cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zcrjdfnhs
title: A case report of an Eurasian Jay (Garrulus glandarius) attacking an incubating adult and depredating the eggs of the Japanese Tit (Parus minor)

description: In May 2021, we opportunistically observed one Eurasian Jay
 (Garrulus glandarius) attacking an
 adult incubating Japanese Tit (Parus minor) and
 depredating nine tit eggs at a nestbox where a woodpecker had
 greatly enlarged the entrance. After the predation event, the
 Japanese tits abandoned the nest. We recommend that when using
 artificial nest boxes to protect hole-nesting birds, the
 appropriate entrance size should be proportional to the body size of the
 target species. This observation gives us a better understanding of the
 potential predators of secondary hole-nesting birds.
description: In 2021 from 27<sup>th</sup> April to
 9<sup>th</sup> May, we used a mini digital video camera
 (CTS-K6, Chuangtianshi Technology Co., Ltd., Shenzhen, China) to monitor
 the incubating behaviors of Japanese tits in 22 nest boxes from 08:00 a.m.
 to 17:00 p.m. (GMT + 8). We fixed the camera on the inner lid of the box
 and adjusted the camera's angle to ensure the recording of the nest
 cup and entrance hole. The entrance hole of one of the nest boxes had been
 enlarged by a woodpecker (<em>Dendrocopos</em> spp.) pecking
 at it, such that the entrance to this box was 7.5 cm in diameter, and the
 depth from the entrance to the bottom was about 14.0 cm. On 1 May 2021, we
 recorded Eurasian jay attacking incubating adult and depredated eggs of
 Japanese tit with a nest hole size of 7.5 cm through the video cameras for
 the first time.
DOI: 10.5061/dryad.kprr4xh8s
title: Soil protist functional composition shifts with atmospheric nitrogen deposition in subtropical forests

description: 1. Soil protist plays a key role in ecological functions through predation
 and parasitism. However, little is known about how nitrogen (N) deposition
 and seasonal variations influence soil protist function in forest soils.
 2. Here, we assessed firstly the impacts of N deposition (control, 50 kg N
 ha-1 yr-1, 100 kg N ha-1 yr-1, and 150 kg N ha-1 yr-1) on the functional
 composition of the soil protist community in summer and winter, using
 amplicon sequencing of environmental DNA from a subtropical natural
 forest. 3. We found that soil protists were dominated by consumers
 (42.6–51.6%), followed by parasites (32.9–40.9%) and phototrophs
 (3.2–13.1%), implying a predominant role of consumers and potential
 top-down effects on the other trophic groups in subtropical forest soils.
 The functional composition of soil protists was greatly influenced by N
 deposition, but these responses were dependent on seasonal variations. The
 diversity of phototrophs was lower in summer than in winter. Instead, an
 opposite pattern was observed for consumers, resulting in a significantly
 higher protist diversity in summer than in winter, which indicates a
 greater sensitivity of soil protists to seasonal variations. Furthermore,
 low and high N deposition simplified the structural complexity of soil
 protist communities, suggesting a nonlinear response of the protist
 structural stability to N deposition. 4. Synthesis and applications. This
 study provides unprecedented evidence that season variation plays an
 important role in regulating responses of soil protist functional
 composition to N deposition, and highlights the nonlinear effects of
 rising N deposition levels on the soil food web.
DOI: 10.5061/dryad.6djh9w15d
title: Data for: The role of MHC and inbreeding in disassortative mating in sand lizards

description: The harmful effects of close inbreeding have been recognized for centuries
 and, with the rise of Mendelian genetics, was realized to be an effect of
 homozygosis. This historical background led to great interest in ways to
 quantify inbreeding, its depression effects on the phenotype and flow-on
 effects on mate choice and other aspects of behavioural ecology. The
 mechanisms and cues used to avoid inbreeding are varied and include major
 histocompatibility complex (MHC) molecules and the peptides they transport
 as predictors of the degree of genetic relatedness. Here we revisit and
 complement data from a Swedish population of sand lizards (Lacerta agilis)
 showing signs of inbreeding depression to assess the effects of genetic
 relatedness on pair formation in the wild. Parental pairs were less
 similar at the MHC than expected under random mating but mated at random
 with respect to microsatellite relatedness. MHC clustered in groups of
 RFLP bands but no partner preference was observed with respect to partner
 MHC cluster genotype. Male MHC band patterns were unrelated to their
 fertilization success in clutches selected for analysis on the basis of
 showing mixed paternity. Thus, our data suggest that MHC plays a role in
 pre-copulatory- but not post-copulatory partner association, suggesting
 that MHC is not the driver of fertilization bias and gamete recognition in
 sand lizards.
DOI: 10.5061/dryad.brv15dvdg
title: Amazonian Odonata trait bank

description: Discussion regarding the gaps of knowledge on Odonata is common in the
 literature. Such gaps are even greater when dealing with basic biological
 data for biodiverse environments like the Amazon Rainforest. Therefore,
 studies that address, classify and standardize functional traits allow the
 elaboration of a wide range of ecological hypotheses.  Here, our
 main goal was to produce a database with 68 functional traits of 218
 Odonata species that occur in the Brazilian Amazon. As a result, we
 provide a functional matrix and identified different functional patterns
 for the suborders, as well as a strong relationship between the different
 categories of traits. For this reason, we recommend choosing key traits
 that represent a set of functional variables, reducing the sampling
 efforts. In conclusion, we detect and discuss gaps in current literature
 and suggest possible paths to be taken or implement to increase our
 knowledge of odonate biology and ecology.
description: We organized a checklist of 218 species occurring in the
 Brazilian Amazon based on approximately 500 collection sites sampled over
 a decade by researchers of the Laboratory of Ecology and Conservation
 (LABECO). Subsequently, we started the selection of traits and their
 categories. We emphasize that some group of traits present different life
 history facets, in this way justifying the classification in different
 groups. Posteriorly, we carried out an active search for information in
 the scientific literature available in the databases: "Web of
 Science", and “Google Scholar”. The search was performed using the
 respective names of the 218 registered species as keywords. Additionally,
 we measured 22 adult morphological traits with the aid of a
 stereomicroscope, a digital caliper, and analytical balance. Finally, we
 surveyed the occurrence records of the 218 studied Amazonian species for
 the entire American continent. Part of these records were obtained from
 the digital platforms “species link” and “gbif”. In addition, data
 provided/shared by different Brazilian research groups were included, as
 well as records available in more than 2400 articles published for South
 America. All the data compiled at this stage added up to more than 40.000
 occurrence records for the Americas. Subsequently, each of these species
 was classified according to its distribution amplitude along the biomes of
 the American continent: (i) short distribution (2 biomes); (ii) dispersed
 distribution (3-4 biomes); (iii) wide (5-6); and (iv) very wide
 (&gt;7) distribution.
description: Office Package and R
DOI: 10.5061/dryad.8931zcrvv
title: Parental effects on inbreeding depression in a beetle with obligate parental care

description: Inbreeding depression occurs when individuals who are closely related mate
 and produce offspring with reduced fitness. Although inbreeding depression
 is a genetic phenomenon, the magnitude of inbreeding depression can be
 influenced by environmental conditions and parental effects. In this
 study, we tested whether size-based parental effects influence the
 magnitude of inbreeding depression in an insect with elaborate and
 obligate parental care (the burying beetle, Nicrophorus
 orbicollis). We first tested for size-dependent maternal effects on
 offspring size using a phenotypic manipulation experiment where we created
 large and small adults by manipulating the amount of time they fed as
 larvae. Consistent with studies of
 other Nicrophorus species, we found that larger mothers
 produced larger offspring. We next tested for size-dependent parental
 effects on the magnitude of inbreeding depression in two traits: mean
 larval mass and survival from larval dispersal to eclosion. As in our
 first experiment, we found that larger parents produced larger offspring.
 However, larval mass was also influenced by the interaction between
 parental body size and inbreeding status: when parents were small, inbred
 larvae were smaller than outbred larvae, but when parents were large this
 pattern was reversed. In contrast, survival from larval dispersal to adult
 emergence showed inbreeding depression that was unaffected by parental
 body size. Our results suggest that size-based parental effects can
 generate variation in the magnitude of inbreeding depression. However,
 further work is needed to dissect the mechanisms through which this might
 occur and to better understand why parental size influences inbreeding
 depression in some traits but not others.
DOI: 10.5061/dryad.73n5tb324
title: Ancient DNA reveals genetic admixture in China during tiger evolution

description: The contrast between the oldest fossil presence of tigers 2–3 Mya and
 extant tigers’ coalescence approximately 110,000 years ago implies a
 complex genomic diversity pattern in ancient tigers that has largely
 escaped scientific scrutiny. Here we collected over 60 historical
 specimens across mainland Asia and generated whole genome sequences from a
 10,600-year-old Russian Far East (RFE) specimen (RUSA21, 8´ coverage), 14
 South China tigers (0.1–12´), three Caspian tigers (4–8´), plus 17 new
 mitogenomes. RUSA21 clustered within modern Northeast Asian phylogroups
 and partially derived from an extinct Late Pleistocene lineage. While some
 of the 8,000–10,000-year-old RFE mitogenomes are basal to all tigers, one
 2,000-year-old specimen resembles present Amur tigers. The Caspian tiger
 likely dispersed from an ancestral Northeast Asian population and
 experienced gene flow from southern Bengal tigers. Lastly, genome-wide
 monophyly supported the South China tiger as a distinct subspecies, albeit
 with mitochondrial paraphyly, hence resolving its longstanding taxonomic
 controversy. The distribution of mitochondrial haplogroups corroborated by
 biogeographical modeling suggested Southwest China was a Late Pleistocene
 refugium for a relic basal lineage. As suitable habitat returned, Eastern
 China became a genetic melting pot to foster divergent lineages to merge
 into South China tigers and other subsequent northern subspecies to
 develop. Genomic information retrieved from ancient tigers hence sheds
 light on the species’ full evolutionary history leading to nine modern
 subspecies and resolves the natural history of surviving tigers.
description: # Ancient DNA reveals genetic admixture in China during tiger evolution
 [https://doi.org/10.5061/dryad.73n5tb324](https://doi.org/10.5061/dryad.73n5tb324) ## Description of the data and file structure | File | Description | | ---- | ----------- | | 11th\_hard\_no\_old.bcf.gz | hard filtered vcf file | | auto\_neutral\_psdo\_gt\_psdo\_miss10\_info\_11th\_hard\_no\_old.bcf.gz | Pseudohaploid vcf file. NB: don't use any field in INFO | | auto\_neutral\_hqc\_miss4\_meanDP5\_info\_11th\_hard\_no\_old.bcf.gz | Strictly filtered vcf file. NB: don't use any field in INFO | | gl\_tv\_mafF\_misF.dp1.beagle.gz | Genotype likelihood file. | | file.md5 | MD5 | ## Code/Software Github link https://github.com/xinsun1/Xin\_etal\_2023\_NEE\_TigerPopGen
DOI: 10.5061/dryad.73n5tb325
title: Short-term, but not long-term grooming reciprocity in a species with high fission-fusion dynamics

description: Reciprocity allows animals to balance the costs and benefits of
 cooperative interactions by switching roles over time. Reciprocity can be
 based on two different processes: partner control and partner choice.
 Although not mutually exclusive, the relative roles of the two processes
 remain debated. We investigated grooming reciprocity in wild
 Geoffroy's spider monkeys (Ateles geoffroyi), a species with low
 grooming rates and reduced opportunities for group members to interact due
 to a high degree of fission-fusion dynamics. We assessed separately the
 roles of partner control and partner choice in grooming exchanges and
 investigated the factors affecting reciprocity. We found short-term
 reciprocity based on partner-control with reciprocation occurring within
 401 s after receiving grooming. In contrast, we did not find evidence for
 long-term reciprocity based on partner choice. Short-term reciprocity
 based on partner control was not affected by kinship, whereas reduced time
 spent together in the same subgroup increased the probability of
 short-term grooming reciprocation. Our results suggest the opportunity to
 interact is a potent modulator of reciprocity. In species characterized by
 a high degree of fission-fusion dynamics and low grooming rates,
 short-term reciprocation based on partner control can be favoured at the
 expense of partner choice.
DOI: 10.5281/zenodo.18403149
title: Mycelium-based biocomposites as key enabling technology in Industry 5.0: Application of AI, laser cutting, 3D scan and X-ray CT scan in heat insulation industrial production – Rad Data

description: Raw data supplementing the following manuscript: “Mycelium-based biocomposites as key enabling technology in Industry 5.0: Application of AI, laser cutting, 3D scan and X-ray CT scan in heat insulation industrial production”
DOI: 10.5281/zenodo.18403148
title: Mycelium-based biocomposites as key enabling technology in Industry 5.0: Application of AI, laser cutting, 3D scan and X-ray CT scan in heat insulation industrial production – Rad Data

description: Raw data supplementing the following manuscript: “Mycelium-based biocomposites as key enabling technology in Industry 5.0: Application of AI, laser cutting, 3D scan and X-ray CT scan in heat insulation industrial production”
DOI: 10.5061/dryad.0gb5mkm5q
title: Data for: Immune genotypes, immune responses, and survival in a wild bird population

description: Individuals vary in their immune genotype, inbreeding coefficient f,
 immune responses, survival to adulthood, and adult longevity. However,
 whether immune genes predict survival or longevity, whether such
 relationships are mediated through immune responses, and how f affects
 immune genotype remain unclear. We use a wild song sparrow (Melospiza
 melodia) population in which survival to adulthood, adult longevity, and f
 were measured precisely, and in which immune responses have previously
 been assessed. We investigate four toll-like receptors (TLR) and the major
 histocompatibility complex (MHC) class IIB exon 2 genes. We test: a)
 whether immune genes predict fitness (survival to adulthood or adult
 longevity); b) whether immune genes predict immune response; c) whether
 immune response predicts fitness; and d) whether fitness, immune
 responses, or immune genotypes are correlated with f. We find that
 survival to adulthood is not associated with immune gene variation, but
 adult longevity is decreased by high MHC allele diversity (especially in
 birds that were relatively outbred), and by the presence of a specific MHC
 supertype. Immune responses were affected by specific immune genotypes.
 Survival to adulthood and adult longevity were not predicted by immune
 response, implying caution in the use of immune response as a predictor
 for fitness. We also found no relationship between f and immune genotype.
 This finding indicates that immune gene associations with longevity and
 immune response are not artefacts of f, and suggests that
 pathogen-mediated selection at functional loci can slow the loss of
 genetic variation arising from genetic drift and small population size.
DOI: 10.5061/dryad.wh70rxws7
title: Scale insects contribute to spider conservation in urban trees and shrubs

description: Urbanization filters arthropod communities and selects for species
 tolerant of urban conditions. Spiders are key generalist predators in
 urban ecosystems, but certain spider families are rare in cities compared
 to rural areas. The unique arthropod communities found in different tree
 species likely affect their ability to conserve spiders by providing
 different prey resources. If arthropods disperse from trees to plants
 growing below trees, the conservation benefits of the arthropod
 communities found in trees may also extend to plants growing beneath them.
 Certain urban tree species can host high densities of scale-insects and
 other arthropods that may provide important prey resources for spiders. To
 assess the conservation value of different arthropod communities in urban
 trees, we collected spiders from scale-infested and scale-uninfested trees
 and from shrubs under these trees. We used hanging cup traps to collect
 spiders that fell from both tree types. Spider abundance was greater
 within, and in shrubs below, scale-infested compared to scale-uninfested
 trees. Scale-infested trees hosted more orb web weaving spiders than
 scale-uninfested trees. Shrubs under scale-infested trees hosted more
 hunting, orb web weaving, and space web weaving spiders than shrubs under
 uninfested trees. Our findings suggest that scale-infested urban trees,
 and the robust arthropod communities they support, conserve certain spider
 guilds, and these benefits extend to other plants in the landscape.
 Implications for insect conservation: The ability of urban trees to
 conserve spider communities is in part attributable to the abundance of
 potential prey available within trees. Therefore, tolerating pests such as
 scale insects in urban trees can conserve spider communities both within
 trees and in shrubs planted below these trees.
DOI: 10.5061/dryad.2bvq83bvd
title: Multimodal immune profiling of SARS-CoV-2 in Uganda – soluble immune mediators

description: Little is known about the pathobiology of SARS-CoV-2 infection in
 sub-Saharan Africa, where severe COVID-19 fatality rates are among the
 highest in the world and the immunological landscape is unique. In a
 prospective cohort study of 306 adults encompassing the entire clinical
 spectrum of SARS-CoV-2 infection in Uganda, we integrated profiling of the
 peripheral blood proteome and transcriptome to dissect the immunopathology
 of COVID-19 across multiple phases of the pandemic. Beyond the prognostic
 importance of myeloid cell-driven immune activation and lymphopenia, we
 show that multifaceted impairment of host protein synthesis and extensive
 redox imbalance define core biological signatures of severe COVID-19, with
 central roles for IL-7, IL-15, and lymphotoxin-α in COVID-19 respiratory
 failure. While prognostic signatures were generally consistent in
 SARS-CoV-2/HIV-coinfection, type I interferon responses uniquely scaled
 with COVID-19 severity in persons living with HIV. Throughout the
 pandemic, COVID-19 severity peaked during phases dominated by A.23/A.23.1
 and Delta B.1.617.2/AY variants. Independent of clinical severity, Delta
 phase COVID-19 was distinguished by exaggerated pro-inflammatory myeloid
 cell and inflammasome activation, NK and CD8+ T-cell depletion, and
 impaired host protein synthesis. Combining these analyses with a
 contemporary Ugandan cohort of adults hospitalized with influenza and
 other severe respiratory infections, we found activation of epidermal and
 platelet-derived growth factor pathways to be distinct features of
 COVID-19, deepening translational understanding of mechanisms potentially
 underlying SARS-CoV-2-associated pulmonary fibrosis. Collectively, our
 findings provide biological rationale for use of broad and targeted
 immunotherapies for severe COVID-19 in sub-Saharan Africa, illustrate the
 relevance of local viral and host factors to SARS-CoV-2 immunopathology,
 and highlight underemphasized yet therapeutically exploitable immune
 pathways driving COVID-19 severity.
description: In cryopreserved serum samples from adults with SARS-CoV-2
 infection and influenza and non-influenza severe acute respiratory
 infection in Uganda, concentrations of 48 soluble immune mediators were
 quantified using the Human Cytokine/Chemokine 48-Plex Discovery Assay
 Array (Eve Technologies, Calgary, Alberta, Canada; MilliporeSigma,
 Burlington, MA, USA). Samples from different pathogen and clinical
 severity groups were randomized across sample plates and analyzed by
 technicians blinded to pathogen and severity status. Soluble mediators
 were quantitated in duplicate with the mean concentration used for
 analysis presented. Values below the lower limit of assay quantification
 were replaced with the lowest value that could be reliably quantified for
 that particular mediator. Values above the upper limit of quantification
 were replaced with the highest standard curve value for each particular
 mediator.
DOI: 10.5061/dryad.pvmcvdnqv
title: Dim artificial light at night alters immediate early gene expression throughout the avian brain

description: Artificial light at night (ALAN) is a pervasive pollutant that alters
 physiology and behavior. However, the underlying mechanisms triggering
 these alterations are unknown, as previous work shows that dim levels of
 ALAN may have a masking effect, bypassing the central clock. Light
 stimulates neuronal activity in numerous brain regions which could in turn
 activate downstream effectors regulating physiological response. In the
 present study, taking advantage of immediate early gene (IEG) expression
 as a proxy for neuronal activity, we determined the brain regions
 activated in response to ALAN. We exposed zebra finches to dim ALAN (1.5
 lux) and analyzed 24 regions throughout the brain. We found that the
 overall expression of two different IEGs, cFos and ZENK, in birds exposed
 to ALAN were significantly different from birds inactive at night.
 Additionally, we found that ALAN-exposed birds had significantly different
 IEG expression from birds inactive at night and active during the day in
 several brain areas associated with vision, movement, learning and memory,
 pain processing, and hormone regulation. These results give insight into
 the mechanistic pathways responding to ALAN that underlie downstream,
 well-documented behavioral and physiological changes.
description: Dim artificial light at night alters immediate early gene expression
 throughout the avian brain === This is the raw data for the manuscript
 cfos\_df --- bird = individual bird group = treatment active = birds
 separated into only two groups of active or inactive (total minutes of
 activity &lt;1 minute) 90 minutes before perfusion pathway = related
 pathway for brain region area = area of the brain in abbreviations, see
 manuscript for detailed area name slice = number of slices for that bird
 for that area cFos\_exact = exact percent of cFos+ cells ZENK\_exact =
 exact percent of ZENK+ cells cFos\_Int = an interger for analysis, it is
 the exact percent multiplied by 10 ZENK\_Int = an interger for analysis,
 it is the exact percent multiplied by 10 Total = total percent of DAPI
 cells for exact Total = total percent of DAPI cells for intergers, total
 percent multiplied by 10 cFos\_percent = exact percent of cFos+ cells cFos
 = rounded percet of cFos+ cells ZENK\_percent = exact percent of ZENK+
 cells ZENK = rounded percent of ZENK+ cells Behavior --- bird = individual
 bird treatment = treatment behavior = birds' behavior time = time
 spent doing specific behavior in minutes total = total time of recording
 percent = percent of time doing specific behavior