cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nvx0k6dr6
title: Data from: Disentangling the aging network of a termite queen

description: Background: Most insects are relatively short-lived, with a maximum
 lifespan of a few weeks, like the aging model organism, the fruit-fly
 Drosophila melanogaster. By contrast, the queens of many social insects
 (termites, ants and some bees) can live from a few years to decades. This
 makes social insects promising models in aging research providing insights
 into how a long reproductive life can be achieved. Yet, aging studies on
 social insect reproductives are hampered by a lack of quantitative data on
 age-dependent survival and time series analyses that cover the whole
 lifespan of such long-lived individuals. We studied aging in queens of the
 drywood termite Cryptotermes secundus by determining survival
 probabilities over a period of 15 years and performed transcriptome
 analyses for queens of known age that covered their whole lifespan.
 Results: The maximum lifespan of C. secundus queens was 13 years, with a
 median maximum longevity of 11.0 years. Time course and co-expression
 network analyses of gene expression patterns over time indicated a
 non-gradual aging pattern. It was characterized by networks of genes that
 became differentially expressed only late in life, namely after ten years,
 which associates well with the median maximum lifespan for queens. These
 old-age gene networks reflect processes of physiological upheaval. We
 detected strong signs of stress, decline, defense and repair at the
 transcriptional level of epigenetic control as well as at the
 post-transcriptional level with changes in transposable element activity
 and the proteostasis network. The latter depicts an upregulation of
 protein degradation, together with protein synthesis and protein folding,
 processes which are often down-regulated in old animals. The simultaneous
 upregulation of protein synthesis and autophagy is indicative of a
 stress-response mediated by the transcription factor cnc, a homolog of
 human nrf genes. Conclusion: Our results show non-linear senescence with a
 rather sudden physiological upheaval at old-age. Most importantly, they
 point to a re-wiring in the proteostasis network and stress as part of the
 aging process of social insect queens, shortly before queens die.
description: Information are provided in the Methods section of the
 study.
DOI: 10.5061/dryad.3r2280gf2
title: Molecular Dynamics trajectories of the human PDZ2 domain

description: Molecular Dynamics trajectories of the human PDZ2 domain. This dataset
 contains simulations of two systems (PDZ2 apo and PDZ2 bound to the
 RA-GEF-2 peptide) started from either a crystal or NMR structure.
description: The .prmtop file is a text file as used by the AMBER
 software for molecular dynamics simulations and contains the
 topology of the molecular system. Any text editor should be able to read
 the file, though it is designed towards being used by the
 program. The .nc file is a binary file format for
 trajectories created by the AMBER
 software.
DOI: 10.5061/dryad.d2547d825
title: Predator community and resource use jointly modulate the inducible defense response in body height of crucian carp

description: Phenotypic plasticity can be expressed as changes in body shape in
 response to environmental variability. Crucian carp (Carassius carassius),
 a widespread cyprinid, displays remarkable plasticity in body morphology
 and increases body depth when exposed to cues from predators, suggesting
 the triggering of an anti-predator defense mechanism. However, these
 morphological changes could also be related to resource use and foraging
 behavior, as an indirect effect of predator presence. In order to
 determine whether phenotypic plasticity in crucian carp is driven by a
 direct or indirect response to predation threat, we compared twelve fish
 communities inhabiting small lakes in southeast Norway grouped by four
 categories of predation regimes: no predator fish, or brown trout (Salmo
 trutta), perch (Perca fluviatilis) or pike (Esox lucius) as main
 piscivores. We predicted the body shape of crucian carp to be associated
 with the species composition of predator communities, and that the
 presence of efficient piscivores results in a deeper body shape. We use
 stable isotope analyses to test if this variation in body shape was
 related to a shift in individual resource use – i.e., littoral rather than
 pelagic resource use would favor the development of a specific body shape
 - or other environmental characteristics. The results showed that
 increasingly efficient predator communities induced progressively deeper
 body shape, larger body size and lower population densities. Predator
 maximum gape size and individual trophic position were the best variables
 explaining crucian carp variation in body depth among predation
 categories, while littoral resource use did not have a clear effect. The
 gradient in predation pressure also corresponded to a shift in lake
 productivity. These results indicate that crucian carp have a fine-tuned
 morphological defense mechanism against predation risk, triggered by the
 combined effect of predator presence and resource availability.
DOI: 10.5061/dryad.34tmpg4j7
title: DragonDrop: passive dynamics and control strategies of aerial righting in the dragonfly

description: Dragonflies perform dramatic aerial manoeuvres when hunting prey or
 chasing rivals but glide leisurely with wings virtually fixed. This makes
 dragonflies a great system to explore how to minimize the trade-off
 between manoeuvrability and stability. We challenged the dragonfly by
 dropping it from selected inverted attitudes and digitised the
 6-degrees-of-freedom aerial recovery kinematics via custom motion capture
 techniques. From these kinematic data we then performed rigid-body inverse
 dynamics to reconstruct the forces and torques involved in the righting
 behaviour. We found that inverted dragonflies typically recover themselves
 with the shortest rotation from the initial body inclination.
 Additionally, they exhibited a strong tendency to pitch up with their head
 leading out of the manoeuvre. Surprisingly, anaesthetised dragonflies
 could also complete the aerial righting. Such passive righting disappears
 in recently dead dragonflies but can be partially recovered by waxing
 their wings to mimic the wing posture of the anesthetised dragonflies. Our
 inverse dynamics model and wind tunnel experiments support the idea that
 certain wing postures readily provide stability and may explain the
 dragonfly’s rotational preference. This work demonstrates for the first
 time that aerodynamically stable body configuration exists in gliding
 insects, and an active insect can leverage this passive stability as
 needed.
description: This kinematic data has been collected using 8 motion capture
 cameras tracking a variable number (generally 5) of markers. Dragonflies
 were dropped from selected inverted orientations as detailed in the paper
 itself and a ReadMe file has been provided with the data to facilitate
 navigation through the many kinematic parameters being measured. All data
 have gone through extensive processing, however raw captured coordinates
 are also included within the files.
description: The Readme file entitled
 "Fabian_et_al_DragonDrop_README.txt" is enclosed with the data
 and should give the relevant information required to access and assess the
 data.
DOI: 10.5061/dryad.pc866t1n3
title: Data from: Higher gametocyte production and mosquito infectivity in chronic compared to incident Plasmodium falciparum infections

description: Plasmodium falciparum gametocyte kinetics and infectivity may differ
 between chronic and incident infections. Children aged 5-10 years were
 recruited from an area of high malaria transmission in Burkina Faso into
 two cohorts: an incident cohort in which new infections were followed
 after parasite clearance (n=48), and a chronic cohort in which
 asymptomatic infections were identified and followed (n=60). Parasite
 kinetics were assessed daily with repeated mosquito feeding assays to
 quantify transmission potential. All participants were treated upon
 detection of symptoms; 92% (44/48) of the incident cohort developed
 symptoms within 35 days, compared to 23% (14/60) of the chronic cohort.
 All individuals with chronic infection became gametocytaemic during
 follow-up, whereas only 35% (17/48) in the incident cohort produced
 gametocytes before becoming symptomatic. Parasite multiplication rate
 (PMR) and the relative abundance of ap2-g and gexp-5 transcripts were
 positively associated with gametocyte production. Antibody responses were
 higher and PMR lower in chronic infections. The presence of symptoms and
 sexual stage immune responses were associated with reductions in
 gametocyte infectivity to mosquitoes. We observed that most incident
 infections required treatment before the density of mature gametocytes was
 sufficient to infect mosquitoes. In contrast, chronic, asymptomatic
 infections represented a significant source of mosquito infections. Our
 observations support the notion that malaria transmission reduction may be
 expedited by enhanced case management, involving both symptom-screening
 and infection detection.
description: Clean datasets with molecular data, mosquito feeding assays and
 serology data. Data are provided as xls with in second tab the variable
 labels
DOI: 10.15468/dl.7ae2yn
title: Occurrence Download

description: A dataset containing 14996 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Stipiturus malachurus",
 "Year 2015-2026"
 ]
}

 The dataset includes 14996 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002709-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.51c59zw75
title: Attack behaviour in naive Gyrfalcons is modelled by the same guidance law as in Peregrines, but at a lower guidance gain

description: The aerial hunting behaviours of birds are strongly influenced by flight
 morphology and ecology, but little is known of how this relates to the
 behavioural algorithms guiding flight. Here we use GPS loggers to record
 the attack trajectories of captive-bred Gyrfalcons (Falco rusticolus)
 during their maiden flights against robotic aerial targets, which we
 compare to existing flight data from Peregrines (Falco peregrinus). The
 attack trajectories of both species are well modelled by a proportional
 navigation (PN) guidance law, which commands turning in proportion to the
 angular rate of the line-of-sight to target, at a guidance gain N.
 However, naïve Gyrfalcons operate at significantly lower values of
 N than Peregrines, producing slower turning and a longer path to
 intercept. Gyrfalcons are less manoeuvrable than Peregrines, but physical
 constraint is insufficient to explain the lower values of N we
 found, which may reflect either the inexperience of the individual birds
 or ecological adaptation at the species level. For example, low values of
 N promote the tail-chasing behaviour that is typical of wild
 Gyrfalcons and which apparently serves to tire their prey in a prolonged
 high-speed pursuit. Likewise, during close pursuit of typical fast evasive
 prey, PN will be less prone to being thrown off by erratic target
 manoeuvres at low guidance gain. The fact that low-gain PN successfully
 models the maiden attack flights of Gyrfalcons suggests that this
 behavioural algorithm is embedded in a guidance pathway ancestral to the
 clade containing Gyrfalcons and Peregrines, though perhaps with much
 deeper evolutionary origins.
DOI: 10.5061/dryad.dfn2z350f
title: Impacts of recurrent dry and wet years alter long-term tree growth trajectories

description: Climate extremes, such as abnormally dry and wet conditions, generate
 abrupt shifts in tree growth, a situation which is expected to increase
 under predicted climate conditions. Thus, it is crucial to understand
 factors determining short- and long-term tree performance in response to
 higher frequency and intensity of climate extremes. We evaluated how three
 successive droughts and wet years influenced short- and long -term growth
 of six dominant Iberian tree species. Within species variation in growth
 response to repeated dry and wet years was evaluated as a function of
 individual traits related to resource and water use (diameter at breast
 height (DBH), wood density (WD) and specific leaf area (SLA)) and
 tree-to-tree competition across climatically contrasted populations.
 Furthermore, we assessed how short-term accumulated impacts of the
 repeated dry and wet years influenced long-term growth performance. All
 species showed strong short-term growth decreases and enhancements due to
 repeated dry and wet years. However, patterns of accumulated growth
 decreases (AcGD) and enhancements (AcGE) across climatically contrasting
 populations were species-specific. Furthermore, individual trait data were
 weakly associated to either AcGD or AcGE and the few relevant associations
 were found for conifers. Intraspecific variations in tree growth responses
 to repeated climates extremes were large, and not explained by
 intraspecific variability in SLA and WD. Accumulated impacts of repeated
 dry and wet years were related to long-term growth trends, showing how the
 recurrence of climate extremes can determine growth trajectories. The
 relationships of AcGD and AcGE with long-term growth trends were more
 common in conifers species. Synthesis. Repeated climate extremes
 do not only cause short-term growth reductions and enhancements, but also
 determine long-term tree growth trajectories. This result shows how
 repeated droughts can lead to growth decline. Conifers were more
 susceptible to the accumulated effects of extreme weather events
 indicating that in the future, more intense and frequent climate extremes
 will alter growth performance in forests dominated by these species.
DOI: 10.5061/dryad.np5hqbzrr
title: Multi-taxa inventory of naturalized species in Chile

description: Here we present a multi-taxa inventory of naturalized alien species
 recorded on continental Chile and adjacent marine habitats, including
 eight taxonomic groups. We identified 1,122 species. These comprise 790
 vascular plants (terrestrial and aquatic); 31 nonvascular plants
 [Bryophyta (mosses), Marchantiophyta (liverworts) and Anthocerotophyta
 (hornworts)]; 18 marine and freshwater macro and micro algae; 71 fungi; 39
 terrestrial vertebrates (amphibians, reptiles, mammals and birds); 108
 insects; 37 marine and freshwater invertebrates and vertebrates (6
 polychaetes, 3 mollusks and 28 Pisces); and 28 terrestrial gastropods. For
 all taxonomic groups, naturalized species were found to mainly be
 distributed in regions with Mediterranean and temperate climates, with few
 at either extreme of the country. The invasion curves show that
 naturalized species first underwent a positive increment, followed by an
 apparent plateau phase, mainly in vascular plants, insects and
 vertebrates. In fungi, marine and freshwater macro and microalgae,
 vertebrates and invertebrates, the cumulative number of naturalized
 species increased sharply starting in the early 20th century; the lack of
 collections before 1900 is also evident. When considering naturalized
 species as a whole, this inventory highlights that the rate of new
 naturalizations consistently increased after 1950, especially for some
 taxonomic groups such as insects, fungi, and vascular plants. This
 multi-taxa inventory of naturalized species provides a platform for
 national reporting on biodiversity indicators and highlights areas where
 Chile must invest resources to manage biological invasions.
description: Exhaustive bibliographic revision and used herbarium and
 zoological collections to identify all the species recorded as naturalized
 in continental Chile and adjacent marine habitats for each of the eight
 taxonomic groups: a) vascular plants (terrestrial and aquatic); b)
 nonvascular plants [Bryophyta (mosses), Marchantiophyta (liverworts), and
 Anthocerotophyta (hornworts)]; c) marine and freshwater macro and micro
 algae; d) fungi; e) terrestrial vertebrate fauna (amphibians, reptiles,
 birds and mammals); f ) insects; g) marine and freshwater vertebrates
 (Pisces) and invertebrates (polychaetes and mollusks); and h) terrestrial
 gastropods. For each taxonomic group, we used the most accepted and
 comprehensive definition of naturalized species.
DOI: 10.5061/dryad.xd2547dg1
title: Temporal instability of lake charr phenotypes: Synchronicity of growth rates and morphology linked to environmental variables?

description: Pathways through which phenotypic variation among individuals arise can be
 complex. One assumption often made in relation to intraspecific diversity
 is that the stability or predictability of the environment will interact
 with expression of the underlying phenotypic variation. To address
 biological complexity below the species level, we investigated variability
 across years in morphology and annual growth increments between and within
 two sympatric lake charr Salvelinus namaycush ecotypes in Rush Lake, USA.
 A rapid phenotypic shift in body and head shape was found within a decade.
 The magnitude and direction of the observed phenotypic change was
 consistent in both ecotypes, which suggests similar pathways caused the
 variation over time. Over the same time period, annual growth increments
 declined for both lake charr ecotypes and corresponded with a consistent
 phenotypic shift of each ecotype. Despite ecotype-specific annual growth
 changes in response to winter conditions, the observed annual growth shift
 for both ecotypes was linked, to some degree, with variation in the
 environment. Particularly, a declining trend in regional cloud cover was
 associated with an increase of early stage (ages 1-3) annual growth for
 lake charr of Rush Lake. Underlying mechanisms causing changes in growth
 rates and constrained morphological modulation are not fully understood.
 An improved knowledge of the biology hidden within the expression of
 phenotypic variation promises to clarify our understanding of temporal
 morphological diversity and instability.
description: PCA and CVA with centroid for each ecotype in Rush Lake
DOI: 10.5061/dryad.j9kd51cb9
title: Data from: Microbial community composition interacts with local abiotic conditions to drive colonization resistance in human gut microbiome samples

description: Biological invasions can alter ecosystem stability and function, and
 predicting what happens when a new species or strain arrives remains a
 major challenge in ecology. In the mammalian gastrointestinal tract,
 susceptibility of the resident microbial community to invasion by
 pathogens has important implications for host health. However, at the
 community level, it is unclear whether susceptibility to invasion depends
 mostly on resident community composition (which microbes are present), or
 also on local abiotic conditions (such as nutrient status). Here, we used
 a gut microcosm system to disentangle some of the drivers of
 susceptibility to invasion in microbial communities sampled from humans.
 We found resident microbial communities inhibited an invading E. coli
 strain, compared to community-free control treatments, sometimes excluding
 the invader completely (colonization resistance). These effects were
 stronger at later time points, coinciding with shifts in microbial
 community composition and nutrient availability. By separating these two
 components (microbial community and abiotic environment), we found
 taxonomic composition played a crucial role in suppressing invasion, but
 this depended critically on local abiotic conditions (adapted communities
 were more suppressive in nutrient-depleted conditions). This helps predict
 when resident communities will be most susceptible to invasion, with
 implications for optimizing treatments based around microbiota management.
DOI: 10.5061/dryad.8w9ghx3ks
title: Among-individual diet variation within a lake trout ecotype: Lack of stability of niche use

description: In a polymorphic species, predictable differences in resource use are
 expected among ecotypes, and homogeneity in resource use is expected
 within an ecotype. Yet, using a broad resource spectrum has been
 identified as a strategy for fishes living in unproductive northern
 environments, where food is patchily distributed and ephemeral. We
 investigated whether specialization of trophic resources by individuals
 occurred within the generalist piscivore ecotype of lake trout from Great
 Bear Lake, Canada, reflective of a form of diversity. Four distinct
 dietary patterns of resource use within this lake trout ecotype were
 detected from fatty acid composition, with some variation linked to
 spatial patterns within Great Bear Lake. Feeding habits of different
 groups within the ecotype were not associated with detectable
 morphological or genetic differentiation, suggesting that behavioral
 plasticity caused the trophic differences. A low level of genetic
 differentiation was detected between exceptionally large-sized individuals
 and other piscivore individuals. We demonstrated that individual trophic
 specialization can occur within an ecotype inhabiting a geologically young
 system (8,000–10,000 yr BP), a lake that sustains high levels of
 phenotypic diversity of lake trout overall. The characterization of niche
 use among individuals, as done in this study, is necessary to understand
 the role that individual variation can play at the beginning of
 differentiation processes.
description: Genepop 3 digit  CVA and PCA
 life-history (length and age) Fatty
 acids