fibroblast activation and collagen production via leptin

description: Aims: Activation of cardiac fibroblasts into myofibroblasts constitutes a
 key step in cardiac remodeling after myocardial infarction (MI), due to
 interstitial fibrosis. Mesenchymal stem cells (MSCs) have been shown to
 improve post-MI remodeling an effect that is enhanced by hypoxia
 preconditioning (HPC). Leptin has been shown to promote cardiac fibrosis.
 The expression of leptin is significantly increased in MSCs after HPC, but
 it is unknown whether leptin contributes to MSC therapy or the fibrosis
 process. The objective of this study was to determine whether leptin
 secreted from MSCs modulates cardiac fibrosis. Methods: Cardiac fibroblast
 (CF) activation was induced by hypoxia (0.5% O2). The effects of MSCs on
 fibroblast activation were analyzed by co-culturing MSCs with CFs and
 detecting the expression of a-SMA, SM22a, and collagen IaI in CFs by
 western blot, immunofluorescence and Sirius red staining. In vivo MSCs
 antifibrotic effects on left ventricular remodeling were investigated
 using an acute MI model involving permanent ligation of the left anterior
 descending coronary artery. Results: Co-cultured MSCs decreased fibroblast
 activation and HPC enhanced the effects. Leptin deficit MSCs from Ob/Ob
 mice did not decrease fibroblast activation. Consistent with this, H-MSCs
 significantly inhibited cardiac fibrosis after MI and mediated decreased
 expression of TGF-b/Smad2 and MRTF-A in CFs. These effects were again
 absent in leptin-deficient MSCs. Conclusion: Our data demonstrate that
 activation of cardiac fibroblast was inhibited by MSCs in a manner that
 was leptin-dependent. The mechanism may involve blocking TGF-b/Smad2 and
 MRTF-A signal pathway.
DOI: 10.5061/dryad.rv15dv4b4
title: Two notorious nodes: A critical examination of relaxed molecular clock age estimates of the bilaterian animals and placental mammals

description: The popularity of relaxed clock Bayesian inference of clade origin timings
 has generated several recent publications with focal results considerably
 older than the fossils of the clades in question. Here we critically
 examine two such clades: the animals (with focus on the bilaterians); and
 the mammals (with focus on the placentals). Each example displays a set of
 characteristic pathologies which, although much commented on, are rarely
 corrected for. We conclude that in neither case does the molecular clock
 analysis provide any evidence for an origin of the clade deeper than what
 is suggested by the fossil record. In addition, both these clades have
 other features (including, in the case of the placental mammals, proximity
 to a large mass extinction) that allow us to generate precise expectations
 of the timings of their origins. Thus, in these instances the fossil
 record can provide a powerful test of molecular clock methodology, and why
 it goes astray; and we have every reason to think these problems are
 general.
DOI: 10.5061/dryad.h44j0zppf
title: Data for: Can heavy metal pollution induce soil bacterial community resistance to antibiotics in boreal forests?

description: The emergence of microbial antibiotic resistance is a central threat to
 global health, food security, and development. It has been shown that
 heavy metal pollution can give rise to microbial resistance to
 antibiotics, but how wide-spread this phenomenon is remains an open
 question that urgently needs filling to enable appropriate environmental
 risk assessments. Here, we determined whether long-term differences in
 heavy metal pollution in boreal forests had affected soil microbial
 communities such that they had increased microbial resistance to
 antibiotics. First, we assessed variation in metal concentrations in
 samples collected across a distance trajectory from the pollution source,
 and also the microbial rates and levels of bacterial community resistance
 to the heavy metal Cu and the antibiotics tetracycline and vancomycin in
 those samples. Second, we tested if the exposure to Cu or tetracycline
 could increase bacterial community resistance to Cu and to antibiotics in
 soils with high versus low background levels of metal contamination. Metal
 pollution had affected microbial community structures and suppressed
 decomposer functioning. Importantly, bacterial community Cu resistance
 increased with higher metal concentrations, which coincided with an
 induced bacterial community resistance to tetracycline, but not to
 vancomycin. Laboratory experiments revealed that bacterial community Cu
 resistance could be further induced in both the low and high end of the
 pollution gradient, but also that these short-term inductions of community
 metal tolerance did not coincide with enhanced antibiotic resistance. This
 yielded a surprising negative correlation between long-term and short-term
 effects by metals on microbial metal and antibiotic resistances. One
 mechanism that could provide protection against both metal cations and
 tetracycline is the small multidrug resistance (SMR) family, which is an
 energy demanding physiological mechanism that may take time to confer
 protection. This may explain the different microbial responses to
 long-term gradients and metal addition experiments. Policy implications.
 We show that metal pollution in boreal forests will promote antibiotic
 resistance in soil bacterial communities, revealing an overlooked
 reservoir of antibiotic resistance. We recommend that environmental risk
 assessments for any activity giving rise to increased soil metal
 concentrations need to also consider the induction of microbial antibiotic
 resistance.
description: All details regarding how the dataset was obtained can be found
 in the open access research paper, or via references literature.
description: The file can be opened with Microsoft Excel or with an
 open-source alternative, like Open Office.
DOI: 10.5061/dryad.kd51c5b94
title: Ecological and metabolomic responses of plants to deer exclosure in a suburban forest

description: Trees and shrubs in suburban forests can be subject to chronic herbivory
 from abundant white-tailed deer, influencing survival, growth, secondary
 metabolites and ecological success in the community. We investigated how
 deer affect the size, cover, and metabolomes of four species in the
 understory of a suburban forest in central New Jersey, USA: the woody
 shrubs Euonymus alatus and Lindera benzoin, the tree Nyssa sylvatica, and
 the semi-woody shrub Rosa multiflora. For each species, we compared plants
 in 38 16 m2 plots with or without deer exclosure, measuring proportion
 cover and mean height after 6.5 years of fencing. We scored each species
 in all plots for deer browsing over eight years and assessed selection by
 deer among the species. We did untargeted metabolomics by sampling leaves
 from three plants of each species in an equal number of fenced and
 unfenced plots, conducting chloroform-methanol extractions followed by
 LC-MS/MS, and conducting statistical analysis on MetaboAnalyst. The
 proportion of a species browsed ranged from 0.24 to 0.35. Nyssa sylvatica
 appeared most selected by and susceptible to deer; in unfenced plots both
 its cover and mean height were significantly lower. Only cover or height
 was lower for E. alatus and L. benzoin in unfenced plots, while R.
 multiflora height was greater. The metabolomic analysis identified 2,333
 metabolites, which clustered by species but not fencing treatment.
 However, targeted analysis of the top metabolites grouped by fencing for
 all samples and for each species alone, and was especially clear in N.
 sylvatica, which also grouped by fencing using all metabolites. The most
 significant metabolites that were upregulated in fenced plants include
 some involved in defense-related metabolic pathways, e.g. monoterpenoid
 biosynthesis. In overbrowsed suburban forests, variation of deer impact on
 species’ ecological success, potentially mediated by metabolome-wide
 chemical responses to deer, may contribute to changes in community
 structure.
DOI: 10.5061/dryad.jm63xsjf5
title: Genotypes of cave, surface and hybrid Astyanax mexicanus

description: Genetic divergence in the presence of gene flow has been well documented,
 but there is little information on the specific factors maintaining
 divergence. The present study investigates this in the Mexican tetra
 (Astyanax mexicanus), an excellent model for studying this question
 because surface and cave populations differ markedly in phenotype and
 genotype, but are interfertile.  Previous population studies
 documented significant gene flow among cave and surface populations but
 they focused on analyses of neutral markers, whose evolutionary dynamics
 likely differ from those of genes involved in cave adaptation. The present
 study advances our understanding of this question by focusing specifically
 on the genetics responsible for eye and pigmentation reduction, signature
 traits of cave populations. Direct observations of two cave populations
 over the course of 63 years verify that surface fish frequently move into
 the caves and even hybridize with the cavefish. Importantly, however,
 historical records show that surface alleles for pigmentation and eye size
 do not persist, but are rapidly eliminated from the cave gene pool. It has
 been argued that the regression of eyes and pigmentation was driven by
 drift, but the results of this study suggest that strong selection
 actively eliminates surface alleles from the cave populations. 
description: The data consist of genotypes of surface and cave fishes and
 their hybrids as determined by the use of an ABI automated
 sequencer.
description: The two files are in csv and txt formats. They can be opened with
 any text editor or Excel. The two files are in a compressed format folder
 which needs to be unzipped to gain access.
DOI: 10.5061/dryad.j6q573nhr
title: Data for: Sex, amitosis, and evolvability in the ciliate Tetrahymena thermophila

description: Understanding the mechanisms that generate genetic variation, and thus
 contribute to the process of adaptation, is a major goal of evolutionary
 biology. Mutation and genetic exchange have been well studied as
 mechanisms to generate genetic variation. However, there are additional
 factors, such as genome architecture, that may also impact the amount of
 genetic variation in some populations, and the extent to which these
 variation generating mechanisms are themselves shaped by natural selection
 is still an open question. To test the effect of genome architecture on
 the generation of genetic variation, and hence evolvability, we studied
 Tetrahymena thermophila, a ciliate with an unusual genome structure and
 mechanism of nuclear division, called amitosis, whereby homologous
 chromosomes are randomly distributed to daughter cells. Amitosis leads to
 genetic variation among the asexual descendants of a newly produced sexual
 progeny because different progeny cells will contain different
 combinations of parental alleles. We hypothesize that amitosis thus
 increases the evolvability of newly produced sexual progeny relative to
 their unmated parents and species that undergo mitosis. To test this
 hypothesis, we used experimental evolution and simulations to compare the
 rate of adaptation in T. thermophila populations founded by a single
 sexual progeny to parental populations that had not had sex in many
 generations. The populations founded by a sexual progeny adapted more
 quickly than parental populations in both laboratory populations and
 simulated populations. This suggests that the additional genetic variation
 generated by amitosis of a heterozygote can increase the rate of
 adaptation following sex and may help explain the evolutionary success of
 the unusual genetic architecture of Tetrahymena and ciliates more
 generally.
DOI: 10.5061/dryad.1vhhmgqwx
title: Chromosome-level assemblies of the Pieris mannii butterfly genome suggest Z-origin and rapid evolution of the W chromosome

description: The insect order Lepidoptera (butterflies and moths) represents the
 largest group of organisms with ZW/ZZ sex determination. While the origin
 of the Z chromosome predates the evolution of the Lepidoptera, the W
 chromosomes are considered younger, but their origin is debated. To shed
 light on the origin of the lepidopteran W, we here produce
 chromosome-level genome assemblies for the butterfly Pieris
 mannii, and compare the sex chromosomes within and between P. mannii and
 its sister species P. rapae. Our analyses clearly indicate a common origin
 of the W chromosomes of the two Pieris species, and reveal similarity
 between the Z and W in chromosome sequence and structure. This supports
 the view that the W in these species originates from Z-autosome fusion
 rather than from a redundant B chromosome. We further demonstrate the
 extremely rapid evolution of the W relative to the other chromosomes and
 argue that this may preclude reliable conclusions about the origins of W
 chromosomes based on comparisons among distantly related Lepidoptera.
 Finally, we find that sequence similarity between the Z and W chromosomes
 is greatest toward the chromosome ends, perhaps reflecting selection for
 the maintenance of recognition sites essential to chromosome segregation.
 Our study highlights the utility of long-read sequencing technology for
 illuminating chromosome evolution.
DOI: 10.5061/dryad.mcvdnck4c
title: Distinctive, fine-scale distribution of Eastern Caribbean sperm whale vocal clans reflects island fidelity rather than environmental variables

description: Environmental variables are often the primary drivers of species’
 distributions as they define their niche. However, individuals, or groups
 of individuals, may sometimes adopt a limited range within this larger
 suitable habitat as a result of social and cultural processes. This is the
 case for Eastern Caribbean sperm whales. While environmental variables are
 reasonably successful in describing the general distribution of sperm
 whales in the region, individuals from different cultural groups have
 distinct distributions around the Lesser Antilles islands. Using data
 collected over two years of dedicated surveys in the Eastern Caribbean, we
 conducted habitat modelling and habitat suitability analyses to
 investigate the mechanisms responsible for such fine-scale distribution
 patterns. Vocal clan-specific models were dramatically more successful at
 predicting distribution than general species models, showing how a failure
 to incorporate social factors can impede accurate predictions. Habitat
 variation between islands did not explain vocal clan distributions,
 suggesting that cultural group segregation in the Eastern Caribbean sperm
 whale is driven by traditions of site/island fidelity (most likely
 maintained through conformism and homophily) rather than habitat type
 specialization. Our results provide evidence for the key role of cultural
 knowledge in shaping habitat use of sperm whales within suitable
 environmental conditions and highlight the importance of cultural factors
 in shaping sperm whale ecology. We recommend that social and cultural
 information be incorporated into conservation and management as culture
 can segregate populations on fine spatial scales in the absence of
 environmental variability.
description: See the full article for detailed methods. R code based on code
 from Pirotta et al. 2011 (Modelling sperm whale habitat preference: a
 novel approach combining transect and follow data) and Eguiguren et al.
 2019 (Habitat use of culturally distinct Galápagos sperm whale
 <em>Physeter</em> <em>macrocephalus</em>
 clans).
DOI: 10.5061/dryad.7h44j0zxw
title: Reciprocal bark exchange helps to disentangle tree species dependent bark and wood trait effects on invertebrate diversity

description: 1. Previous studies showed that bark cover at early-decay stage had
 profound control on the invertebrate assemblages of bark and wood, with
 possible consequence for the decomposition process. However, previous
 experimental designs could not disentangle how bark versus wood traits
 affect the invertebrate assemblage process in bark and/or wood separately
 because wood traits of different tree species may vary independently from
 bark traits. Furthermore, we do not know whether such tree species
 specific bark trait effects are still influential at mid-decay stage. 2.
 To unravel whether and how bark and wood traits influence invertebrate
 communities in tree logs at mid-decay stage, we introduce reciprocal bark
 transplantation within pairs of different tree species as a new method. We
 applied this method to two pairs of phylogenetically contrasting species
 of gymnosperms (pair I: Araucaria araucana and Cryptomeria japonica, pair
 II: Picea abies and Thuja plicata) and another gymnosperm (Chamaecyparis
 lawsoniana) set as disturbance control to test for potential bark
 manipulation artefacts on invertebrate community composition. 3. Our bark
 exchange experiment revealed that both bark and wood host abundant and
 divergent subsets of invertebrates on mid-decay logs of different tree
 species. We further documented that the invertebrate community composition
 was predominantly shaped by the traits of host tissue per se, while also
 being significantly but less strongly affected by the traits of the other
 tissue, i.e. the adjacent bark or wood. Our results indicated that bark
 trait effects faded with time and how long bark trait effects persist
 greatly depends on bark thickness. 4. Synthesis. Our study suggests that
 maintaining deadwood heterogeneity related to variation between tree
 species, and to bark versus wood, is important for nursing a large
 biodiversity of invertebrates. Combined with bark removal methodology, our
 bark exchange method can be further extended to more decay stages and more
 forest biomes to track bark trait effects and bark induced priority
 effects on deadwood decomposition, and its associated invertebrate and
 microbial communities.