cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g79cnp5r4
title: Investigating population dynamics from parentage analysis in the highly endangered fan mussel Pinna nobilis

description: Understanding dispersal patterns is a major focus for conservation biology
 as it influences local survival and resilience in case of local
 disturbance, particularly for sessile species. Dispersal can be assessed
 through parentage analyses by estimating family structure and
 self-recruitment. This study documents the family structure of a pelagic
 spawner, Pinna nobilis, which is facing a major crisis that threatens its
 survival as most of its populations have been decimated by a parasite,
 Haplosporidium pinnae. In this context, we focused on a single population
 (Peyrefite, Banyuls-sur-mer, France) where 640 individuals were sampled in
 2011, 2015 and 2018 and genotyped for 22 microsatellite markers. Genetic
 diversity was high and homogeneous among years, with mean allele numbers
 ranging between 13.6 and 14.8 and observed heterozygosities (Ho) between
 0.7121 and 0.7331. Low, but significant, genetic differentiations were
 found between 2011 - 2015 and 2015 - 2018. A parentage analysis described
 11 clusters, including one prevailing, and revealed that 46.9 % of
 individuals were involved in half-sib relationships, even between years,
 suggesting that source populations were recurrent year after year. There
 were few individuals resampled between years (30 in 2015 and 14 in 2018),
 indicating a rapid turnover. Considering the large number of half-sib
 relationships but the low number of relations per individual, we conclude
 that P. nobilis exhibit homogeneous reproductive success. Self-recruitment
 was not detected, making this population highly vulnerable as
 replenishment only relies on connectivity from neighboring populations. In
 the context of the pandemic caused by H. pinnae, these results will have
 to be considered when choosing a location to reintroduce individuals in
 potential future rescue plans.
DOI: 10.15468/dl.4hupbe
title: Occurrence Download

description: A dataset containing 890 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Kenya, Tanzania, United Republic of)",
 "OccurrenceStatus is Present",
 "TaxonKey is Bitis arietans"
 ]
}

 The dataset includes 890 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003008-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.wm37pvmpg
title: Plant and soil microbial diversity and related spatial and environmental factors in the grasslands of northern China

description: Plant and soil microbial diversity and related spatial and environmental
 factors in the grasslands of northern China from 2018 and 2019. The data
 included 54 and 27 sites in 2018 and 2019 respectively. The data table
 contains two sheets, one for 2018 and the other for 2019. Spatial factors
 include longitude and latitude; climatic factors include mean annual
 temperature, mean annual precipitation, temperature seasonality,
 precipitation seasonality, potential evapotranspiration, and aridity
 index; soil factors include soil bulk density, soil moisture, soil pH,
 soil organic carbon, soil clay content, soil silt content, soil sand
 content, soil total carbon, soil total nitrogen, and soil C:N ratio; plant
 functional diversity include    functional
 richness (FRic), functional evenness (FEve), functional divergence (FDiv),
 functional dispersion (FDis), Rao's quadratic entropy (RaoQ);
 community-weighted mean (CWM) traits include specific leaf area (SLA),
 leaf dry matter content (LDMC), leaf nitrogen content (leafN),ratio of
 leaf carbon to nitrogen (leaf C:N), and stem density; soil microbial
 diversity include bacterial diversity and fungal diversity; fungal
 functional guilds include pathotrophic fungi, saprotrophic fungi,
 arbuscular mycorrhizal fungi, and ectomycorrhizal fungi; bacterial
 functional guilds include aerobic chemoheterotrophy, predatory or
 exoparasitic, cellulolysis, aerobic nitrite oxidation, sulfur respiration,
 nitrate reduction, ureolysis, aromatic compound degradation, intracellular
 parasites, fermentation, and methanotrophy in the data sheet of
 2018.  Soil microbial diversity include bacterial diversity and
 fungal diversity; fungal functional guilds include pathotrophic fungi,
 saprotrophic fungi, arbuscular mycorrhizal fungi, and ectomycorrhizal
 fungi; bacterial functional guilds include aerobic chemoheterotrophy,
 predatory or exoparasitic, cellulolysis, aerobic nitrite oxidation, sulfur
 respiration, nitrate reduction, ureolysis, aromatic compound degradation,
 intracellular parasites, fermentation, and methanotrophy in the data sheet
 of 2019.
DOI: 10.5061/dryad.sxksn034j
title: UCE Phylogenomics resolves major relationships among Ectaheteromorph ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A new classification for the subfamilies and the description of a new genus

description: Uncovering the evolutionary history of the subfamilies Ectatomminae and
 Heteroponerinae, or ectaheteromorphs, is key to understanding a major
 branch of the ant tree of life. Despite their diversity and ecological
 importance, phylogenetic relationships in the group have not been well
 explored. One particularly suitable tool for resolving phylogeny is the
 use of ultraconserved elements (UCEs), which have been shown to be ideal
 markers at a variety of evolutionary time scales. In the present study, we
 enriched and sequenced 2,127 UCEs from 135 specimens of ectaheteromorph
 ants and investigated phylogeny using a variety of model-based
 phylogenomic methods. Trees recovered from partitioned maximum-likelihood
 and species-tree analyses were well resolved and largely congruent. The
 results are consistent with an expanded concept of Ectatomminae that now
 includes the subfamily Heteroponerinae new synonym and its single tribe
 Heteroponerini new combination. Eleven monophyletic groups are recognized
 as genera: Acanthoponera, Alfaria status revived, Boltonia Camacho and
 Feitosa new genus, Ectatomma, Gnamptogenys, Heteroponera, Holcoponera
 status revived, Poneracantha status revived, Rhytidoponera, Stictoponera
 status revived, and Typhlomyrmex. The new phylogenetic framework and
 classification proposed here will shed light on the study of Ectatomminae
 taxonomy and systematics, as well as on the morphological evolution of the
 groups that it comprises.
DOI: 10.5061/dryad.rbnzs7hcj
title: Behavioral responses by a bumble bee to competition with a niche-constructing congener

description: While feeding, foragers can alter their environment. Such alteration
 constitutes ecological niche construction (ENC) if it enables future
 benefits for the constructor and conspecific individuals. The
 environmental modification may also affect non-constructing, bystander
 species, especially if they share resources with constructor species. If
 so, ENC could confer the constructor species a competitive advantage by
 both enhancing its foraging returns and reducing those of bystander
 species. Expectations – (E1) ENC frequency should vary positively with the
 recent and current density of the constructor species, and (E2)
 constructors should use modifications disproportionately. In contrast,
 bystanders should (E3) experience intensified competition for the affected
 resource, and (E4) exhibit diverse, possibly mitigating, responses to ENC,
 depending on opportunity and relative benefits. We investigated these
 expectations in Argentina for competition for Fuchsia magellanica nectar
 between an invasive bumble bee, Bombus terrestris (terr: putative
 constructor), that often bites holes at the bases of floral tubes to rob
 nectar, and native B. dahlbomii (dahl: bystander), which normally accesses
 Fuchsia nectar through the flower mouth (front visits). Robbing holes
 constitute ENC, as they persist until the 7-day flowers wilt. The dynamics
 of the incidence of robbed flowers, abundance of both bees, and the number
 and types of their flower visits (front or robbing) were characterised by
 alternate-day surveys of plants during 2.5 months. After initially
 accessing Fuchsia nectar via front visits, terr switched to robbing and
 its abundance on Fuchsia increased 20-fold within 10 days (E2).
 Correspondingly, the incidence of robbed flowers varied positively with
 recent and past terr abundance (E1).  In contrast, dahl abundance
 remained low and varied negatively with the incidence of robbed flowers
 (E3). When terr ceased visiting Fuchsia, dahl abundance increased six-fold
 within 10 days (E3), possibly because many dahl previously had avoided
 competition with terr by feeding on other plant species (E4). While terr
 was present, dahl on Fuchsia used front visits (tolerance) or used
 existing robbing holes (adoption: E4). The diverse dahl responses suggest
 partial compensation for competition with terr. ENC alters competitive
 asymmetry, favouring constructor species. However, bystander responses can
 partially offset this advantage, perhaps facilitating coexistence.
DOI: 10.5061/dryad.1c59zw3wm
title: Survey data from: Can community laboratory facilities increase access and inclusivity in geoscience?

description: Geochronology and geochemistry are critical tools in geoscience research
 and research training, but students and faculty at many institutions have
 little or no access to the specialized and expensive facilities needed for
 sample preparation and analysis. Here, we assess whether community
 laboratories, dedicated to hosting visitors, can help address these
 inequities by increasing access to cutting-edge methods and the resulting
 data. We report the first three years of outcomes from such a community
 laboratory, the goal of which is to improve access, equity, and diversity
 in geoscience by making an increasingly important analytical technique
 more widely available. Although the community sample preparation facility
 we describe here focuses on the cosmogenic nuclides 10Be and 26Al, the
 model we present is viable across the geosciences. Three years of
 development, assessment, and refinement demonstrate that the community
 laboratory model shows promise for including a greater diversity of users
 and applications. However, challenges to fostering a diverse community
 still exist; the costs of supplies, isotopic analysis, and travel to the
 community facility are roadblocks to diversification. Our experience
 suggests that supporting more community laboratory facilities could be an
 important and efficient way to further diversify the geosciences, both in
 terms of the people involved and the types of research performed.
description: During January of 2021, three years after the opening of the
 Community Cosmogenic Facility, we administered an anonymous online survey
 to all laboratory users including anyone who visited the laboratory as
 well as advisors of student visitors. The survey was administered by an
 external evaluator under a protocol approved by the Institutional Review
 Board and disseminated via Google Forms. It consisted of 12
 multiple-response questions focused on demographics, experience in the
 laboratory, and outcomes. Five of the 12 survey questions invited
 respondents to explain or elaborate on their responses. We invited 85
 individuals (comprising both laboratory visitors as well as their
 advisors, if applicable) to take the survey. The response rate was 74% (n
 = 63); all survey data are included in the Supplemental Data.
DOI: 10.5061/dryad.kh189326t
title: Location and condition of gorgonian forests in Italian coastal waters

description: Gorgonian forests are among the most complex of subtidal habitats in the
 Mediterranean Sea, supporting high biodiversity and providing diverse
 ecosystem services. Despite their iconic status, the geographical
 distribution and condition of gorgonian species is poorly known. Using
 multiple online data types our primary aims were to compile, map and
 analyse observations of gorgonian forests in Italian coastal waters to
 assess the biological complexity of gorgonian forests; evaluate impacts
 and vulnerable species, and identify areas of special interest inside and
 outside of existing MPAs to help prioritise conservation strategies and
 actions. Location: Italy. Mediterranean Sea. Methods: Using a multi-source
 data integration approach we collected and integrated data from scientific
 publications, online databases, citizen science projects, SCUBA diver
 questionnaires and social media into a unified spatial framework providing
 up-to-date information on the geographical distribution, abundance, and
 health of major habitat-forming gorgonian species in Italian coastal
 waters. Results: Higher abundance and complexity of gorgonian species
 occurred outside MPAs. Areas of Special Interest (n=167) were identified
 (80 inside and 87 outside MPAs). Three locations supported all seven focal
 species: Capo Caccia MPA, Portofino MPA and Catania (unprotected). The
 purple gorgonian (Paramuricea clavata), the most abundant and
 geographically widespread species with highest forest complexity, also
 experienced the highest impact, possibly linked to thermal stress events,
 disease and fishing. Main conclusions: The multi-source approach was a
 rapid and cost-effective tool to gather, analyse and map disparate data on
 gorgonian forests spanning 27 years of underwater observations both inside
 and outside of marine protected areas (MPAs). The unique perspective given
 by this approach demonstrates the suboptimal protection of several
 habitat-forming gorgonian species. The approach has great potential for
 wider application and offers a more inclusive participatory model for
 crowdsourcing and repurposing underutilised observations while also
 increasing ocean literacy.
description: Using a multi-source data integration approach we collected and
 integrated data from<br> scientific publications, online databases,
 citizen science projects, SCUBA diver questionnaires and social media into
 a unified spatial framework providing up-to-date information on the
 geographical distribution, abundance, and health of major habitat-forming
 gorgonian species in Italian coastal waters.
description: Null = no data recorded or not applicable.
DOI: 10.5061/dryad.v9s4mw6xj
title: Rhesus macaques compensate for reproductive delay following ecological adversity early in life

description: Adversity early in life can shape the reproductive potential of
 individuals through negative effects on health and life span. However,
 long-lived populations with multiple reproductive events may present
 alternative life history strategies to optimize reproductive schedules and
 compensate for shorter life spans. Here, we quantify the effects of major
 hurricanes and density dependence as sources of early-life ecological
 adversity on Cayo Santiago rhesus macaque female reproduction and
 decompose their effects onto the mean age-specific fertility, reproductive
 pace, and lifetime reproductive success (LRS). Females experiencing major
 hurricanes exhibit a delayed reproductive debut but maintain the pace of
 reproduction past debut and show a higher mean fertility during prime
 reproductive ages, relative to unaffected females. Increasing density at
 birth is associated to a decrease in mean fertility and reproductive pace,
 but such association is absent at intermediate densities. When combined,
 our study reveals that hurricanes early in life predict a delay-overshoot
 pattern in mean age-specific fertility that supports the maintenance of
 LRS. In contrast to predictive adaptive response models of accelerated
 reproduction, this long-lived population presents a novel reproductive
 strategy where females who experience major natural disasters early in
 life ultimately overcome their initial reproductive penalty with no major
 negative fitness outcomes. Density presents a more complex relation with
 reproduction that suggests females experiencing a population regulated at
 intermediate densities early in life will escape density dependence and
 show optimized reproductive schedules. Our results support hypotheses
 about life history trade-offs in which adversity-affected females ensure
 their future reproductive potential by allocating more energy to growth or
 maintenance processes at younger adult ages.
description: This data is based on census data collected by the Caribbean
 Primate Research Center of the University of Puerto Rico-Medical Sciences
 Campus.
description: The data has nine variables:
 <strong>season</strong> - birth season of focal
 female <strong>id</strong> - id of focal
 female <strong>age</strong> - age of focal
 female <strong>offspring</strong> - 0 =
 focal female did not produce an offspring, 1 = focal female produced an
 offspring <strong>exit</strong> - age at
 exit from the population due to death or right censorship
 <strong>cohort</strong> - birth cohort (hurricane or
 non-hurricane) <strong>censorship</strong>
 - no = focal female died in the population, yes = focal female was right
 censored <strong>denisty_birth</strong> -
 number of adult females at the onset of the annual birth season
 <strong>denisty_mating</strong> - number of adult
 females at the onset of the annual mating season
DOI: 10.5061/dryad.3j9kd51kh
title: A global analysis of aerial displays in passerines revealed an effect of habitat, mating system and migratory traits

description: Aerial displaying is a flamboyant part of the sexual behaviour of several
 volant animal groups, including birds. Nevertheless, little attention has
 been focused on identifying correlates of large-scale diversity in this
 trait. In this study, we scored the presence and absence of aerial
 displays in males of 1,732 species of passerine birds (Passeriformes) and
 employed Bayesian phylogenetically informed mixed models to test for
 associations between aerial displays and a set of life-history and
 environmental predictors. Our multivariate models revealed that species
 with males that perform aerial displays inhabited open rather than closed
 (forested) habitats. These species also exhibited higher levels of
 polygyny, had more elongated wings, migrated over longer distances and
 bred at higher latitudes. When we included species where the sexual
 function of displays has not been explicitly described but is likely to
 occur, we found that aerial displaying was also associated with smaller
 body size and increased male plumage colouration. Our results suggest that
 both sexual selection and natural selection have been important sources of
 selection on aerial displays in passerines.
DOI: 10.5061/dryad.g1jwstqs7
title: Local plant richness predicts bee abundance and diversity in a study of urban residential yards

description: Understanding the drivers of biodiversity in cities is a central goal of
 urban ecology. There is currently intense scientific and public interest
 in the factors that influence pollinator diversity in cities and their
 surroundings. Existing studies point to a variety of landscape and local
 factors as potentially important, including urbanization (often defined as
 impervious surface cover in the surrounding lands), tree canopy cover and
 the diversity and abundance of locally flowering plants. However, few
 studies have sought to weigh the relative importance of these predictors
 of bee community metrics. Using a set of 27 residential yards chosen to
 represent a gradient of both urbanization and tree canopy cover at a
 landscape scale, we used pan trapping and netting to assess the abundance
 and diversity of local bee communities across the City of Ottawa, Ontario,
 Canada. Surprisingly, the landscape factors (urbanization and tree cover)
 described only a tiny fraction (&lt; 1%) of the total
 variance in bee abundance and diversity across sites. This was true
 regardless of the scale of analysis at which the landscape factors were
 measured. Instead, a yard's floral richness, and, to a somewhat
 lesser extent, its floral abundance, emerged as the most important
 predictors of a yard's bee community abundance and diversity. Our
 study offers an important counterpoint to a growing body of work
 emphasizing the impacts of landscape factors on bee communities. Instead,
 our research suggests that improving bee floral resources by increasing
 the plant species richness and abundance locally is a powerful tool to
 support bee conservation, regardless of the level of urbanization or tree
 cover in the surrounding landscape. Our work highlights that the practice
 of promoting ‘bee-friendly’ plantings in private yards,
 currently being undertaken by a number of non-profits around the world,
 can play an important role in restoring and maintaining urban pollinator
 communities.
DOI: 10.5061/dryad.cz8w9gj4s
title: Serotonin neurons modulate learning rate through uncertainty

description: Regulating how fast to learn is critical for flexible behavior. Learning
 about the consequences of actions should be slow in stable environments,
 but accelerate when that environment changes. Recognizing stability and
 detecting change is difficult in environments with noisy relationships
 between actions and outcomes. Under these conditions, theories propose
 that uncertainty can be used to modulate learning rates
 ("meta-learning"). We show that mice behaving in a dynamic
 foraging task exhibit choice behavior that varied as a function of two
 forms of uncertainty estimated from a meta-learning model. The activity of
 dorsal raphe serotonin neurons tracked both types of uncertainty in the
 foraging task, as well as in a dynamic Pavlovian task. Reversible
 inhibition of serotonin neurons in the foraging task reproduced changes in
 learning predicted by a simulated lesion of meta-learning in the model. We
 thus provide a quantitative link between serotonin neuron activity,
 learning, and decision making.
DOI: 10.5061/dryad.f1vhhmgz9
title: Can we implement mechanistic niche models without measuring traits?

description: Despite increasing demand for more mechanistic models of species’
 distributions, they remain difficult to implement due to their intense
 data requirements. Here, we suggest that three existing tools might help
 researchers estimate missing trait data that can fill necessary
 requirements: phylogenetic imputation (incorporating evolutionary
 relationships into the imputation process), allometry, and biophysics.
 These tools can bridge the gap between species for which we have fairly
 little data and ecological models of their distributions. We focus on
 ecophysiological traits of salamanders; a simple theoretical model of
 water loss showed that changing body mass results in a decrease in
 mass-specific water loss, driven by both increasing total size and
 increasing the thickness of the epidermis. Yet this has two costs –
 mass-specific oxygen absorption decreases with the surface area-to-volume
 ratio, and a thicker epidermis slows the rate of respiration. Using a
 mechanistic distribution model, we modeled the ranges of six species of
 lungless, terrestrial salamanders. The model performed well for two
 species of Plethodon and one species of Desmognathus, but poorly for three
 other species; this discrepancy likely reflects biases in the data
 available to build the imputation model and biological assumptions on
 which the mechanistic distribution model is based. Though overall model
 performance was mediocre, the parameter estimates used in this study may
 be useful when fewer total parameters are missing. We provide relevant R
 functions for the mechanistic niche model in the package ‘ManderGander’.
description: Body mass, resting metabolic rate, and epidermal thickness were
 all collated from published sources.