cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dz08kps13
title: Can age-related changes in parental care modulate inbreeding depression? A test using the burying beetle, Nicrophorus orbicollis

description: Parental care has been shown to reduce the magnitude of inbreeding
 depression in some species with facultative care. However, parents often
 vary in the quality or amount of care they provide to their offspring and
 it is less clear whether this variation also impacts the magnitude of
 inbreeding depression. Here, we tested whether age related changes in
 parental care modulate the expression of inbreeding depression in the
 burying beetle, Nicrophorus orbicollis. Consistent with previous studies,
 we found that older parents produced larger broods of offspring than
 younger parents without sacrificing mean larval mass. Inbreeding
 depression was evident in several fitness-related traits: brood size at
 dispersal, the proportion of the brood that survived to eclosion, and mean
 age at death were all reduced in inbred broods compared to outbred broods.
 Surprisingly, inbred offspring were heavier at dispersal than outbred
 offspring. This was likely due to reduced sibling competition in inbred
 broods. Despite evidence for age related changes in parental investment
 and the existence of inbreeding depression, there was no evidence that an
 interaction between the two influenced any of the traits we measured. Our
 results suggest that age-related changes in parental care may be too
 slight to influence the expression of inbreeding depression.
DOI: 10.5061/dryad.k0p2ngfbs
title: Data from: Treated like dirt: Robust forensic and ecological inferences from soil eDNA after challenging sample storage

description: We investigated the effect of storage duration and conditions on the
 assessment of the soil biota with eDNA metabarcoding. We extracted eDNA
 from freshly collected soil samples and again from the same samples after
 storage under contrasting temperature conditions and contrasting exposure
 (open/closed tubes). We used four different primer sets targeting
 bacteria, fungi, protists (cercozoans), and general eukaryotes. We
 quantified differences in richness, evenness, and community composition.
 Subsequently, we tested whether we could correctly infer habitat type and
 original sample identity after storage using a large reference dataset.
 This repository contains the un-demultiplexed fastq sequences.
description: A soil sample was split into 108 smaller samples, that were
 stored in different ways (temperature, exposure and time). Biodiversity
 changes were assessed with metabarcoding using 4 different
 markers. This repository contains the paired end
 Illumina MiSeg fastq data for all amplicons in the study.
description: Information for reproducing the analyses is given in the GitHub
 repository (https://github.com/tobiasgf/sample_storage) and in the article. The data should ideally be analysed with dada2. The demultiplexed samplewise paired reads are deposited in ENA/SRA under the project number: PRJEB56039 (https://www.ebi.ac.uk/ena/browser/view/PRJEB56039).
DOI: 10.6078/d11q63
title: Female dewlap ornaments are evolutionarily labile and associated with increased influence diversification rates in Anolis lizards

description: The evolution of costly signaling traits has largely focused on male
 ornaments. However, our understanding of the ornament evolution is
 necessarily incomplete without investigating the causes and consequences
 of variation in female ornamentation. Here, we study the Anolis lizard
 dewlap, a trait extensively studied as a male secondary sexual
 characteristic but present in females of several species. We characterized
 female dewlaps for 339 species to test hypotheses about their evolution.
 Our results did not support the hypothesis that female dewlaps are
 selected against throughout the anole phylogeny. Rather, we found that
 female dewlaps were evolutionary labile. We also did not find support for
 the adaptive hypothesis that interspecific competition drove the evolution
 of female dewlaps. However, we did find support for the non-adaptive
 pleiotropy hypothesis as species with larger females and reduced sexual
 size dimorphism were more likely to possess female dewlaps. Lastly, we
 found that female dewlap presence influenced diversification rates in
 anoles, but only secondarily to a hidden state. Our results demonstrate
 that female ornamentation is widespread in anoles and the traditional
 hypothesis of divergent selection between the sexes does not fully explain
 their evolution. Instead, female ornamentation is likely subject to
 complex adaptive and non-adaptive evolutionary forces.
DOI: 10.5061/dryad.c59zw3rbn
title: Elastic pinch biomechanisms can yield consistent launch speeds regardless of projectile mass

description: Energetic trade-offs are particularly pertinent to bio-ballistic systems
 which impart energy to projectiles exclusively during launch.  We
 investigated such tradeoffs in the spring-propelled seeds of Loropetalum
 chinense, Hamamelis virginiana, and Fortunearia sinensis. Using similar
 seed-shooting mechanisms, fruits of these confamilial plants
 (Hamamelidaceae) span an order of magnitude in spring and seed mass. We
 expected that as seed mass increased, ejection speed would decrease.
 Instead, ejection speed remained relatively constant. We tested if fruits
 shoot larger seeds by storing more elastic potential energy (PE). Spring
 mass and PE increased as seed mass increased (in order of increasing seed
 mass: L. chinense, H. virginiana, F. sinensis). As seed mass to
 spring mass ratio increased (ratios: H. virginiana = 0.503, F. sinensis =
 0.653, L. chinense = 0.842), mass-specific PE storage increased.
 Conversion efficiency of PE to seed kinetic energy (KE) decreased with
 increasing fruit mass. Therefore, similar ejection speeds across scales
 occurred because (1) larger fruits stored more PE and (2) smaller fruits
 had higher mass-specific PE storage and improved PE to KE conversion. By
 examining integrated spring and projectile mechanics in our focal species,
 we revealed diverse, energetic scaling strategies relevant to
 spring-propelled systems navigating energetic trade-offs.
DOI: 10.5281/zenodo.15847134
title: A feature-optimized deep learning framework for mapping and spatial 1 characterization of tea plantations in complex mountain landscapes
DOI: 10.5281/zenodo.18360843
title: A feature-optimized deep learning framework for mapping and spatial 1 characterization of tea plantations in complex mountain landscapes
DOI: 10.5061/dryad.g79cnp5sx
title: Gastrointestinal helminths increase Bordetella bronchiseptica shedding and host variation in supershedding

description: Co-infected hosts, individuals that carry more than one infectious agent
 at any one time, have been suggested to facilitate pathogen transmission,
 including the emergence of supershedding events. However, how the host
 immune response mediates the interactions between co-infecting pathogens
 and how these affect the dynamics of shedding remains largely unclear. We
 used laboratory experiments and a modeling approach to examine temporal
 changes in the shedding of the respiratory bacterium Bordetella
 bronchiseptica in rabbits with one or two gastrointestinal
 helminth species. Experimental data showed that rabbits co-infected with
 one or both helminths shed significantly more B. bronchiseptica,
 by direct contact with an agar petri dish than rabbits with bacteria
 alone. Co-infected hosts generated supershedding events of higher
 intensity and more frequently than hosts with no helminths. To explain
 this variation in shedding an infection-immune model was developed and
 fitted to rabbits of each group. Simulations suggested that differences in
 the magnitude and duration of shedding could be explained by the effect of
 the two helminths on the relative contribution of neutrophils and specific
 IgA and IgG to B. bronchiseptica neutralization in the respiratory tract.
 However, the interactions between infection and immune response at the
 scale of analysis that we used could not capture the rapid variation in
 the intensity of shedding of every rabbit. We suggest that fast and local
 changes at the level of respiratory tissue probably played a more
 important role. This study indicates that co-infected hosts are an
 important source of variation in shedding, and provides a quantitative
 explanation of the role of helminths in the dynamics of respiratory
 bacterial infections.
description: We
 used laboratory data from rabbits infected with: i- <em>B.
 bronchiseptica</em> (B), ii- <em>B. bronchiseptica-Graphidium
 strigosum</em> (BG),  iii- <em>B. bronchiseptica-T.
 retortaeformis</em> (BT) and iv- the three infections together. Data
 on the level of <em>B. bronchiseptica</em> shed and related
 antibody (IgA and IgG) and neutrophil responses to the bacterial infection
 were collected over a four-month period. Full details on data collection
 and processing are reported in the paper associated with these
 datasets. 
description: The file can be opened with Excel. Within the file there are
 spreadsheets with data for every variables used in the modeling.
DOI: 10.5061/dryad.m63xsj45h
title: Troubled waters: Water availability drives human-baboon encounters in a protected, semi-arid landscape

description: Most animal habitats are affected by humans. While some species tolerate
 and even benefit from these changes, others suffer. Understanding when and
 how human-altered landscapes affect animal behavior, health, reproduction,
 and survival is essential to species management in a human-dominated
 world. Here we use 27 years of data on human-baboon encounters in
 a protected, semi-arid ecosystem in Kenya to: (i) identify spatial,
 environmental, and group-level predictors of baboon encounters with
 pastoralists; (ii) test whether human-built water sources alter baboon
 ranging patterns; and (iii) test if human encounters are linked to baboon
 survival, reproduction, and health. We find that the primary driver of
 human-baboon encounters is water availability. During dry periods,
 pastoralists migrate into baboon rangelands, leading to frequent
 human-baboon encounters, especially near water wells. Further, the baboons
 shift their ranges to encompass newly built wells and move away from
 abandoned, dried-up wells. Since 2006, a third of adult baboon deaths were
 linked to violent encounters with humans or their dogs. Human encounters
 were also linked to high infant mortality and parasite diversity in
 females (but this effect could not be disentangled from seasonal
 confounds). For wild baboons, life in protected, pastoralist conservancies
 presents a double-edged sword: human-built wells enable the baboons to
 access water during dry periods, but these wells lead to encounters with
 humans, which have become a common source of baboon mortality. Together,
 our results serve as a comprehensive case study of anthropogenic effects
 on wild primates, highlighting the complex interactions between humans and
 wildlife in protected areas.
DOI: 10.5061/dryad.2280gb5wd
title: Data from: Nitrogen enrichment alters multiple dimensions of grassland functional stability via changing compositional stability

description: Anthropogenic nutrient enrichment is known to alter the composition and
 functioning of plant communities. However, how nutrient enrichment
 influences multiple dimensions of community- and ecosystem-level stability
 remains poorly understood. Using data from a nitrogen (N) and phosphorus
 (P) addition experiment in a temperate semi-arid grassland that
 experienced a natural drought, we show that N enrichment, not P
 enrichment, decreased grassland functional and compositional temporal
 stability, resistance, and recovery, but increased functional and
 compositional resilience. Compositional stability and species asynchrony,
 rather than species diversity, were identified as key determinants of all
 dimensions of grassland functional stability, except for recovery. Whereas
 grassland functional recovery was decoupled from compositional recovery, N
 enrichment altered other dimensions of functional stability primarily
 through changing their corresponding compositional stability
 dimensions. Our findings highlight the need to examine ecological
 stability at the community level for a more mechanistic understanding
 of ecosystem dynamics in the face of environmental change.
DOI: 10.5061/dryad.nk98sf7wq
title: Data for: Paternity sharing in insects with female competition for nuptial gifts

description: Male parental investment is expected to be associated with high confidence
 of paternity. Studies of species with exclusive male parental care have
 provided support for this hypothesis because mating typically co-occurs
 with each oviposition, allowing control over paternity and the allocation
 of care. However, in systems where males invest by feeding mates
 (typically arthropods) mating (and thus the investment) is separated from
 egg-laying, resulting in less control over insemination (as male
 ejaculates compete with rival sperm stored by females) and a greater risk
 of investing in unrelated offspring (cuckoldry). As strong selection on
 males to increase paternity would compromise the fitness of all a female’s
 other mates that make costly nutrient contributions, paternity sharing
 (males not excluded from siring offspring) is an expected outcome of sperm
 competition. Using wild-caught females in an orthopteran and a dipteran
 species, in which sexually selected, ornamented females compete for male
 nuptial food gifts needed for successful reproduction, we examined
 paternity patterns and compared them to findings in other insects. We used
 microsatellite analysis of offspring (lifetime reproduction in the
 orthopteran) and stored sperm from wild-caught females in both study
 species, and as predicted there was evidence of shared paternity as few
 males failed to sire offspring. Further support for paternity-sharing is
 the lack of last-male sperm precedence in our study species. Although
 paternity was not equal among sires, our estimates of paternity bias were
 similar to other insects with valuable nuptial gifts and contrasted with
 the finding that males are frequently excluded from siring offspring in
 species where males supply little more than sperm. This suggests paternity
 bias may be reduced in nuptial-gift systems and may help facilitate the
 evolution of these paternal investments.
DOI: 10.5061/dryad.np5hqbzx5
title: Gut metabolome and cytokine profiling of MSM prior to and following HIV seroconversion

description: Alterations in the gut microbiome have been associated with HIV infection,
 but the relative impact of HIV versus other factors on the gut microbiome
 has been difficult to determine in cross-sectional studies. To address
 this, we examined the gut microbiome, serum metabolome, and cytokines
 longitudinally within individuals before and after HIV seroconversion. We
 identified few changes in the microbiome following HIV infection, but
 greater differences including decreased Bacteroides were seen between
 pre-HIV infection visits compared to matched controls. Those who acquired
 HIV also had elevated inflammatory cytokines and bioactive lipids prior to
 HIV acquisition compared to matched controls. Following HIV
 seroconversion, alterations in serum metabolites involving secondary bile
 acid metabolism and amino acid metabolism were observed. These data
 highlight the importance of understanding the role of the microbiome in
 HIV susceptibility.
DOI: 10.5061/dryad.rfj6q57f0
title: Black-tailed deer distance sampling on Blakely Island (WA), 2007 - 2021

description: Removal of predators and creation of early seral habitat has, in many
 systems, caused substantial population growth of herbivores. Hyperabundant
 herbivores, in turn, induce cascading ecosystem effects, but few studies
 have investigated long-term browser density trends in relation to
 succession and stochastic climate events. Here, for the first time, we use
 annual population estimates of a forest browser to relate forest
 succession to the long-term decline of an herbivore that prefers early
 seral habitat. From 2007 – 2021, concurrent with reduced timber harvest,
 we used line-transect distance sampling to document annual changes in
 Columbian black-tailed deer (Odocoileus hemionus columbianus) density on a
 mid-sized (17.3km2) predator-free island. We documented successional
 changes associated with forest aggradation and decreased forage quality
 for deer: early successional shrub/scrub habitat declined 3.8%/year;
 timber volume increased 4.5%/year; and canopy coverage increased 2.5%. In
 2007 – 2008, deer densities were the greatest observed (~44/km2), but then
 an historic snowstorm reduced deer density by 39%. Density increased
 slightly in 2010 but from 2010 – 2021, as forests matured, deer density
 decreased 4.0% per year, declining to 20 deer/km2. Despite declines, deer
 density on the island exceeds mainland densities, and overbrowsing likely
 continues to disrupt ecosystem processes.
description: The distance sampling data are formatted to be used in Program
 DISTANCE.
description: # Black-tailed deer distance sampling on Blakely Island (WA), 2007 - 2021
 [https://doi.org/10.5061/dryad.rfj6q57f0](https://doi.org/10.5061/dryad.rfj6q57f0) The attached Excel file contains two sheets. The first worksheet contains used in population estimation of black-tailed on Blakely Island (WA).  Each row corresponds to an observation of a deer, identifying the transect name, length, cluster size (i.e., # of deer seen together), and perpendicular distance from the transect to the deer (or centerpoint of the group).  If a transect was surveyed and no deer were observed, the distance of the transect is included (so that sampling effort can be calculated), but cluster size and perpendicular distance are marked as "n/a." The second sheet contains historical landcover data on Blakely Island, pulled from CCAP.
DOI: 10.5061/dryad.8cz8w9gv7
title: Data for: Context dependency in interference competition among birds in an endangered woodland ecosystem

description: Aim Much research has quantified species responses to human-modified
 ecosystems. However, there has been relatively limited work on how
 human-modified ecosystems may reshape competitive interactions between
 species. Using extensive data gathered over 19 years across an area
 exceeding three million ha, we asked: Are levels of interference
 competition between bird species context-dependent and influenced by
 habitat structure and productivity? We focussed on the hyper-aggressive
 behaviour of the Noisy Miner, which has been recognised as a Key
 Threatening Process for other woodland bird species. Location Temperate
 woodlands of south-eastern Australia Methods We constructed Bayesian
 multi-species occupancy/detection models of bird species in woodland
 patches and tested the fixed and interactive effects of Noisy Miner
 presence, the amount of tree cover, net primary productivity, and time. We
 quantified the responses of 31 species, many with known interactions with
 the Noisy Miner documented in previous studies at fine spatial scales.
 However, whether environmental conditions such as amount of forest cover
 and net primary productivity mediate the impact of Noisy Miners remains
 untested at large spatial scales and over decadal time scales. Results We
 identified negative associations between the Noisy Miner and 18 bird
 species, including, unexpectedly, both small- and large-bodied taxa. Site
 occupancy in some species was influenced by interactions between Noisy
 Miner presence and increasing amounts of tree cover or productivity. Our
 results suggest that for some species, interference competition by the
 Noisy Miner is context-dependent and mitigated by increasing tree cover
 and/or increasing net primary productivity Main conclusions Areas of high
 productivity or tree cover may be important refugia for some species of
 woodland birds. Vegetation clearing that reduces tree cover could likely
 strengthen interference competition by the Noisy Miner on parts of the
 remaining woodland bird community, including species of conservation
 concern.
description: Dataset contains data collected by on-the-ground bird surveys,
 then used in as part of a Bayesian multi-species occupancy/detection
 model, used to attempt to answer the question:  <em>Are levels of
 interference competition between the Noisy Miner and other bird species
 context-dependent and influenced by habitat structure and productivity?
 </em>
DOI: 10.15468/dl.b3ysmu
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eperua grandiflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 81 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003288-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m0cfxpp72
title: Do functional and phylogenetic nestedness follow the same mechanisms as taxonomic nestedness? Evidence from amphibians in the largest archipelago of China

description: 1. Nested subset pattern (nestedness) has been raised to explain the
 distribution of species on islands and habitat fragments for over 60
 years. However, previous studies on nestedness focused on species richness
 and composition and overlooked the role of species traits and phylogeny in
 generating and explaining the nestedness. 2. To address this gap, we
 sampled amphibians on 37 land-bridge islands in the Zhoushan Archipelago
 to explore nestedness as well as the underlying causal processes through
 three facets of diversity, i.e. taxonomic, functional and phylogenetic
 diversity. The taxonomic nestedness was measured through organizing the
 species incidence matrix to achieve a maximum value, while the functional
 and phylogenetic nestedness were quantified by incorporating the
 similarity of species in terms of their ecological traits and phylogeny.
 We also obtained six island characteristics and seven species traits as
 predictors of nestedness. 3. Amphibian metacommunities were significantly
 nested in these three facets of diversity. When relating different
 predictors to nestedness, island area, habitat diversity and species
 traits were highly correlated with taxonomic nestedness. Moreover, island
 area and habitat diversity significantly influenced functional and
 phylogenetic nestedness. Therefore, the results support the selective
 extinction and habitat nestedness hypotheses. 4. Interestingly, although
 we did not observe significant influences of isolation on taxonomic
 nestedness, functional and phylogenetic diversities were significantly
 higher than expected when matrices were ordered by increasing distance to
 mainland. The result suggests that there are more functionally and
 phylogenetically diverse species on less-isolated islands, reflecting a
 selective colonization process overlooked by the traditional analysis of
 taxonomic nestedness. 5. Although the three facets of nestedness and
 underlying processes were largely congruent, we detected the
 distance-related functional and phylogenetic nestedness for amphibian
 assemblages. Therefore, we highlight that a framework that simultaneously
 considers taxonomic, functional and phylogenetic nestedness contributes to
 a complementary understanding of nestedness processes. In addition, it
 also improves our ability to conserve insular biodiversity from different
 perspectives.