cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0vt4b8h1m
title: Comparative analysis of passerine feather traits: data and script

description: Tropical bird species are characterised by a comparatively slow pace of
 life, being predictably different from their temperate zone counterparts
 in their investments in growth, survival and reproduction. In birds, the
 development of functional plumage is often considered energetically
 demanding investment, with consequences on individual fitness and
 survival. However, current knowledge of interspecific variation in feather
 growth patterns is mostly based on species of the northern temperate zone.
 We evaluated patterns in tail feather growth rates (FGR) and feather
 quality (stress-induced fault bar occurrence; FBO), using 1518 individuals
 of 167 species and 39 passerine families inhabiting Afrotropical and
 northern temperate zones. We detected a clear difference in feather traits
 between species breeding in the temperate and tropical zones, with the
 latter having significantly slower FGR and three times higher FBO.
 Moreover, trans-Saharan latitudinal migrants resembled temperate zone
 residents in that they exhibited a comparatively fast FGR and low FBO,
 despite sharing moulting environments with tropical species. Our results
 reveal convergent latitudinal shifts in feather growth investments
 (latitudinal syndrome) across unrelated passerine families and underscore
 the importance of breeding latitude in determining cross-species variation
 in key avian life-history traits.
DOI: 10.5281/zenodo.17521170
title: Urea transporter evolution: deep conservation, recent adaptation in mammals, and  maintenance of the Jka/Jkb polymorphism in the past ~110,000 years
DOI: 10.5281/zenodo.18399451
title: Urea transporter evolution: deep conservation, recent adaptation in mammals, and  maintenance of the Jka/Jkb polymorphism in the past ~110,000 years
DOI: 10.5061/dryad.m63xsj43n
title: Image data set based on the age of giant pandas

description: The conservation of the giant panda (Ailuropoda melanoleuca), as an iconic
 vulnerable species, has received great attention in the past few decades.
 As an important part of the giant panda population survey, the age
 distribution of giant pandas can not only provide useful instruction but
 also verify the effectiveness of conservation measures. The current
 methods for determining the age groups of giant pandas are mainly based on
 the size and length of giant panda feces and the bite value of intact
 bamboo in the feces, or in the case of a skeleton, through the wear of
 molars and the growth line of teeth. These methods have certain flaws that
 limit their applications. In this study, we developed a deep learning
 method to study age group classification based on facial images of captive
 giant pandas and achieved an accuracy of 85.99% on EfficientNet. The
 experimental results show that the faces of giant pandas contain some age
 information which is mainly concentrated between the eyes of giant pandas.
 In addition, the results also indicate that it is feasible to identify the
 age groups of giant pandas through the analysis of facial images.
description: The image data set of captive giant pandas used in this study are
 all from the Chengdu Research Base of Giant Panda Breeding and its partner
 units, such as: Yunnan Wildlife Park, Suzhou Wildlife Park, Shenzhen
 Wildlife Park, etc. By using a Panasonic dvx200 video camera and three
 digital cameras (Canon 1DXmarkII, Canon 5DmarkIII, and a Panasonic Lumix
 DMC-GH4), the image data of 218 captive pandas was collected. All data
 were cleaned and annotated to establish a larger giant panda age image
 database.
description: Juvenile The facial images of juvenile giant
 pandas. Subadult The facial images of subadult giant
 pandas. Adult The facial images of adult giant
 pandas. Old The facial images of the old
 pandas.
DOI: 10.5061/dryad.k98sf7m7f
title: Data from: Climatic niche lability but growth form conservatism in the African woody flora

description: Climatic niche evolution during the diversification of tropical plants has
 received little attention in Africa. To address this, we characterized the
 climatic niche of &gt;4000 tropical African woody species,
 distinguishing two broad bioclimatic groups (forest vs. savanna) and six
 subgroups. We quantified niche conservatism versus lability at the genus
 level and for higher clades, using a molecular phylogeny of &gt;800
 genera. Although niche stasis at speciation is prevalent, numerous clades
 individually cover vast climatic spaces suggesting a general ease in
 transcending ecological limits, especially across bioclimatic subgroups.
 The forest biome was the main source of diversity, providing many lineages
 to savanna, but reverse shifts also occurred. We identified clades that
 diversified in savanna after shifts from forest. The forest-savanna
 transition was not consistently associated with a growth form change,
 though we found evolutionarily labile clades whose presence in forest or
 savanna is associated respectively with climbing or shrubby species
 diversification.
description: Two sets of data are provided: 1) The climatic
 niches of 4154 woody species occuring in tropical Africa.
 2) The bioclimatic affiliations of these species.
 All information on the methods used to create these data is
 provided in the attached manuscript.<br>Please read the READ_ME.txt
 file provided with the datasets.
DOI: 10.15468/dl.uvdh35
title: Occurrence Download

description: A dataset containing 392 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fagus hayatae"
 ]
}

 The dataset includes 392 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003056-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0zpc86707
title: Pathogen prevalence modulates medication behavior in ant Formica fusca

description: Ants face unique challenges regarding pathogens, as the sociality which
 has allowed them to form large and complex colonies also raises the
 potential for transmission of disease within these colonies. To cope with
 the threat of pathogens, ants have developed a variety of behavioral and
 physiological strategies. One of these strategies is self-medication, in
 which animals use biologically active compounds to combat pathogens in a
 way which would be harmful in the absence of them. Formica fusca ants are
 to date the only species of ants proven to successfully self-medicate
 against an active infection caused by a fungal pathogen by supplementing
 their diet with food containing hydrogen peroxide. Here, we build on that
 research by investigating how the prevalence of disease in colonies of F.
 fusca affects the strength of the self-medication response. We exposed
 either half of the workers of each colony or all of them to a fungal
 pathogen and offered them different combinations of diets. We see that
 workers of F. fusca engage in self-medication behavior even if exposed to
 a low lethal dose of a pathogen, and that the strength of that response is
 affected by the prevalence of the disease in the colonies. We also saw
 that the infection status of the individual foragers did not significantly
 affect their decision to forage on either control food or medicinal food
 as uninfected workers were also foraging on hydrogen peroxide food, which
 opens up the possibility of kin medication in partially infected colonies.
 Our results further affirm the ability of ants to self-medicate against
 fungal pathogens, shed new light on plasticity of self-medication and
 raise new questions to be investigated on the role self-medication has in
 social immunity.
description: The dataset was collected by analyzing pictures of foraging bouts
 of ant colonies suffering from different levels of pathogen infection (0%
 workers infected, 50% workers infected, 100% workers infected). Pictures
 were taken 4 times a day for a total of 6 days, and from the pictures we
 collected data on how many ants were foraging on either one of the two
 foods available to them spatially placed either on the left or
 right. The foods available varied according to which of
 the three diet treatments the colonies were subjected to: both foods
 control food, both foods treated, choice between control and treated
 food. Data was also collected on the infection status
 of the foragers and what type of food they were foraging on, as half of
 the ants in all colonies were marked to note whether they were infected or
 non-infected. Data on the survival of ants in the
 colonies were also gathered to discern whether any of the combinations of
 infection treatment an diet were affecting survival of workers in the
 colonies.
DOI: 10.5061/dryad.3ffbg79km
title: Identification of microbial taxa present in Ctenocephalides felis (cat flea) reveals widespread co-infection and associations with vector phylogeny

description: Background Ctenocephalides felis, the cat flea, is the most common
 ectoparasite of cats and dogs worldwide. As a cause of flea allergy
 dermatitis and a vector for two genera of zoonotic pathogens (Bartonella
 and Rickettsia spp.), the effect of the C. felis microbiome on pathogen
 transmission and vector survival is of substantial medical importance to
 both human and veterinary medicine. The aim of this study was to assay the
 pathogenic and commensal eubacterial microbial communities of individual
 C. felis from multiple geographic locations and analyze these findings by
 location, qPCR pathogen prevalence, and flea genetic diversity. Methods
 16S Next Generation Sequencing (NGS) was utilized to sequence the
 microbiome of fleas collected from free-roaming cats, and the cox1 gene
 was used for flea phylogenetic analysis. NGS data were analyzed for 168
 individual fleas from seven locations within the US and UK. Given
 inconsistency in the genera historically reported to constitute the C.
 felis microbiome, we utilized the decontam prevalence method followed by
 literature review to separate contaminants from true microbiome members.
 Results NGS identified a single dominant and cosmopolitan amplicon
 sequence variant (ASV) from Rickettsia and Wolbachia while identifying one
 dominant Bartonella clarridgeiae and one dominant Bartonella
 henselae/Bartonella koehlerae ASV. Multiple less common ASVs from these
 genera were detected within restricted geographical ranges. Co-detection
 of two or more genera (Bartonella, Rickettsia, and/or Wolbachia) or
 multiple ASVs from a single genus in a single flea was common.
 Achromobacter, Peptoniphilus, and Rhodococcus were identified as
 additional candidate members of the C. felis microbiome on the basis of
 decontam analysis and literature review. Ctenocephalides felis
 phylogenetic diversity as assessed by the cox1 gene fell within currently
 characterized clades while identifying seven novel haplotypes. NGS
 sensitivity and specificity for Bartonella and Rickettsia spp. DNA
 detection was compared to targeted qPCR. Conclusions Our findings confirm
 the widespread coinfection of fleas with multiple bacterial genera and
 strains, proposing three additional microbiome members. The presence of
 minor Bartonella, Rickettsia, and Wolbachia ASVs was found to vary by
 location and flea haplotype. These findings have important implications
 for flea-borne pathogen transmission and control.
DOI: 10.5061/dryad.4mw6m90c7
title: Molecular evolution and depth-related adaptations of rhodopsin in the adaptive radiation of cichlid fishes in Lake Tanganyika

description: The visual sensory system is essential for animals to perceive their
 environment and is thus under strong selection. In aquatic environments,
 light intensity and spectrum differ primarily along a depth gradient.
 Rhodopsin (RH1) is the only opsin responsible for dim-light vision in
 vertebrates and has been shown to evolve in response to the respective
 light conditions, including along a water depth gradient in fishes. In
 this study, we examined the diversity and sequence evolution of RH1 in the
 virtually entire adaptive radiation of cichlid fishes in Lake Tanganyika,
 focusing on adaptations to the achromatic environment with respect to
 depth. We show that Tanganyikan cichlid genomes contain a single copy of
 RH1. The 76 variable amino acid sites detected in RH1 across the radiation
 were not uniformly distributed along the protein sequence, and 31 of these
 variable sites show signals of positive selection. Moreover, the amino
 acid substitutions at 15 positively selected sites appeared to be
 depth-related, including three key tuning sites that directly mediate
 shifts in the peak spectral sensitivity, one site involved in protein
 stability, and 11 sites that may be functionally important on the basis of
 their physicochemical properties. Among the strongest candidate
 sites for deep-water adaptations are two known key tuning sites (positions
 292 and 299) and three newly identified variable sites (37, 104 and 290).
 Our study, which is th first compralehensive analysis of RH1 evolution in
 a massive adaptive radiation of cichlid fishes, provides novel insights
 into the evolution of RH1 in a freshwater environment.
description: For this study, we revisited
 the Illumina sequence data from our previous work, in which we had
 produced whole genome sequences for a nearly taxonomically complete sample
 of the cichlid fish fauna of LT (raw sequencing data are available on NCBI
 under the BioProject accession number PRJNA550295, https://www.ncbi.nlm.nih.gov/bioproject/; Ronco et al., 2021). Making use of the available raw DNA reads, we (<em>i</em>) identified and newly assembled the intron-less RH1 coding sequence; (<em>ii</em>) quantified the diversity of both nucleotides and amino acid sequences of RH1; (<em>iii</em>) tested if environmental pressures have shaped RH1 protein sequence evolution; and (<em>iv</em>) screened for candidate amino acid substitutions that are associated with water depth and hence potentially represent depth-related adaptations.
description: A GitHub reposit is available for further information:
 https://github.com/Ninet93/RH1_Ricci_et_al.git
DOI: 10.5061/dryad.qz612jmh6
title: Canopy gaps facilitate upslope shifts in montane conifers but not in temperate deciduous trees in the Northeastern United States

description: Many montane tree species are expected to migrate upslope as climate
 warms, but it is not clear if forest canopy gaps, which can facilitate
 tree seedling recruitment, serve as an important mechanism driving tree
 species range shifts. Patterns of tree seedling establishment can inform
 us about early stages of tree species migrations and are critical to
 examine in the context of global climate change. We contrasted elevational
 distributions of tree seedlings both within and outside of forest canopy
 gaps with the distributions of conspecific adults and saplings across the
 deciduous-coniferous ecotone on ten mountains in four states of the
 northeastern United States. We tested if seedling distributions of four
 dominant tree species (Abies balsamea, Picea rubens, Acer saccharum, and
 Fagus grandifolia) were shifted upslope of conspecific adult and sapling
 distributions. We also examined if this shift was facilitated by canopy
 gaps and what environmental drivers affected species distributions. There
 was limited seedling recruitment of dominant tree species at the
 temperate-coniferous ecotone, which we attributed to (i) an observed
 downslope shift of seedling distributions of the low-elevation deciduous
 species (Acer saccharum, Fagus grandifolia) and (ii) an upslope shift in
 seedling distributions of the high-elevation conifers (Abies balsamea,
 Picea rubens). The upslope shift of conifer seedlings contrasts with our
 previous research at these sites which observed downslope shifts of
 sapling distributions in Picea rubens, suggesting that seedlings may be
 responding to more recent climate warming. Canopy gaps in high-elevation
 conifer forests facilitated these upslope shifts by promoting conifer
 seedling recruitment. However, gaps at lower elevations did not play a
 significant role in seedling recruitment or the observed downslope shifts
 of the dominant deciduous species. Climate was the dominant predictor of
 adult tree distributions whereas both climate and soil were important
 predictors of seedling distributions. Synthesis. Our study illustrates
 that tree seedlings have the potential for monitoring the early stages of
 tree species migrations, and particularly so in canopy gaps in
 high-elevation conifer forests. Further, we stress that species range
 shifts are sensitive to local scale heterogeneity in light availability
 (i.e., canopy gaps) and other non-climatic factors.
description: See associated README excel file
DOI: 10.5061/dryad.ngf1vhhw4
title: Coping with seasonality: dynamics of adult body mass and survival in an alpine hibernator

description: Alpine mammals are highly vulnerable to current and projected climate
 change because they are confined to a certain elevation range.
 Physiological and behavioural adaptations in burrowing species, such as
 finding shelter in burrows when the summer conditions are unfavorable and
 hibernating in winter during the stressful period of resource shortage,
 could partly buffer the negative impacts of these forecasted changes. We
 studied the links between environmental factors and annual variations in
 adult mass and survival over 14 years in hoary marmots. We hypothesized
 that annual variation in seasonal environmental factors determines
 individual mass and survival through direct effects on food quality and
 availability, expecting greater survival when marmots reach higher mass
 before hibernation. We found that harsh winters decreased mass at
 emergence from hibernation by 47% compared with mild winters. Nonetheless,
 adult marmots had a greater mass gain in summers following harsh winters
 and reached a similar mass at the end of the summer compared with summers
 following mild winters. This result suggests individuals can adopt a
 resource allocation strategy that allows maximizing summer mass gain to
 survive hibernation. Earlier springs also increased summer mass gain by 15
 g/day, and tended to increase apparent adult survival by 23%, compared
 with late springs. While these findings suggest a warming climate could
 have positive effects on summer mass gain and survival, survival also
 tended to decrease by 24% in summers with more precipitation. This result
 suggests the forecasted changes in precipitation extremes could also
 trigger considerable negative effects on the demography of burrowing
 species in the long term. Our study shows that, although burrowing and
 hibernating behaviours could buffer responses to environmental changes,
 these behaviours are not an indefectible shield against climate change.
description: See article and readme file.
DOI: 10.5061/dryad.73n5tb2zp
title: Targeted grazing and mechanical thinning enhance forest stand resilience under a narrow range of wildfire scenarios

description: Increasing wildfire activity has spurred ecological resilience-based
 management that aims to reduce the vulnerability of forest stands to
 wildfire by reducing the probability of crown fire. Targeted grazing is
 increasingly being used to build forest resilience to wildfire, either on
 its own or in combination with treatments like mechanical thinning;
 however, it is unclear how effective this method is at altering the
 probability of crown fire in forest stands. We use crown fire simulation
 models to quantify to what extent targeted grazing, mechanical thinning
 targeting the vertical fuel stratum, and a combination of both treatments
 alter eastern ponderosa pine savanna stand resilience to wildfire by
 modelling their relative impacts on fuel stratum gap and subsequent crown
 fire occurrence under six different wildfire risk scenarios generated by
 altering wind and fuel moisture conditions. We then model changes in the
 probability of crown fire occurrence resulting from treatments across 75
 field-sampled sites in the Pine Ridge region of Nebraska relative to
 predicted crown fire occurrence when sites are left untreated. We find
 that mechanical (vertical) thinning has the potential to alter the
 probability of crown fire in ponderosa pine stands to a much greater
 extent than targeted grazing. Combining both approaches had a slightly
 higher probability of reducing crown fire risk across the greatest range
 of wildfire risk scenarios. Across 75 sample sites, targeted grazing was
 only predicted to prevented crown fire occurrence at 2 sites expected to
 experience crown fire under observed stand conditions across all six of
 our wildfire risk scenarios. In contrast, targeted grazing combined with
 mechanical thinning was predicted to prevent crown fire at approximately
 half of the sites expected to experience crown fire under observed
 conditions under mild and moderate wildfire risk scenarios. Thus, targeted
 grazing should be combined with mechanical thinning to best enhance forest
 resilience to wildfire. No combination of targeted grazing or mechanical
 thinning was able to alter the probability of crown fire under wildfire
 risk scenarios most conducive wildfire, confirming that relying solely on
 vertical thinning and targeted grazing is unlikely to sufficiently enhance
 resilience of forest stands to future wildfire conditions.
description: Crown fire probabilities for each scenario were calculated using
 Crown Fire Initiation Software (CFIS). Fuel Calculator Inputs used to
 generate fuel structural characteristics are included in the tab
 "Site_FuelCalculator_Inputs". This data was collected by
 Renewable Resource Solutions, LLC (2018). A full report on data collection
 for Renewable Resource Solutions is available upon request from the
 Nebraska Forest Service, University of Nebraska, Lincoln, NE.